Phosphorus in PDB 13pk: Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei

Enzymatic activity of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei

All present enzymatic activity of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei:
2.7.2.3;

Protein crystallography data

The structure of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei, PDB code: 13pk was solved by B.E.Bernstein, P.A.M.Michels, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.213, 115.959, 171.327, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 29.1

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Phosphorus atom in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei (pdb code 13pk). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 16 binding sites of Phosphorus where determined in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei, PDB code: 13pk:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 16 in 13pk

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Phosphorus binding site 1 out of 16 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P701

b:87.4
occ:1.00
 P A:PO4701 0.0 87.4 1.0
O4 A:PO4701 1.5 80.8 1.0
O3 A:PO4701 1.5 73.8 1.0
O1 A:PO4701 1.5 81.4 1.0
O2 A:PO4701 1.5 77.7 1.0
O A:LEU103 4.0 28.6 1.0
O D:PHE344 4.3 35.0 1.0
NH2 A:ARG105 4.4 42.0 1.0
O D:GLU345 4.7 43.9 1.0
CD2 D:LEU384 4.7 14.2 1.0
CG D:LEU384 4.8 25.3 1.0
CG2 D:VAL347 4.8 43.0 1.0
CE2 D:PHE354 4.8 32.0 1.0
CD1 A:LEU51 4.9 22.0 1.0
CZ D:PHE354 4.9 37.9 1.0
CG A:LYS48 4.9 42.2 1.0

Phosphorus binding site 2 out of 16 in 13pk

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Phosphorus binding site 2 out of 16 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P704

b:61.4
occ:1.00
 P A:PO4704 0.0 61.4 1.0
O3 A:PO4704 1.5 44.2 1.0
O1 A:PO4704 1.5 52.9 1.0
O4 A:PO4704 1.5 44.6 1.0
O2 A:PO4704 1.5 51.8 1.0
O A:HOH789 3.0 32.9 1.0
CG D:LYS48 4.4 32.8 1.0
O D:LEU103 4.4 31.6 1.0
CG A:LEU384 4.4 37.2 1.0
CE2 A:PHE354 4.5 37.0 1.0
O A:PHE344 4.6 36.4 1.0
CZ A:PHE354 4.7 34.6 1.0
CG2 A:VAL347 4.7 37.0 1.0
CD2 A:LEU384 4.7 35.0 1.0
NH2 D:ARG105 4.8 45.1 1.0

Phosphorus binding site 3 out of 16 in 13pk

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Phosphorus binding site 3 out of 16 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P421

b:29.9
occ:1.00
 PB A:ADP421 0.0 29.9 1.0
O3B A:ADP421 1.5 28.9 1.0
O1B A:ADP421 1.5 28.2 1.0
O3A A:ADP421 1.6 32.8 1.0
O2B A:ADP421 1.6 32.7 1.0
PA A:ADP421 2.9 30.5 1.0
O1A A:ADP421 3.4 32.3 1.0
O A:HOH842 3.5 32.8 1.0
O2A A:ADP421 3.6 30.9 1.0
CA A:GLY375 3.8 27.2 1.0
O5' A:ADP421 3.9 27.1 1.0
OD2 A:ASP377 4.0 31.4 1.0
N A:ASP377 4.0 25.8 1.0
ND2 A:ASN338 4.0 28.2 1.0
N A:GLY376 4.0 29.6 1.0
OG A:SER378 4.1 18.7 1.0
MG A:MG422 4.1 47.0 1.0
C A:GLY375 4.2 29.5 1.0
CB A:ASP377 4.2 24.2 1.0
N A:SER378 4.2 26.8 1.0
C5' A:ADP421 4.2 28.2 1.0
CG A:ASP377 4.6 29.6 1.0
O A:GLY374 4.6 31.2 1.0
CA A:ASP377 4.6 27.6 1.0
CD A:PRO340 4.6 20.2 1.0
CA A:GLY339 4.7 22.4 1.0
CB A:SER378 4.7 22.1 1.0
N A:GLY339 4.7 23.9 1.0
NZ A:LYS223 4.8 45.0 1.0
C A:GLY376 4.9 28.3 1.0
C A:ASP377 4.9 27.2 1.0
CA A:GLY376 4.9 28.3 1.0

