Atomistry » Magnesium » PDB 101d-1amu » 13pk
Atomistry »
  Magnesium »
    PDB 101d-1amu »
      13pk »

Magnesium 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

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei, PDB code: 13pk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 13pk

Go back to Magnesium Binding Sites List in 13pk
Magnesium binding site 1 out of 4 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg422

b:47.0
occ:1.00
OD2 A:ASP377 2.6 31.4 1.0
O1A A:ADP421 2.7 32.3 1.0
O2B A:ADP421 2.8 32.7 1.0
O A:HOH762 3.1 48.2 1.0
O A:HOH861 3.4 56.7 1.0
O A:HOH848 3.6 45.0 1.0
CG A:ASP377 3.8 29.6 1.0
CE A:LYS219 3.8 56.8 1.0
PA A:ADP421 3.9 30.5 1.0
O A:HOH842 4.1 32.8 1.0
PB A:ADP421 4.1 29.9 1.0
O3A A:ADP421 4.1 32.8 1.0
OD1 A:ASP377 4.4 34.1 1.0
NZ A:LYS219 4.7 53.4 1.0
O2A A:ADP421 4.8 30.9 1.0
CB A:ASP377 4.8 24.2 1.0
O3B A:ADP421 4.8 28.9 1.0
N A:ASP377 4.8 25.8 1.0
O1 A:3PG423 4.9 48.1 1.0
O5' A:ADP421 4.9 27.1 1.0
C5' A:ADP421 4.9 28.2 1.0
CD A:LYS219 5.0 57.2 1.0

Magnesium binding site 2 out of 4 in 13pk

Go back to Magnesium Binding Sites List in 13pk
Magnesium binding site 2 out of 4 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg422

b:33.5
occ:1.00
OD2 B:ASP377 2.4 40.2 1.0
O1A B:ADP421 2.6 29.7 1.0
O2B B:ADP421 2.7 34.3 1.0
O B:HOH444 3.5 35.1 1.0
CG B:ASP377 3.6 40.6 1.0
O B:HOH579 3.6 58.0 1.0
PA B:ADP421 3.8 24.8 1.0
O B:HOH556 4.0 9.9 1.0
PB B:ADP421 4.0 27.5 1.0
O3A B:ADP421 4.1 29.4 1.0
CE B:LYS219 4.2 54.2 1.0
OD1 B:ASP377 4.2 44.4 1.0
O2A B:ADP421 4.5 22.3 1.0
CB B:ASP377 4.6 33.2 1.0
N B:ASP377 4.7 23.9 1.0
O3B B:ADP421 4.8 27.3 1.0
O5' B:ADP421 4.9 27.9 1.0
C5' B:ADP421 4.9 29.7 1.0
O B:HOH450 5.0 39.8 1.0

Magnesium binding site 3 out of 4 in 13pk

Go back to Magnesium Binding Sites List in 13pk
Magnesium binding site 3 out of 4 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg422

b:62.0
occ:1.00
O2 C:PO4624 2.4 66.1 1.0
O1A C:ADP421 2.7 53.4 1.0
O2B C:ADP421 2.7 56.8 1.0
OD2 C:ASP377 2.7 43.4 1.0
O C:HOH759 3.2 51.6 1.0
P C:PO4624 3.7 65.8 1.0
PA C:ADP421 3.7 49.4 1.0
O4 C:PO4624 3.7 66.5 1.0
CE C:LYS219 3.9 85.2 1.0
PB C:ADP421 3.9 50.6 1.0
CG C:ASP377 3.9 46.5 1.0
O3A C:ADP421 4.0 50.7 1.0
O2A C:ADP421 4.1 47.6 1.0
O3B C:ADP421 4.4 53.7 1.0
O1 C:PO4624 4.5 64.3 1.0
NZ C:LYS219 4.7 90.6 1.0
OD1 C:ASP377 4.7 46.1 1.0
N C:ASP377 4.7 36.7 1.0
O3 C:PO4624 4.8 65.0 1.0
CB C:ASP377 4.9 40.8 1.0
O5' C:ADP421 4.9 40.9 1.0

Magnesium binding site 4 out of 4 in 13pk

Go back to Magnesium Binding Sites List in 13pk
Magnesium binding site 4 out of 4 in the Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ternary Complex of Phosphoglycerate Kinase From Trypanosoma Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg422

b:36.3
occ:1.00
O2B D:ADP421 2.2 36.4 1.0
OD2 D:ASP377 2.4 35.9 1.0
O1A D:ADP421 2.4 43.5 1.0
O2 D:PO4625 2.7 66.1 1.0
PA D:ADP421 3.4 36.2 1.0
PB D:ADP421 3.4 37.9 1.0
O3A D:ADP421 3.5 35.5 1.0
O4 D:PO4625 3.5 58.1 1.0
CG D:ASP377 3.5 41.0 1.0
P D:PO4625 3.6 58.9 1.0
O3B D:ADP421 3.9 28.3 1.0
O2A D:ADP421 4.0 41.1 1.0
CE D:LYS219 4.1 64.8 1.0
O1 D:PO4625 4.2 65.3 1.0
N D:ASP377 4.3 31.2 1.0
CB D:ASP377 4.3 38.4 1.0
OD1 D:ASP377 4.4 47.3 1.0
O5' D:ADP421 4.6 36.7 1.0
O1B D:ADP421 4.7 37.9 1.0
N D:GLY376 4.7 33.1 1.0
C5' D:ADP421 4.8 34.1 1.0
O3 D:PO4625 4.9 62.2 1.0
CA D:ASP377 5.0 32.2 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: Mon Dec 14 03:23:11 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy