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Magnesium in PDB 2y3i: The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride

Enzymatic activity of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride

All present enzymatic activity of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride:
2.7.2.3;

Protein crystallography data

The structure of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride, PDB code: 2y3i was solved by M.W.Bowler, L.Chaloin, C.Lionne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.419, 103.877, 203.094, 90.00, 90.00, 90.00
R / Rfree (%) 26.3 / 30.3

Other elements in 2y3i:

The structure of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride also contains other interesting chemical elements:

Aluminium (Al) 2 atoms
Fluorine (F) 8 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride (pdb code 2y3i). 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 Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride, PDB code: 2y3i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2y3i

Go back to Magnesium Binding Sites List in 2y3i
Magnesium binding site 1 out of 2 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1416

b:20.9
occ:1.00
O1A A:LA81418 1.7 27.0 1.0
F3 A:ALF1419 1.8 30.4 1.0
OD1 A:ASP374 2.0 25.7 1.0
O3B A:LA81418 2.3 27.1 1.0
PA A:LA81418 3.1 26.6 1.0
CG A:ASP374 3.2 25.5 1.0
PB A:LA81418 3.3 27.1 1.0
AL A:ALF1419 3.5 28.5 1.0
O3A A:LA81418 3.5 27.0 1.0
O5' A:LA81418 3.6 28.1 1.0
NZ A:LYS215 3.7 28.7 1.0
F1 A:ALF1419 3.8 28.2 1.0
O1B A:LA81418 3.9 27.7 1.0
CE A:LYS215 4.0 28.9 1.0
OD2 A:ASP374 4.0 25.5 1.0
F4 A:ALF1419 4.1 29.1 1.0
O1 A:3PG1420 4.2 31.0 1.0
N A:ASP374 4.2 25.1 1.0
CB A:ASP374 4.2 25.5 1.0
O2A A:LA81418 4.3 26.7 1.0
O2B A:LA81418 4.7 25.9 1.0
O2 A:3PG1420 4.7 31.9 1.0
C1 A:3PG1420 4.9 30.7 1.0
C5' A:LA81418 4.9 28.1 1.0
CA A:ASP374 4.9 25.6 1.0
CA A:GLY373 4.9 24.9 1.0
N A:GLY373 4.9 24.7 1.0
C A:GLY373 5.0 24.9 1.0

Magnesium binding site 2 out of 2 in 2y3i

Go back to Magnesium Binding Sites List in 2y3i
Magnesium binding site 2 out of 2 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1418

b:18.2
occ:1.00
F3 D:ALF1417 2.0 32.4 1.0
O1A D:LA81416 2.0 29.4 1.0
OD1 D:ASP374 2.2 36.4 1.0
O3B D:LA81416 2.2 26.8 1.0
CG D:ASP374 3.4 34.9 1.0
PB D:LA81416 3.4 27.1 1.0
PA D:LA81416 3.5 29.2 1.0
AL D:ALF1417 3.6 30.6 1.0
F1 D:ALF1417 3.7 31.0 1.0
NZ D:LYS215 3.7 27.0 1.0
O1 D:3PG1420 3.8 33.0 1.0
O1B D:LA81416 3.9 27.2 1.0
O5' D:LA81416 3.9 30.4 1.0
O3A D:LA81416 4.0 27.7 1.0
CE D:LYS215 4.1 26.5 1.0
N D:ASP374 4.1 32.4 1.0
OD2 D:ASP374 4.1 34.8 1.0
F4 D:ALF1417 4.3 30.2 1.0
CB D:ASP374 4.3 33.9 1.0
CA D:GLY373 4.6 32.0 1.0
N D:GLY373 4.6 31.8 1.0
O2A D:LA81416 4.7 29.6 1.0
C1 D:3PG1420 4.7 32.5 1.0
O2 D:3PG1420 4.7 32.8 1.0
O2B D:LA81416 4.7 27.3 1.0
C D:GLY373 4.8 31.7 1.0
CA D:ASP374 4.9 32.9 1.0

Reference:

P.Lallemand, L.Chaloin, B.Roy, T.Barman, M.W.Bowler, C.Lionne. Interaction of Human 3-Phosphoglycerate Kinase with Its Two Substrates: Is Substrate Antagonism A Kinetic Advantage? J.Mol.Biol. V. 409 742 2011.
ISSN: ISSN 0022-2836
PubMed: 21549713
DOI: 10.1016/J.JMB.2011.04.048
Page generated: Wed Aug 14 07:23:16 2024

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