Phosphorus in PDB 1abb: Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate

Enzymatic activity of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate

All present enzymatic activity of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate:
2.4.1.1;

Protein crystallography data

The structure of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate, PDB code: 1abb was solved by D.D.Leonidas, N.G.Oikonomakos, A.C.Papageorgiou, K.R.Acharya, D.Barford, L.N.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 119.000, 188.100, 88.100, 90.00, 109.29, 90.00
R / Rfree (%) 21 / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Phosphorus atom in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate (pdb code 1abb). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 12 binding sites of Phosphorus where determined in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate, PDB code: 1abb:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 12 in 1abb

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Phosphorus binding site 1 out of 12 in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P931

b:21.1
occ:1.00
PA A:PDP931 0.0 21.1 1.0
O1A A:PDP931 1.5 25.9 1.0
O2A A:PDP931 1.5 25.9 1.0
O5A A:PDP931 1.6 22.2 1.0
O3A A:PDP931 1.7 41.5 1.0
C5A A:PDP931 2.8 10.0 1.0
PB A:PDP931 2.9 65.8 1.0
NZ A:LYS568 3.2 26.7 1.0
O3B A:PDP931 3.3 65.7 1.0
O2B A:PDP931 3.5 62.0 1.0
C5 A:PDP931 4.0 4.9 1.0
CE A:LYS568 4.0 18.0 1.0
O1B A:PDP931 4.1 61.3 1.0
N A:GLY677 4.3 10.0 1.0
CD A:LYS568 4.3 11.9 1.0
C6 A:PDP931 4.4 3.4 1.0
N A:THR676 4.7 16.3 1.0
CA A:GLY675 4.9 20.7 1.0
CA A:GLY677 4.9 5.4 1.0
C A:GLY675 4.9 19.1 1.0
C4 A:PDP931 5.0 3.1 1.0

Phosphorus binding site 2 out of 12 in 1abb

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Phosphorus binding site 2 out of 12 in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P931

b:65.8
occ:1.00
PB A:PDP931 0.0 65.8 1.0
O1B A:PDP931 1.5 61.3 1.0
O2B A:PDP931 1.5 62.0 1.0
O3B A:PDP931 1.5 65.7 1.0
O3A A:PDP931 1.7 41.5 1.0
PA A:PDP931 2.9 21.1 1.0
O2A A:PDP931 3.5 25.9 1.0
O5A A:PDP931 3.7 22.2 1.0
CE A:LYS574 3.9 12.7 1.0
NZ A:LYS574 4.0 9.9 1.0
O1A A:PDP931 4.0 25.9 1.0
NZ A:LYS568 4.0 26.7 1.0
CD A:LYS568 4.2 11.9 1.0
CB A:ARG569 4.3 28.1 1.0
N A:ARG569 4.3 18.8 1.0
CD A:ARG569 4.5 50.3 1.0
CE A:LYS568 4.7 18.0 1.0
C5A A:PDP931 4.8 10.0 1.0
OE2 A:GLU672 4.8 58.7 1.0

Phosphorus binding site 3 out of 12 in 1abb

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Phosphorus binding site 3 out of 12 in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P920

b:45.4
occ:1.00
P A:IMP920 0.0 45.4 1.0
O3P A:IMP920 1.4 51.7 1.0
O1P A:IMP920 1.5 49.0 1.0
O2P A:IMP920 1.5 42.6 1.0
O5' A:IMP920 1.7 40.9 1.0
C5' A:IMP920 2.8 34.6 1.0
NH2 A:ARG310 3.2 10.8 1.0
NH2 A:ARG309 3.4 44.2 1.0
NE A:ARG310 3.5 4.6 1.0
OH A:TYR75 3.7 79.6 1.0
CZ A:ARG310 3.8 10.6 1.0
C4' A:IMP920 4.2 32.8 1.0
CE1 A:TYR75 4.3 79.2 1.0
O4' A:IMP920 4.3 33.7 1.0
CZ A:TYR75 4.4 80.8 1.0
CG A:ARG310 4.6 21.5 1.0
CZ A:ARG309 4.7 42.6 1.0
CD A:ARG310 4.7 6.8 1.0
C3' A:IMP920 4.9 35.0 1.0
C8 A:IMP920 5.0 44.4 1.0