Phosphorus binding site 4 out of 16 in 13pk

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Phosphorus binding site 4 out of 16 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P421

b:30.5
occ:1.00
 PA A:ADP421 0.0 30.5 1.0
O1A A:ADP421 1.5 32.3 1.0
O2A A:ADP421 1.5 30.9 1.0
O5' A:ADP421 1.6 27.1 1.0
O3A A:ADP421 1.6 32.8 1.0
C5' A:ADP421 2.6 28.2 1.0
PB A:ADP421 2.9 29.9 1.0
O2B A:ADP421 3.4 32.7 1.0
O3B A:ADP421 3.4 28.9 1.0
C4' A:ADP421 3.5 29.7 1.0
N A:ALA218 3.6 34.8 1.0
O A:HOH861 3.8 56.7 1.0
NZ A:LYS223 3.9 45.0 1.0
MG A:MG422 3.9 47.0 1.0
CA A:GLY217 4.0 32.2 1.0
OD2 A:ASP377 4.0 31.4 1.0
O4' A:ADP421 4.1 35.6 1.0
O1B A:ADP421 4.1 28.2 1.0
C A:GLY217 4.3 33.4 1.0
CD A:LYS219 4.4 57.2 1.0
CE A:LYS219 4.5 56.8 1.0
CA A:ALA218 4.6 38.2 1.0
O A:ALA218 4.6 43.4 1.0
CD A:PRO340 4.6 20.2 1.0
C A:ALA218 4.7 40.1 1.0
CB A:ALA218 4.7 37.7 1.0
C3' A:ADP421 4.8 30.9 1.0
CE A:LYS223 4.9 45.4 1.0
CG A:LYS219 4.9 53.1 1.0
CA A:GLY339 4.9 22.4 1.0
CG A:ASP377 5.0 29.6 1.0

Phosphorus binding site 5 out of 16 in 13pk

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Phosphorus binding site 5 out of 16 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P423

b:34.4
occ:1.00
 P A:3PG423 0.0 34.4 1.0
O2P A:3PG423 1.5 28.3 1.0
O3P A:3PG423 1.5 35.8 1.0
O4P A:3PG423 1.5 37.1 1.0
O1P A:3PG423 1.7 36.4 1.0
C3 A:3PG423 2.9 36.1 1.0
NH2 A:ARG172 3.4 41.3 1.0
NZ A:LYS219 3.5 53.4 1.0
NH1 A:ARG135 3.5 32.4 1.0
O A:HOH724 3.6 34.2 1.0
O A:HOH876 3.6 51.8 1.0
NH2 A:ARG135 3.7 33.2 1.0
NE A:ARG65 3.7 29.8 1.0
NH2 A:ARG65 3.9 29.8 1.0
O A:HOH752 4.0 45.0 1.0
NE A:ARG172 4.0 40.4 1.0
C2 A:3PG423 4.1 40.8 1.0
CZ A:ARG135 4.1 34.3 1.0
CZ A:ARG172 4.2 38.0 1.0
C1 A:3PG423 4.2 43.8 1.0
NE2 A:HIS62 4.3 27.6 1.0
CZ A:ARG65 4.3 28.2 1.0
O2 A:3PG423 4.3 48.0 1.0
CG A:ARG65 4.6 31.7 1.0
CD A:ARG65 4.8 28.2 1.0
O1 A:3PG423 4.8 48.1 1.0
CE A:LYS219 4.9 56.8 1.0
O3 A:3PG423 4.9 45.9 1.0
ND2 A:ASN26 4.9 27.6 1.0

