Phosphorus in PDB 1aky: High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer

Enzymatic activity of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer

All present enzymatic activity of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer:
2.7.4.3;

Protein crystallography data

The structure of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer, PDB code: 1aky was solved by U.Abele, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.63
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.300, 40.500, 45.700, 110.80, 109.00, 63.30
R / Rfree (%) 19.4 / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer (pdb code 1aky). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 5 binding sites of Phosphorus where determined in the High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer, PDB code: 1aky:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5;

Phosphorus binding site 1 out of 5 in 1aky

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Phosphorus binding site 1 out of 5 in the High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P301

b:14.9
occ:1.00
 PA A:AP5301 0.0 14.9 1.0
O2A A:AP5301 1.5 17.3 1.0
O1A A:AP5301 1.5 17.4 1.0
O5F A:AP5301 1.5 16.1 1.0
O3A A:AP5301 1.5 16.4 1.0
C5F A:AP5301 2.6 13.0 1.0
H1 A:HOH530 2.8 0.0 1.0
PB A:AP5301 2.9 14.7 1.0
HH11 A:ARG132 3.2 0.0 1.0
O2B A:AP5301 3.3 13.1 1.0
O1B A:AP5301 3.6 18.1 1.0
O A:HOH530 3.7 27.4 1.0
H A:GLY18 3.7 0.0 1.0
OG1 A:THR19 3.7 16.2 1.0
NH1 A:ARG132 3.8 17.9 1.0
H A:THR19 3.8 0.0 1.0
C4F A:AP5301 3.8 16.6 1.0
HH12 A:ARG132 3.8 0.0 1.0
H2 A:HOH530 3.9 0.0 1.0
O3B A:AP5301 3.9 14.8 1.0
H A:GLY16 4.0 0.0 1.0
C3F A:AP5301 4.0 23.8 1.0
OG A:SER141 4.0 40.8 1.0
HG1 A:THR19 4.1 0.0 1.0
C2F A:AP5301 4.2 20.6 1.0
CA A:GLY16 4.2 13.4 1.0
HG A:SER141 4.3 0.0 1.0
N A:GLY18 4.4 14.6 1.0
N A:THR19 4.4 15.9 1.0
N A:GLY16 4.4 14.8 1.0
H A:LYS17 4.5 0.0 1.0
O4F A:AP5301 4.5 16.5 1.0
C A:GLY16 4.6 12.1 1.0
C8A A:AP5301 4.6 18.4 1.0
CB A:SER141 4.6 30.8 1.0
N A:LYS17 4.7 12.6 1.0
C1F A:AP5301 4.7 15.6 1.0
CA A:GLY18 4.7 15.3 1.0
CB A:THR19 4.8 16.0 1.0
CD A:ARG132 4.8 20.0 1.0
CZ A:ARG132 4.8 18.8 1.0
O2G A:AP5301 4.9 14.0 1.0
C A:GLY18 4.9 15.0 1.0
CA A:GLY14 4.9 16.3 1.0
H A:GLY14 5.0 0.0 1.0
PG A:AP5301 5.0 14.3 1.0

Phosphorus binding site 2 out of 5 in 1aky

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Phosphorus binding site 2 out of 5 in the High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P301

b:14.7
occ:1.00
 PB A:AP5301 0.0 14.7 1.0
O1B A:AP5301 1.5 18.1 1.0
O2B A:AP5301 1.5 13.1 1.0
O3A A:AP5301 1.5 16.4 1.0
O3B A:AP5301 1.5 14.8 1.0
PA A:AP5301 2.9 14.9 1.0
PG A:AP5301 2.9 14.3 1.0
H A:GLY18 3.0 0.0 1.0
H A:LYS17 3.1 0.0 1.0
H A:GLY14 3.1 0.0 1.0
H A:GLY16 3.1 0.0 1.0
HN1 A:IMD302 3.3 0.0 1.0
O2G A:AP5301 3.3 14.0 1.0
O1A A:AP5301 3.3 17.4 1.0
HH12 A:ARG132 3.5 0.0 1.0
O3G A:AP5301 3.7 13.0 1.0
N A:LYS17 3.7 12.6 1.0
O2A A:AP5301 3.8 17.3 1.0
O5F A:AP5301 3.8 16.1 1.0
H1 A:HOH530 3.8 0.0 1.0
N A:GLY14 3.8 13.8 1.0
O1G A:AP5301 3.9 15.6 1.0
N A:GLY16 4.0 14.8 1.0
N1 A:IMD302 4.0 20.7 1.0
N A:GLY18 4.0 14.6 1.0
H A:ALA15 4.0 0.0 1.0
CA A:GLY14 4.1 16.3 1.0
NH1 A:ARG132 4.1 17.9 1.0
HH11 A:ARG132 4.2 0.0 1.0
CB A:LYS17 4.3 13.0 1.0
CE A:LYS17 4.3 27.9 1.0
N A:ALA15 4.3 13.5 1.0
C5F A:AP5301 4.3 13.0 1.0
C A:GLY14 4.3 15.4 1.0
O A:HOH530 4.4 27.4 1.0
CA A:GLY16 4.4 13.4 1.0
C A:GLY16 4.4 12.1 1.0
CA A:LYS17 4.4 13.8 1.0
C2 A:IMD302 4.6 30.2 1.0
C A:LYS17 4.8 13.7 1.0
H A:THR19 4.8 0.0 1.0
CG A:LYS17 4.8 16.2 1.0
CA A:GLY18 4.9 15.3 1.0
H2 A:HOH530 4.9 0.0 1.0
C5 A:IMD302 5.0 32.1 1.0

