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Magnesium in PDB 2dxe: Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gdp

Enzymatic activity of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gdp

All present enzymatic activity of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gdp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gdp, PDB code: 2dxe was solved by M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.08 / 1.70
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 69.802, 69.802, 107.093, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 19

Other elements in 2dxe:

The structure of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gdp also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gdp (pdb code 2dxe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gdp, PDB code: 2dxe:

Magnesium binding site 1 out of 1 in 2dxe

Go back to Magnesium Binding Sites List in 2dxe
Magnesium binding site 1 out of 1 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:25.8
occ:1.00
 O1A A:GDP501 2.2 27.2 1.0
O1B A:GDP501 2.3 29.2 1.0
O A:HOH769 2.3 22.4 1.0
O A:HOH760 2.4 23.3 1.0
O A:HOH765 2.5 21.1 1.0
O A:HOH774 3.2 34.2 1.0
PB A:GDP501 3.5 28.3 1.0
PA A:GDP501 3.6 27.8 1.0
O3A A:GDP501 4.0 28.0 1.0
O3B A:GDP501 4.1 29.3 1.0
NH1 A:ARG91 4.1 22.0 1.0
OE2 A:GLU57 4.1 25.8 1.0
O A:HOH718 4.2 15.4 1.0
CE1 A:HIS124 4.3 13.1 1.0
NE2 A:HIS58 4.3 17.1 1.0
O A:HOH727 4.4 15.8 1.0
C5' A:GDP501 4.5 25.4 1.0
OD2 A:ASP127 4.5 21.5 1.0
OE1 A:GLU57 4.5 23.8 1.0
O5' A:GDP501 4.5 26.1 1.0
CD A:GLU57 4.6 24.9 1.0
O2A A:GDP501 4.6 28.1 1.0
ND1 A:HIS124 4.7 11.7 1.0
O A:HOH733 4.8 15.6 1.0
O A:HOH729 4.8 15.2 1.0
CB A:ASP127 4.8 17.8 1.0
O2B A:GDP501 4.8 26.7 1.0
O A:HOH790 4.8 25.3 1.0
O A:ALA125 4.9 12.5 1.0
CE1 A:HIS58 4.9 17.3 1.0
CG A:ASP127 4.9 19.5 1.0
NH2 A:ARG91 4.9 24.2 1.0
CZ A:ARG91 5.0 24.0 1.0

Reference:

M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama. Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gdp To Be Published.
Page generated: Sun Aug 10 10:31:32 2025

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