Phosphorus in PDB 1afk: Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate

Enzymatic activity of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate

All present enzymatic activity of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate:
3.1.27.5;

Protein crystallography data

The structure of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate, PDB code: 1afk was solved by D.D.Leonidas, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.540, 33.360, 73.250, 90.00, 90.09, 90.00
R / Rfree (%) 21.1 / 26.6

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate (pdb code 1afk). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate, PDB code: 1afk:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6;

Phosphorus binding site 1 out of 6 in 1afk

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Phosphorus binding site 1 out of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P125

b:26.9
occ:1.00
PB A:PAP125 0.0 26.9 1.0
O1B A:PAP125 1.5 24.2 1.0
O3B A:PAP125 1.5 28.2 1.0
O2B A:PAP125 1.5 26.9 1.0
O3A A:PAP125 1.6 29.9 1.0
PA A:PAP125 3.1 31.2 1.0
O A:HOH197 3.4 62.1 1.0
NE2 A:HIS12 3.6 10.6 1.0
O A:HOH200 3.6 15.8 1.0
O2A A:PAP125 3.6 32.6 1.0
ND1 A:HIS119 3.7 16.3 1.0
C5' A:PAP125 3.8 29.1 1.0
O5' A:PAP125 3.8 30.1 1.0
NE2 A:GLN11 3.9 19.5 1.0
N A:PHE120 4.1 9.7 1.0
O1A A:PAP125 4.2 32.4 1.0
NZ A:LYS41 4.2 21.9 1.0
CE1 A:HIS12 4.3 10.0 1.0
CA A:HIS119 4.4 11.2 1.0
CE1 A:HIS119 4.5 16.9 1.0
O A:PHE120 4.5 8.7 1.0
CG A:HIS119 4.6 14.6 1.0
CD2 A:HIS12 4.6 10.1 1.0
CB A:HIS119 4.7 12.2 1.0
O A:HOH196 4.8 36.1 1.0
C A:HIS119 4.8 10.4 1.0

Phosphorus binding site 2 out of 6 in 1afk

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Phosphorus binding site 2 out of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P125

b:31.2
occ:1.00
PA A:PAP125 0.0 31.2 1.0
O2A A:PAP125 1.5 32.6 1.0
O1A A:PAP125 1.5 32.4 1.0
O5' A:PAP125 1.6 30.1 1.0
O3A A:PAP125 1.7 29.9 1.0
C5' A:PAP125 2.6 29.1 1.0
PB A:PAP125 3.1 26.9 1.0
O3B A:PAP125 3.3 28.2 1.0
NE2 A:GLN11 3.7 19.5 1.0
C4' A:PAP125 3.9 30.7 1.0
O2B A:PAP125 4.0 26.9 1.0
CE A:LYS7 4.0 24.1 1.0
O1B A:PAP125 4.0 24.2 1.0
NZ A:LYS7 4.2 26.1 1.0
O A:HOH200 4.3 15.8 1.0
C3' A:PAP125 4.3 32.0 1.0
O3 A:PAP125 4.6 40.6 1.0
O A:HOH201 4.6 21.6 1.0
CD A:GLN11 4.7 20.0 1.0
OE1 A:GLN11 4.8 23.8 1.0
O A:HOH197 4.9 62.1 1.0
O4' A:PAP125 5.0 30.6 1.0

Phosphorus binding site 3 out of 6 in 1afk

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Phosphorus binding site 3 out of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P125

b:39.7
occ:1.00
P A:PAP125 0.0 39.7 1.0
O1 A:PAP125 1.5 40.5 1.0
O2 A:PAP125 1.5 39.4 1.0
O3 A:PAP125 1.5 40.6 1.0
O3' A:PAP125 1.7 36.2 1.0
C3' A:PAP125 2.8 32.0 1.0
NZ A:LYS7 3.5 26.1 1.0
C4' A:PAP125 3.7 30.7 1.0
C2' A:PAP125 4.0 31.0 1.0
O2' A:PAP125 4.0 29.1 1.0
O5' A:PAP125 4.3 30.1 1.0
CE A:LYS7 4.4 24.1 1.0
C1' A:PAP125 4.5 29.6 1.0
C5' A:PAP125 4.7 29.1 1.0
CB A:ALA4 4.7 20.7 1.0
O4' A:PAP125 4.7 30.6 1.0

