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Magnesium in PDB 3c3a: Crystal Structure of Human Phosphoglycerate Kinase Bound to 3-Phosphoglycerate and L-Adp

Enzymatic activity of Crystal Structure of Human Phosphoglycerate Kinase Bound to 3-Phosphoglycerate and L-Adp

All present enzymatic activity of Crystal Structure of Human Phosphoglycerate Kinase Bound to 3-Phosphoglycerate and L-Adp:
2.7.2.3;

Protein crystallography data

The structure of Crystal Structure of Human Phosphoglycerate Kinase Bound to 3-Phosphoglycerate and L-Adp, PDB code: 3c3a was solved by S.T.Arold, C.Gondeau, C.Lionne, L.Chaloin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.20 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 35.629, 55.949, 95.441, 101.88, 95.20, 82.91
R / Rfree (%) 17.9 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphoglycerate Kinase Bound to 3-Phosphoglycerate and L-Adp (pdb code 3c3a). 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 Human Phosphoglycerate Kinase Bound to 3-Phosphoglycerate and L-Adp, PDB code: 3c3a:

Magnesium binding site 1 out of 1 in 3c3a

Go back to Magnesium Binding Sites List in 3c3a
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Phosphoglycerate Kinase Bound to 3-Phosphoglycerate and L-Adp


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 Human Phosphoglycerate Kinase Bound to 3-Phosphoglycerate and L-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg417

b:52.7
occ:1.00
 O2A B:ADP419 2.3 73.4 1.0
O3B B:ADP419 2.9 91.0 1.0
O2B B:ADP419 3.0 92.4 1.0
OD2 B:ASP218 3.2 44.7 1.0
PB B:ADP419 3.3 91.8 1.0
O3A B:ADP419 3.3 82.2 1.0
PA B:ADP419 3.4 72.2 1.0
N B:LYS215 3.7 30.3 1.0
CE B:LYS219 3.8 38.3 1.0
CB B:LYS215 4.0 32.4 1.0
CG B:ASP218 4.0 40.2 1.0
N B:ALA214 4.0 26.8 1.0
OD1 B:ASP218 4.0 37.7 1.0
O B:LYS215 4.2 33.9 1.0
O5' B:ADP419 4.2 70.3 1.0
CB B:ALA214 4.3 27.4 1.0
NZ B:LYS219 4.3 38.1 1.0
CA B:LYS215 4.4 32.1 1.0
CA B:ALA214 4.6 27.4 1.0
CG B:LYS215 4.6 34.5 1.0
C5' B:ADP419 4.6 66.7 1.0
O B:HOH576 4.6 25.3 1.0
O1A B:ADP419 4.6 68.4 1.0
C B:ALA214 4.6 28.0 1.0
CD B:LYS215 4.7 43.4 1.0
C B:LYS215 4.8 32.9 1.0
O1B B:ADP419 4.8 90.6 1.0
CA B:GLY213 4.9 24.8 1.0
C B:GLY213 5.0 26.6 1.0

Reference:

C.Gondeau, L.Chaloin, P.Lallemand, B.Roy, C.Perigaud, T.Barman, A.Varga, M.Vas, C.Lionne, S.T.Arold. Molecular Basis For the Lack of Enantioselectivity of Human 3-Phosphoglycerate Kinase Nucleic Acids Res. V. 36 3620 2008.
ISSN: ISSN 0305-1048
PubMed: 18463139
DOI: 10.1093/NAR/GKN212
Page generated: Sun Aug 10 17:59:28 2025

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