Phosphorus binding site 4 out of 12 in 1abb

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Phosphorus binding site 4 out of 12 in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P932

b:23.8
occ:1.00
PA B:PDP932 0.0 23.8 1.0
O1A B:PDP932 1.5 17.6 1.0
O2A B:PDP932 1.5 24.4 1.0
O3A B:PDP932 1.6 37.9 1.0
O5A B:PDP932 1.6 26.0 1.0
C5A B:PDP932 2.7 22.1 1.0
PB B:PDP932 2.8 59.2 1.0
O3B B:PDP932 3.2 67.7 1.0
O2B B:PDP932 3.3 60.2 1.0
NZ B:LYS568 3.3 18.8 1.0
N B:GLY677 3.9 6.4 1.0
O1B B:PDP932 4.0 61.7 1.0
C5 B:PDP932 4.0 14.5 1.0
N B:THR676 4.2 23.0 1.0
CE B:LYS568 4.3 13.3 1.0
C6 B:PDP932 4.6 15.4 1.0
CA B:GLY675 4.6 19.0 1.0
CA B:GLY677 4.7 3.6 1.0
C B:GLY675 4.7 21.1 1.0
CD B:LYS568 4.8 9.9 1.0
C B:THR676 4.8 6.5 1.0
C4 B:PDP932 4.9 9.5 1.0
CA B:THR676 5.0 13.2 1.0
C4A B:PDP932 5.0 11.1 1.0

Phosphorus binding site 5 out of 12 in 1abb

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Phosphorus binding site 5 out of 12 in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P932

b:59.2
occ:1.00
PB B:PDP932 0.0 59.2 1.0
O2B B:PDP932 1.5 60.2 1.0
O3B B:PDP932 1.5 67.7 1.0
O1B B:PDP932 1.5 61.7 1.0
O3A B:PDP932 1.6 37.9 1.0
PA B:PDP932 2.8 23.8 1.0
O5A B:PDP932 3.2 26.0 1.0
O2A B:PDP932 3.6 24.4 1.0
NE B:ARG569 3.8 60.5 1.0
NH2 B:ARG569 3.9 71.6 1.0
O1A B:PDP932 3.9 17.6 1.0
NZ B:LYS568 3.9 18.8 1.0
CZ B:ARG569 3.9 66.7 1.0
NZ B:LYS574 4.0 19.6 1.0
N B:ARG569 4.2 23.8 1.0
CD B:LYS568 4.2 9.9 1.0
CE B:LYS574 4.4 8.1 1.0
CB B:ARG569 4.5 33.7 1.0
C5A B:PDP932 4.5 22.1 1.0
CA B:LYS568 4.5 17.6 1.0
CE B:LYS568 4.6 13.3 1.0
CD B:ARG569 4.6 52.5 1.0
CG B:LYS568 4.7 3.0 1.0
CB B:LYS568 4.7 9.6 1.0
NH1 B:ARG569 4.8 68.7 1.0
CD B:LYS574 4.9 7.9 1.0
C B:LYS568 4.9 22.5 1.0
CA B:ARG569 5.0 26.6 1.0
CG B:ARG569 5.0 44.1 1.0

Phosphorus binding site 6 out of 12 in 1abb

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Phosphorus binding site 6 out of 12 in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P920

b:28.2
occ:1.00
P B:IMP920 0.0 28.2 1.0
O1P B:IMP920 1.5 32.0 1.0
O3P B:IMP920 1.5 25.1 1.0
O2P B:IMP920 1.5 21.5 1.0
O5' B:IMP920 1.6 23.2 1.0
C5' B:IMP920 2.7 23.1 1.0
NH2 B:ARG309 3.1 62.8 1.0
OH B:TYR75 3.2 55.1 1.0
NH2 B:ARG310 3.4 10.8 1.0
NE B:ARG310 3.6 9.1 1.0
CZ B:ARG310 4.0 8.8 1.0
CZ B:TYR75 4.2 56.8 1.0
C4' B:IMP920 4.2 18.0 1.0
O4' B:IMP920 4.3 18.9 1.0
CZ B:ARG309 4.4 58.7 1.0
C8 B:IMP920 4.7 23.1 1.0
CD B:ARG310 4.7 11.1 1.0
CG B:ARG310 4.7 10.4 1.0
CE1 B:TYR75 4.7 57.5 1.0
CE2 B:TYR75 5.0 55.5 1.0

Phosphorus binding site 7 out of 12 in 1abb

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Phosphorus binding site 7 out of 12 in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P933

b:18.5
occ:1.00
PA C:PDP933 0.0 18.5 1.0
O1A C:PDP933 1.5 30.6 1.0
O2A C:PDP933 1.5 28.7 1.0
O3A C:PDP933 1.6 40.1 1.0
O5A C:PDP933 1.6 20.8 1.0
C5A C:PDP933 2.7 11.9 1.0
PB C:PDP933 2.9 66.0 1.0
O2B C:PDP933 3.3 62.2 1.0
O3B C:PDP933 3.4 66.3 1.0
NZ C:LYS568 3.6 36.8 1.0
N C:GLY677 3.7 12.8 1.0
CA C:GLY677 3.8 10.5 1.0
O1B C:PDP933 4.0 67.7 1.0
C5 C:PDP933 4.0 7.9 1.0
CE C:LYS568 4.4 24.4 1.0
CD C:LYS568 4.6 23.1 1.0
C6 C:PDP933 4.7 6.0 1.0
N C:THR676 4.8 19.0 1.0
C4 C:PDP933 4.8 7.2 1.0
C4A C:PDP933 4.8 2.0 1.0
C C:THR676 4.8 15.8 1.0
O C:VAL567 4.9 29.7 1.0