Phosphorus binding site 3 out of 5 in 1aky

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Phosphorus binding site 3 out of 5 in the High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P301

b:14.3
occ:1.00
 PG A:AP5301 0.0 14.3 1.0
O2G A:AP5301 1.5 14.0 1.0
O1G A:AP5301 1.5 15.6 1.0
O3G A:AP5301 1.5 13.0 1.0
O3B A:AP5301 1.6 14.8 1.0
HH12 A:ARG132 2.6 0.0 1.0
HN1 A:IMD302 2.8 0.0 1.0
PD A:AP5301 2.9 15.9 1.0
PB A:AP5301 2.9 14.7 1.0
HH22 A:ARG132 3.0 0.0 1.0
H A:GLY14 3.1 0.0 1.0
HH12 A:ARG165 3.1 0.0 1.0
O3D A:AP5301 3.2 17.7 1.0
O2B A:AP5301 3.3 13.1 1.0
O2D A:AP5301 3.4 22.2 1.0
NH1 A:ARG132 3.5 17.9 1.0
HH21 A:ARG176 3.5 0.0 1.0
HH22 A:ARG165 3.6 0.0 1.0
O3A A:AP5301 3.7 16.4 1.0
HH22 A:ARG176 3.7 0.0 1.0
N1 A:IMD302 3.8 20.7 1.0
NH2 A:ARG132 3.8 17.9 1.0
NH1 A:ARG165 3.9 14.1 1.0
O1B A:AP5301 3.9 18.1 1.0
O1D A:AP5301 4.0 15.9 1.0
N A:GLY14 4.0 13.8 1.0
NH2 A:ARG176 4.0 15.3 1.0
CZ A:ARG132 4.1 18.8 1.0
HH11 A:ARG132 4.2 0.0 1.0
NH2 A:ARG165 4.3 11.4 1.0
HZ3 A:LYS17 4.4 0.0 1.0
CA A:PRO13 4.4 16.8 1.0
C5 A:IMD302 4.5 32.1 1.0
PE A:AP5301 4.5 13.3 1.0
HH11 A:ARG165 4.5 0.0 1.0
CZ A:ARG165 4.5 9.7 1.0
H1 A:HOH530 4.6 0.0 1.0
HH21 A:ARG132 4.7 0.0 1.0
O1E A:AP5301 4.7 14.6 1.0
C A:PRO13 4.7 16.2 1.0
CB A:PRO13 4.9 14.2 1.0
CE A:LYS17 4.9 27.9 1.0
O A:HOH530 4.9 27.4 1.0
C2 A:IMD302 4.9 30.2 1.0
CA A:GLY14 4.9 16.3 1.0
H1 A:HOH510 5.0 0.0 1.0
H2 A:HOH550 5.0 0.0 1.0
O2E A:AP5301 5.0 13.1 1.0
PA A:AP5301 5.0 14.9 1.0

Phosphorus binding site 4 out of 5 in 1aky

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Phosphorus binding site 4 out of 5 in the High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P301