Phosphorus binding site 6 out of 16 in 13pk

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Phosphorus binding site 6 out of 16 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P421

b:27.5
occ:1.00
 PB B:ADP421 0.0 27.5 1.0
O1B B:ADP421 1.5 29.7 1.0
O3B B:ADP421 1.5 27.3 1.0
O3A B:ADP421 1.5 29.4 1.0
O2B B:ADP421 1.6 34.3 1.0
PA B:ADP421 2.8 24.8 1.0
O1A B:ADP421 3.3 29.7 1.0
O2A B:ADP421 3.4 22.3 1.0
OD2 B:ASP377 3.7 40.2 1.0
O B:HOH556 3.8 9.9 1.0
O5' B:ADP421 3.8 27.9 1.0
N B:ASP377 3.9 23.9 1.0
CB B:ASP377 3.9 33.2 1.0
MG B:MG422 4.0 33.5 1.0
CA B:GLY375 4.1 23.3 1.0
N B:GLY376 4.1 27.1 1.0
C5' B:ADP421 4.1 29.7 1.0
ND2 B:ASN338 4.2 21.1 1.0
N B:SER378 4.2 25.6 1.0
C B:GLY375 4.2 25.0 1.0
CG B:ASP377 4.3 40.6 1.0
OG B:SER378 4.3 22.4 1.0
CA B:ASP377 4.4 27.4 1.0
CD B:PRO340 4.4 24.1 1.0
CA B:GLY339 4.6 18.8 1.0
N B:GLY339 4.7 19.4 1.0
C B:ASP377 4.8 27.7 1.0
C B:GLY376 4.8 20.8 1.0
NZ B:LYS223 4.8 28.5 1.0
CB B:SER378 4.9 23.2 1.0
CA B:GLY376 4.9 24.6 1.0
O B:GLY374 4.9 27.1 1.0
O B:GLY375 5.0 25.3 1.0

Phosphorus binding site 7 out of 16 in 13pk

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Phosphorus binding site 7 out of 16 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P421

b:24.8
occ:1.00
 PA B:ADP421 0.0 24.8 1.0
O1A B:ADP421 1.4 29.7 1.0
O2A B:ADP421 1.5 22.3 1.0
O3A B:ADP421 1.5 29.4 1.0
O5' B:ADP421 1.5 27.9 1.0
C5' B:ADP421 2.5 29.7 1.0
PB B:ADP421 2.8 27.5 1.0
O2B B:ADP421 3.3 34.3 1.0
C4' B:ADP421 3.4 29.8 1.0
O3B B:ADP421 3.4 27.3 1.0
OD2 B:ASP377 3.7 40.2 1.0
MG B:MG422 3.8 33.5 1.0
N B:ALA218 3.8 33.5 1.0
O1B B:ADP421 3.9 29.7 1.0
O4' B:ADP421 4.0 38.0 1.0
CA B:GLY217 4.0 27.6 1.0
NZ B:LYS223 4.2 28.5 1.0
CD B:PRO340 4.4 24.1 1.0
C B:GLY217 4.5 29.9 1.0
CG B:ASP377 4.6 40.6 1.0
CE B:LYS219 4.6 54.2 1.0
CD B:LYS219 4.6 55.0 1.0
C3' B:ADP421 4.7 32.7 1.0
CB B:ASP377 4.7 33.2 1.0
O B:HOH579 4.7 58.0 1.0
CA B:ALA218 4.8 32.5 1.0
CB B:ALA218 4.9 35.1 1.0