Phosphorus binding site 8 out of 12 in 1abb

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Phosphorus binding site 8 out of 12 in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P933

b:66.0
occ:1.00
PB C:PDP933 0.0 66.0 1.0
O1B C:PDP933 1.5 67.7 1.0
O2B C:PDP933 1.5 62.2 1.0
O3B C:PDP933 1.5 66.3 1.0
O3A C:PDP933 1.6 40.1 1.0
PA C:PDP933 2.9 18.5 1.0
O5A C:PDP933 3.4 20.8 1.0
O1A C:PDP933 3.7 30.6 1.0
O2A C:PDP933 3.8 28.7 1.0
NZ C:LYS574 3.8 22.7 1.0
NZ C:LYS568 4.0 36.8 1.0
CE C:LYS574 4.2 21.5 1.0
C5A C:PDP933 4.3 11.9 1.0
CD C:LYS568 4.4 23.1 1.0
CB C:ARG569 4.6 23.0 1.0
N C:ARG569 4.7 14.8 1.0
CE C:LYS568 4.8 24.4 1.0
CD C:ARG569 4.9 34.6 1.0

Phosphorus binding site 9 out of 12 in 1abb

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Phosphorus binding site 9 out of 12 in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P920

b:26.2
occ:1.00
P C:IMP920 0.0 26.2 1.0
O3P C:IMP920 1.5 20.3 1.0
O1P C:IMP920 1.5 33.3 1.0
O2P C:IMP920 1.5 25.6 1.0
O5' C:IMP920 1.6 18.4 1.0
C5' C:IMP920 2.7 20.9 1.0
NH2 C:ARG309 3.4 43.8 1.0
NH2 C:ARG310 3.6 7.4 1.0
NE C:ARG310 3.6 9.4 1.0
OH C:TYR75 3.6 53.1 1.0
C4' C:IMP920 4.1 17.0 1.0
CZ C:ARG310 4.1 8.1 1.0
O4' C:IMP920 4.3 19.4 1.0
CE1 C:TYR75 4.3 46.3 1.0
CZ C:TYR75 4.4 49.2 1.0
CD C:ARG310 4.7 8.1 1.0
CZ C:ARG309 4.7 39.1 1.0
C8 C:IMP920 4.7 21.9 1.0
C3' C:IMP920 4.8 20.6 1.0

Phosphorus binding site 10 out of 12 in 1abb

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Phosphorus binding site 10 out of 12 in the Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:P934

b:26.1
occ:1.00
PA D:PDP934 0.0 26.1 1.0
O1A D:PDP934 1.5 26.3 1.0
O2A D:PDP934 1.5 22.1 1.0
O5A D:PDP934 1.6 31.0 1.0
O3A D:PDP934 1.7 45.2 1.0
C5A D:PDP934 2.7 31.3 1.0
PB D:PDP934 3.0 58.7 1.0
O3B D:PDP934 3.3 60.5 1.0
NZ D:LYS568 3.4 22.3 1.0
N D:GLY677 3.4 2.0 1.0
O2B D:PDP934 3.5 58.2 1.0
CA D:GLY677 3.8 9.2 1.0
C5 D:PDP934 4.0 26.0 1.0
O1B D:PDP934 4.1 59.1 1.0
CE D:LYS568 4.3 24.5 1.0
N D:THR676 4.4 21.9 1.0
C D:THR676 4.6 7.7 1.0
C6 D:PDP934 4.6 22.0 1.0
CD D:LYS568 4.6 19.7 1.0
CA D:GLY675 4.9 29.4 1.0
C4 D:PDP934 4.9 23.8 1.0
CB D:THR676 4.9 15.7 1.0
OD1 D:ASN678 4.9 32.4 1.0
CA D:THR676 5.0 10.4 1.0
C D:GLY677 5.0 9.7 1.0

Reference:

D.D.Leonidas, N.G.Oikonomakos, A.C.Papageorgiou, K.R.Acharya, D.Barford, L.N.Johnson. Control of Phosphorylase B Conformation By A Modified Cofactor: Crystallographic Studies on R-State Glycogen Phosphorylase Reconstituted with Pyridoxal 5'-Diphosphate. Protein Sci. V. 1 1112 1992.
ISSN: ISSN 0961-8368
PubMed: 1304390
Page generated: Fri Sep 25 12:42:20 2020

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