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Magnesium in PDB 4axx: The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp 3-Phosphoglycerate and Beryllium Trifluoride

Enzymatic activity of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp 3-Phosphoglycerate and Beryllium Trifluoride

All present enzymatic activity of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp 3-Phosphoglycerate and Beryllium Trifluoride:
2.7.2.3;

Protein crystallography data

The structure of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp 3-Phosphoglycerate and Beryllium Trifluoride, PDB code: 4axx was solved by M.W.Bowler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.820, 90.800, 108.540, 90.00, 90.00, 90.00
R / Rfree (%) 16.976 / 20.65

Other elements in 4axx:

The structure of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp 3-Phosphoglycerate and Beryllium Trifluoride also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp 3-Phosphoglycerate and Beryllium Trifluoride (pdb code 4axx). 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 The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp 3-Phosphoglycerate and Beryllium Trifluoride, PDB code: 4axx:

Magnesium binding site 1 out of 1 in 4axx

Go back to Magnesium Binding Sites List in 4axx
Magnesium binding site 1 out of 1 in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp 3-Phosphoglycerate and Beryllium Trifluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp 3-Phosphoglycerate and Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1418

b:15.4
occ:1.00
 O3B A:ADP1420 1.8 12.7 1.0
O2A A:ADP1420 1.9 14.0 1.0
OD2 A:ASP375 2.0 15.0 1.0
F1 A:BEF1422 2.1 16.2 1.0
O A:HOH2388 2.3 16.6 1.0
O A:HOH2236 2.4 19.9 1.0
PB A:ADP1420 2.6 13.9 1.0
PA A:ADP1420 3.0 14.0 1.0
O3A A:ADP1420 3.0 14.4 1.0
CG A:ASP375 3.1 14.4 1.0
O1B A:ADP1420 3.4 14.2 1.0
BE A:BEF1422 3.5 15.7 1.0
CB A:ASP375 3.8 13.9 1.0
O A:HOH2418 3.8 16.2 1.0
N A:ASP375 3.9 13.3 1.0
O2B A:ADP1420 3.9 14.6 1.0
NZ A:LYS216 4.0 15.4 1.0
F3 A:BEF1422 4.0 15.7 1.0
C5' A:ADP1420 4.0 13.4 1.0
O5' A:ADP1420 4.0 14.3 1.0
O1A A:ADP1420 4.2 15.9 1.0
OD1 A:ASP375 4.2 15.6 1.0
O1 A:3PG1421 4.3 13.0 1.0
CE A:LYS216 4.3 16.4 1.0
O A:HOH2386 4.4 21.8 1.0
CA A:ASP375 4.5 13.7 1.0
O A:HOH2020 4.5 33.1 1.0
N A:GLY374 4.6 11.9 1.0
F2 A:BEF1422 4.6 17.5 1.0
O A:HOH2049 4.7 16.0 1.0
CD A:LYS216 4.7 15.6 1.0
O2 A:3PG1421 4.8 13.2 1.0
C A:GLY374 4.8 13.5 1.0
CA A:GLY374 4.8 12.7 1.0
O A:HOH2387 4.9 22.6 1.0
C1 A:3PG1421 5.0 12.0 1.0

Reference:

M.W.Bowler, M.J.Cliff, G.M.Blackburn, J.P.Waltho. Catalytic Activity in the Transitions State Analogue Stabilised Conformation of A Phosphoryl Transfer Enzyme To Be Published.
Page generated: Mon Aug 11 06:06:06 2025

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