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Magnesium in PDB 2wzb: The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride

Enzymatic activity of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride

All present enzymatic activity of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium 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, 3PG and Magnesium Trifluoride, PDB code: 2wzb was solved by M.W.Bowler, M.J.Cliff, J.P.M.Marston, N.J.Baxter, A.M.H.Hownslow, A.V.Varga, J.Szabo, M.Vas, G.M.Blackburn, J.P.Waltho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.430, 92.180, 109.000, 90.00, 90.00, 90.00
R / Rfree (%) 16.094 / 18.63

Other elements in 2wzb:

The structure of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium 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, 3PG and Magnesium Trifluoride (pdb code 2wzb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride, PDB code: 2wzb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2wzb

Go back to Magnesium Binding Sites List in 2wzb
Magnesium binding site 1 out of 2 in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium 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, 3PG and Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1417

b:8.6
occ:1.00
 F1 A:MGF1421 2.0 8.1 1.0
O1A A:ADP1419 2.1 7.2 1.0
O1B A:ADP1419 2.1 7.3 1.0
OD2 A:ASP374 2.1 5.5 1.0
O A:HOH2614 2.1 3.0 1.0
O A:HOH2608 2.1 6.2 1.0
PB A:ADP1419 3.2 7.3 1.0
CG A:ASP374 3.2 5.5 1.0
PA A:ADP1419 3.3 7.2 1.0
O3A A:ADP1419 3.5 7.1 1.0
MG A:MGF1421 3.5 7.9 1.0
O3B A:ADP1419 3.7 7.2 1.0
O A:HOH2611 3.9 9.7 1.0
CB A:ASP374 3.9 5.2 1.0
NZ A:LYS215 3.9 4.6 1.0
N A:ASP374 4.1 4.1 1.0
O1 A:3PG1420 4.2 9.5 1.0
CE A:LYS215 4.2 4.0 1.0
O A:HOH2557 4.2 12.6 1.0
OD1 A:ASP374 4.2 6.1 1.0
C5' A:ADP1419 4.3 8.3 1.0
O5' A:ADP1419 4.3 7.9 1.0
O A:HOH2280 4.3 11.6 1.0
F2 A:MGF1421 4.4 8.1 1.0
O2A A:ADP1419 4.4 8.2 1.0
O A:HOH2047 4.4 4.1 1.0
O2B A:ADP1419 4.4 7.7 1.0
O A:HOH2558 4.6 7.9 1.0
CA A:ASP374 4.7 4.7 1.0
CD A:LYS215 4.7 5.1 1.0
O2 A:3PG1420 4.7 7.6 1.0
N A:GLY373 4.8 4.5 1.0
C1 A:3PG1420 4.9 7.2 1.0
C A:GLY373 4.9 3.9 1.0
CA A:GLY373 4.9 4.4 1.0

Magnesium binding site 2 out of 2 in 2wzb

Go back to Magnesium Binding Sites List in 2wzb
Magnesium binding site 2 out of 2 in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1421

b:7.9
occ:1.00
 MG A:MGF1421 0.0 7.9 1.0
F2 A:MGF1421 1.9 8.1 1.0
F3 A:MGF1421 1.9 8.2 1.0
F1 A:MGF1421 1.9 8.1 1.0
O2 A:3PG1420 2.1 7.6 1.0
O3B A:ADP1419 2.2 7.2 1.0
C1 A:3PG1420 3.0 7.2 1.0
PB A:ADP1419 3.2 7.3 1.0
O1B A:ADP1419 3.2 7.3 1.0
O1 A:3PG1420 3.2 9.5 1.0
MG A:MG1417 3.5 8.6 1.0
O A:HOH2614 3.8 3.0 1.0
O A:HOH2303 3.8 4.2 1.0
NZ A:LYS219 3.9 6.6 1.0
NZ A:LYS215 3.9 4.6 1.0
O A:HOH2617 4.0 3.1 1.0
CA A:GLY395 4.1 4.5 1.0
N A:GLY396 4.2 5.0 1.0
N A:GLY373 4.2 4.5 1.0
O1A A:ADP1419 4.2 7.2 1.0
O3A A:ADP1419 4.3 7.1 1.0
O2B A:ADP1419 4.3 7.7 1.0
NH2 A:ARG38 4.3 4.2 1.0
C2 A:3PG1420 4.4 7.9 1.0
N A:GLY395 4.5 4.5 1.0
CA A:GLY372 4.5 3.8 1.0
PA A:ADP1419 4.6 7.2 1.0
CD A:LYS215 4.6 5.1 1.0
C A:GLY395 4.7 4.4 1.0
CE A:LYS215 4.7 4.0 1.0
CE A:LYS219 4.8 6.8 1.0
O2A A:ADP1419 4.8 8.2 1.0
ND2 A:ASN336 4.8 4.0 1.0
C A:GLY372 4.9 4.4 1.0
O A:HOH2608 4.9 6.2 1.0

Reference:

M.J.Cliff, M.W.Bowler, J.Szabo, J.P.M.Marston, A.V.Varga, A.M.H.Hownslow, N.J.Baxter, G.M.Blackburn, M.Vas, J.P.Waltho. Transition State Analogue Structures of Human Phosphoglycerate Kinase Establish the Importance of Charge Balance in Catalysis. J.Am.Chem.Soc. V. 132 6507 2010.
ISSN: ISSN 0002-7863
PubMed: 20397725
DOI: 10.1021/JA100974T
Page generated: Sun Aug 10 15:56:24 2025

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