Phosphorus in PDB 16pk: Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog

Enzymatic activity of Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog

All present enzymatic activity of Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog:
2.7.2.3;

Protein crystallography data

The structure of Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog, PDB code: 16pk was solved by B.E.Bernstein, J.Bressi, M.Blackburn, M.Gelb, 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 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.710, 79.760, 81.320, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.5

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog (pdb code 16pk). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 3 binding sites of Phosphorus where determined in the Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog, PDB code: 16pk:
Jump to Phosphorus binding site number: 1; 2; 3;

Phosphorus binding site 1 out of 3 in 16pk

Go back to Phosphorus Binding Sites List in 16pk
Phosphorus binding site 1 out of 3 in the Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P499

b:18.0
occ:1.00
PB A:BIS499 0.0 18.0 1.0
O3B A:BIS499 1.5 19.3 1.0
O3A A:BIS499 1.5 17.2 1.0
O2B A:BIS499 1.6 16.0 1.0
C11 A:BIS499 1.8 20.3 1.0
F12 A:BIS499 2.5 19.9 1.0
F11 A:BIS499 2.6 22.0 1.0
C12 A:BIS499 2.7 19.9 1.0
PA A:BIS499 2.9 15.9 1.0
O2A A:BIS499 3.5 14.1 1.0
O1A A:BIS499 3.7 18.9 1.0
O A:HOH781 3.7 27.0 1.0
O A:HOH768 3.7 11.8 1.0
O5' A:BIS499 3.9 13.7 1.0
O A:HOH766 3.9 13.1 1.0
O A:HOH862 4.1 47.4 1.0
C13 A:BIS499 4.1 23.0 1.0
CA A:GLY339 4.1 8.8 1.0
C5' A:BIS499 4.2 12.8 1.0
CD A:PRO340 4.3 8.0 1.0
NZ A:LYS223 4.4 13.2 1.0
N A:GLY339 4.5 8.0 1.0
O A:HOH776 4.5 23.0 1.0
O A:HOH1020 4.9 42.9 1.0
O A:HOH1037 4.9 44.0 1.0
O A:HOH799 4.9 24.8 1.0

Phosphorus binding site 2 out of 3 in 16pk

Go back to Phosphorus Binding Sites List in 16pk
Phosphorus binding site 2 out of 3 in the Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P499

b:15.9
occ:1.00
PA A:BIS499 0.0 15.9 1.0
O2A A:BIS499 1.5 14.1 1.0
O1A A:BIS499 1.5 18.9 1.0
O3A A:BIS499 1.6 17.2 1.0
O5' A:BIS499 1.6 13.7 1.0
C5' A:BIS499 2.6 12.8 1.0
PB A:BIS499 2.9 18.0 1.0
O3B A:BIS499 3.4 19.3 1.0
F11 A:BIS499 3.6 22.0 1.0
C4' A:BIS499 3.7 12.3 1.0
O A:HOH571 3.7 20.2 1.0
O A:HOH1020 3.8 42.9 1.0
C11 A:BIS499 3.8 20.3 1.0
O2B A:BIS499 4.0 16.0 1.0
CA A:GLY217 4.0 9.5 1.0
O A:HOH799 4.1 24.8 1.0
O A:HOH806 4.1 38.8 1.0
N A:ALA218 4.1 10.4 1.0
O A:HOH776 4.2 23.0 1.0
O4' A:BIS499 4.2 12.9 1.0
NZ A:LYS223 4.2 13.2 1.0
C12 A:BIS499 4.3 19.9 1.0
C A:GLY217 4.6 11.5 1.0
O A:HOH512 4.7 13.6 1.0
O A:HOH768 4.8 11.8 1.0
C3' A:BIS499 5.0 12.8 1.0
CD A:PRO340 5.0 8.0 1.0

Phosphorus binding site 3 out of 3 in 16pk

Go back to Phosphorus Binding Sites List in 16pk
Phosphorus binding site 3 out of 3 in the Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Phosphoglycerate Kinase From Trypanosoma Brucei Bisubstrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P499

b:24.1
occ:1.00
PN A:BIS499 0.0 24.1 1.0
ON3 A:BIS499 1.5 24.0 1.0
ON1 A:BIS499 1.5 20.0 1.0
ON2 A:BIS499 1.5 25.4 1.0
C15 A:BIS499 1.8 25.5 1.0
F52 A:BIS499 2.5 22.4 1.0
F51 A:BIS499 2.6 29.6 1.0
C14 A:BIS499 2.8 24.3 1.0
O A:HOH505 3.5 13.5 1.0
O A:HOH1032 3.5 36.5 1.0
N A:GLY398 3.6 12.3 1.0
O A:HOH902 3.6 30.4 1.0
C13 A:BIS499 3.7 23.0 1.0
O A:HOH1034 3.8 42.6 1.0
O A:HOH872 3.8 46.6 1.0
O A:HOH874 3.9 43.8 1.0
N A:GLY399 4.0 11.0 1.0
O A:HOH779 4.1 28.0 1.0
CA A:GLY398 4.2 10.5 1.0
C A:GLY397 4.5 11.9 1.0
CA A:GLY397 4.6 12.5 1.0
C A:GLY398 4.6 10.8 1.0
O A:HOH981 4.7 45.4 1.0
CA A:GLY399 4.9 10.3 1.0

Reference:

B.E.Bernstein, D.M.Williams, J.C.Bressi, P.Kuhn, M.H.Gelb, G.M.Blackburn, W.G.Hol. A Bisubstrate Analog Induces Unexpected Conformational Changes in Phosphoglycerate Kinase From Trypanosoma Brucei. J.Mol.Biol. V. 279 1137 1998.
ISSN: ISSN 0022-2836
PubMed: 9642090
DOI: 10.1006/JMBI.1998.1835
Page generated: Fri Sep 25 11:39:25 2020

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