Phosphorus binding site 4 out of 6 in 1afk

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Phosphorus binding site 4 out of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P125

b:42.7
occ:1.00
PB B:PAP125 0.0 42.7 1.0
O1B B:PAP125 1.5 41.5 1.0
O3B B:PAP125 1.5 42.4 1.0
O2B B:PAP125 1.5 44.0 1.0
O3A B:PAP125 1.7 43.6 1.0
PA B:PAP125 3.2 45.4 1.0
O B:HOH161 3.3 23.1 1.0
O5' B:PAP125 3.3 41.4 1.0
C5' B:PAP125 3.3 37.6 1.0
NE2 B:HIS12 3.5 9.9 1.0
ND1 B:HIS119 3.6 22.2 1.0
O1A B:PAP125 3.7 44.6 1.0
N B:PHE120 3.7 10.3 1.0
NE2 B:GLN11 3.8 18.3 1.0
CA B:HIS119 4.2 12.1 1.0
O B:PHE120 4.2 12.5 1.0
CE1 B:HIS119 4.3 21.9 1.0
O2A B:PAP125 4.4 45.2 1.0
CG B:HIS119 4.4 20.1 1.0
CE1 B:HIS12 4.4 8.0 1.0
CD2 B:HIS12 4.4 9.1 1.0
C B:HIS119 4.5 12.2 1.0
CB B:HIS119 4.6 15.7 1.0
CB B:PHE120 4.7 9.9 1.0
CA B:PHE120 4.7 10.5 1.0
C4' B:PAP125 4.8 37.6 1.0
C B:PHE120 4.9 11.0 1.0
CD B:GLN11 5.0 17.8 1.0

Phosphorus binding site 5 out of 6 in 1afk

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Phosphorus binding site 5 out of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P125

b:45.4
occ:1.00
PA B:PAP125 0.0 45.4 1.0
O1A B:PAP125 1.5 44.6 1.0
O2A B:PAP125 1.5 45.2 1.0
O5' B:PAP125 1.7 41.4 1.0
O3A B:PAP125 1.7 43.6 1.0
C5' B:PAP125 2.6 37.6 1.0
NZ B:LYS7 3.0 35.2 1.0
PB B:PAP125 3.2 42.7 1.0
C3' B:PAP125 3.6 38.8 1.0
C4' B:PAP125 3.7 37.6 1.0
NE2 B:GLN11 3.8 18.3 1.0
O1B B:PAP125 3.8 41.5 1.0
O2B B:PAP125 3.8 44.0 1.0
O3B B:PAP125 3.8 42.4 1.0
O B:HOH161 4.1 23.1 1.0
O B:HOH160 4.2 18.9 1.0
CE B:LYS7 4.3 29.2 1.0
C2' B:PAP125 4.3 37.5 1.0
CD B:LYS7 4.5 25.1 1.0
O2' B:PAP125 4.6 37.8 1.0
O3' B:PAP125 4.7 45.3 1.0
CD B:GLN11 4.7 17.8 1.0
CG B:LYS7 4.8 18.0 1.0
O4' B:PAP125 4.9 36.2 1.0
OE1 B:GLN11 4.9 22.2 1.0
ND1 B:HIS119 5.0 22.2 1.0

Phosphorus binding site 6 out of 6 in 1afk

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Phosphorus binding site 6 out of 6 in the Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Crystal Structure of Ribonuclease A in Complex with 5'- Diphosphoadenosine-3'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P125

b:50.9
occ:1.00
P B:PAP125 0.0 50.9 1.0
O3 B:PAP125 1.5 48.8 1.0
O1 B:PAP125 1.5 47.8 1.0
O2 B:PAP125 1.5 48.9 1.0
O3' B:PAP125 1.7 45.3 1.0
C3' B:PAP125 3.0 38.8 1.0
CB B:ALA4 3.5 13.5 1.0
NZ B:LYS7 3.8 35.2 1.0
C4' B:PAP125 3.8 37.6 1.0
O2' B:PAP125 4.2 37.8 1.0
C1' B:PAP125 4.2 36.0 1.0
C2' B:PAP125 4.2 37.5 1.0
CA B:ALA4 4.2 14.4 1.0
CE B:LYS7 4.5 29.2 1.0
O4' B:PAP125 4.6 36.2 1.0
O B:HOH160 4.6 18.9 1.0
O5' B:PAP125 4.7 41.4 1.0
C5' B:PAP125 4.9 37.6 1.0
N B:ALA4 5.0 16.6 1.0

Reference:

D.D.Leonidas, R.Shapiro, L.I.Irons, N.Russo, K.R.Acharya. Crystal Structures of Ribonuclease A Complexes with 5'-Diphosphoadenosine 3'-Phosphate and 5'-Diphosphoadenosine 2'-Phosphate at 1.7 A Resolution. Biochemistry V. 36 5578 1997.
ISSN: ISSN 0006-2960
PubMed: 9154942
DOI: 10.1021/BI9700330
Page generated: Fri Sep 25 12:47:23 2020

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