Phosphorus binding site 8 out of 16 in 13pk

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Phosphorus binding site 8 out of 16 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P423

b:62.9
occ:1.00
 P B:3PG423 0.0 62.9 1.0
O3P B:3PG423 1.5 65.0 1.0
O2P B:3PG423 1.5 60.0 1.0
O4P B:3PG423 1.5 59.2 1.0
O1P B:3PG423 1.7 61.8 1.0
C3 B:3PG423 2.9 61.3 1.0
NH1 B:ARG135 3.2 41.3 1.0
NE B:ARG65 3.5 57.1 1.0
NH2 B:ARG135 3.7 48.0 1.0
NZ B:LYS219 3.8 61.1 1.0
CZ B:ARG135 3.9 46.4 1.0
NH2 B:ARG65 4.0 58.2 1.0
C2 B:3PG423 4.1 63.0 1.0
NE2 B:HIS62 4.1 31.8 1.0
O B:HOH480 4.1 51.1 1.0
CG B:ARG65 4.2 51.9 1.0
CZ B:ARG65 4.3 57.5 1.0
C1 B:3PG423 4.3 65.8 1.0
NH2 B:ARG172 4.3 78.7 1.0
O2 B:3PG423 4.3 67.7 1.0
CD B:ARG65 4.5 52.0 1.0
O B:GLY64 4.5 32.8 1.0
ND2 B:ASN26 4.7 29.0 1.0
CD2 B:HIS62 4.8 29.6 1.0
NE B:ARG172 4.9 81.2 1.0
O1 B:3PG423 5.0 68.9 1.0

Phosphorus binding site 9 out of 16 in 13pk

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Phosphorus binding site 9 out of 16 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P624

b:65.8
occ:1.00
 P C:PO4624 0.0 65.8 1.0
O4 C:PO4624 1.5 66.5 1.0
O2 C:PO4624 1.5 66.1 1.0
O3 C:PO4624 1.5 65.0 1.0
O1 C:PO4624 1.5 64.3 1.0
O3B C:ADP421 3.4 53.7 1.0
O2B C:ADP421 3.6 56.8 1.0
MG C:MG422 3.7 62.0 1.0
O C:HOH759 3.7 51.6 1.0
N C:GLY376 3.7 44.4 1.0
NH1 C:ARG39 3.8 41.1 1.0
NH2 C:ARG39 3.8 42.7 1.0
CA C:GLY398 4.0 68.3 1.0
PB C:ADP421 4.0 50.6 1.0
CE C:LYS219 4.2 85.2 1.0
CA C:GLY375 4.2 44.5 1.0
CZ C:ARG39 4.3 36.3 1.0
C C:GLY375 4.5 44.5 1.0
ND2 C:ASN26 4.6 49.0 1.0
CA C:GLY376 4.6 39.4 1.0
NZ C:LYS219 4.6 90.6 1.0
N C:GLY398 4.7 62.0 1.0
O2A C:ADP421 4.9 47.6 1.0
O1B C:ADP421 5.0 54.7 1.0

Phosphorus binding site 10 out of 16 in 13pk

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Phosphorus binding site 10 out of 16 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P702

b:65.3
occ:1.00
 P C:PO4702 0.0 65.3 1.0
O3 C:PO4702 1.5 60.9 1.0
O2 C:PO4702 1.5 62.9 1.0
O4 C:PO4702 1.5 61.3 1.0
O1 C:PO4702 1.5 58.7 1.0
O C:HOH789 3.1 26.2 1.0
CG B:LYS48 3.9 45.3 1.0
CD2 C:LEU384 4.4 33.3 1.0
CG C:LEU384 4.4 37.6 1.0
CE2 C:PHE354 4.4 37.1 1.0
CZ C:PHE354 4.5 35.3 1.0
O B:LEU103 4.6 36.1 1.0
CB B:LYS48 4.6 33.6 1.0
CA B:LYS48 4.7 35.6 1.0
CD B:LYS48 4.8 51.9 1.0
O C:PHE344 4.9 46.8 1.0
CD1 B:LEU51 4.9 25.4 1.0

Reference:

B.E.Bernstein, P.A.Michels, W.G.Hol. Synergistic Effects of Substrate-Induced Conformational Changes in Phosphoglycerate Kinase Activation. Nature V. 385 275 1997.
ISSN: ISSN 0028-0836
PubMed: 9000079
DOI: 10.1038/385275A0
Page generated: Fri Sep 25 11:24:18 2020

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