b:15.9
occ:1.00
 PD A:AP5301 0.0 15.9 1.0
O2D A:AP5301 1.5 22.2 1.0
O1D A:AP5301 1.5 15.9 1.0
O3D A:AP5301 1.5 17.7 1.0
O3G A:AP5301 1.5 13.0 1.0
PG A:AP5301 2.9 14.3 1.0
PE A:AP5301 2.9 13.3 1.0
HZ3 A:LYS17 3.0 0.0 1.0
H2 A:HOH501 3.0 0.0 1.0
HH12 A:ARG93 3.0 0.0 1.0
HH21 A:ARG176 3.1 0.0 1.0
HH22 A:ARG93 3.2 0.0 1.0
O2E A:AP5301 3.3 13.1 1.0
O1G A:AP5301 3.3 15.6 1.0
HH22 A:ARG165 3.4 0.0 1.0
O5J A:AP5301 3.5 15.0 1.0
O2G A:AP5301 3.5 14.0 1.0
NZ A:LYS17 3.8 22.2 1.0
HZ1 A:LYS17 3.9 0.0 1.0
O A:HOH501 3.9 15.8 1.0
O1E A:AP5301 3.9 14.6 1.0
O3B A:AP5301 3.9 14.8 1.0
NH1 A:ARG93 4.0 21.6 1.0
NH2 A:ARG176 4.0 15.3 1.0
HN1 A:IMD302 4.0 0.0 1.0
O A:HOH550 4.1 28.2 1.0
H1 A:HOH501 4.1 0.0 1.0
NH2 A:ARG93 4.1 11.1 1.0
H2 A:HOH550 4.2 0.0 1.0
C5J A:AP5301 4.2 13.9 1.0
HH12 A:ARG165 4.2 0.0 1.0
HH22 A:ARG176 4.4 0.0 1.0
HE A:ARG176 4.4 0.0 1.0
NH2 A:ARG165 4.4 11.4 1.0
CA A:PRO13 4.4 16.8 1.0
CE A:LYS17 4.6 27.9 1.0
CZ A:ARG93 4.6 19.4 1.0
CB A:PRO13 4.6 14.2 1.0
HZ2 A:LYS17 4.6 0.0 1.0
H A:GLY14 4.7 0.0 1.0
HH11 A:ARG93 4.7 0.0 1.0
N1 A:IMD302 4.8 20.7 1.0
HH22 A:ARG132 4.9 0.0 1.0
HH21 A:ARG93 4.9 0.0 1.0
H1 A:HOH550 5.0 0.0 1.0
HH21 A:ARG165 5.0 0.0 1.0
H1 A:HOH513 5.0 0.0 1.0
O A:HOH513 5.0 22.6 1.0

Phosphorus binding site 5 out of 5 in 1aky

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Phosphorus binding site 5 out of 5 in the High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P301

b:13.3
occ:1.00
 PE A:AP5301 0.0 13.3 1.0
O1E A:AP5301 1.5 14.6 1.0
O2E A:AP5301 1.5 13.1 1.0
O5J A:AP5301 1.5 15.0 1.0
O3D A:AP5301 1.5 17.7 1.0
C5J A:AP5301 2.6 13.9 1.0
PD A:AP5301 2.9 15.9 1.0
HH22 A:ARG93 3.0 0.0 1.0
HH22 A:ARG165 3.2 0.0 1.0
H1 A:HOH511 3.3 0.0 1.0
O1D A:AP5301 3.3 15.9 1.0
HH22 A:ARG40 3.3 0.0 1.0
HH12 A:ARG40 3.4 0.0 1.0
O3G A:AP5301 3.7 13.0 1.0
HH12 A:ARG165 3.7 0.0 1.0
NH2 A:ARG93 3.7 11.1 1.0
O2D A:AP5301 3.8 22.2 1.0
O A:HOH511 3.8 20.6 1.0
C4J A:AP5301 3.9 13.8 1.0
O A:HOH550 4.0 28.2 1.0
NH2 A:ARG165 4.0 11.4 1.0
CA A:GLY36 4.0 12.2 1.0
O2G A:AP5301 4.1 14.0 1.0
HH21 A:ARG93 4.1 0.0 1.0
HN1 A:IMD302 4.1 0.0 1.0
HH12 A:ARG93 4.2 0.0 1.0
NH2 A:ARG40 4.3 18.3 1.0
H A:GLY36 4.3 0.0 1.0
N1 A:IMD302 4.4 20.7 1.0
NH1 A:ARG40 4.4 13.0 1.0
O4J A:AP5301 4.4 13.3 1.0
NH1 A:ARG165 4.4 14.1 1.0
PG A:AP5301 4.5 14.3 1.0
C3J A:AP5301 4.5 11.4 1.0
C5 A:IMD302 4.5 32.1 1.0
C8B A:AP5301 4.5 9.5 1.0
H1 A:HOH550 4.6 0.0 1.0
HH21 A:ARG165 4.6 0.0 1.0
N A:GLY36 4.6 13.8 1.0
CZ A:ARG93 4.6 19.4 1.0
CZ A:ARG165 4.6 9.7 1.0
H2 A:HOH550 4.7 0.0 1.0
H2 A:HOH511 4.7 0.0 1.0
NH1 A:ARG93 4.8 21.6 1.0
H2 A:HOH501 4.8 0.0 1.0
CZ A:ARG40 4.8 12.4 1.0
HZ1 A:LYS17 4.9 0.0 1.0
HH21 A:ARG176 5.0 0.0 1.0
HZ3 A:LYS17 5.0 0.0 1.0

Reference:

U.Abele, G.E.Schulz. High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer. Protein Sci. V. 4 1262 1995.
ISSN: ISSN 0961-8368
PubMed: 7670369
Page generated: Fri Sep 25 13:06:55 2020

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