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Magnesium in PDB 2ybe: The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution

Enzymatic activity of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution

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 at 2.0 A Resolution:
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 at 2.0 A Resolution, PDB code: 2ybe 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.202, 91.030, 108.807, 90.00, 90.00, 90.00
R / Rfree (%) 19.316 / 24.329

Other elements in 2ybe:

The structure of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Aluminium (Al) 1 atom
Fluorine (F) 4 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 at 2.0 A Resolution (pdb code 2ybe). 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 Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution, PDB code: 2ybe:

Magnesium binding site 1 out of 1 in 2ybe

Go back to Magnesium Binding Sites List in 2ybe
Magnesium binding site 1 out of 1 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution


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 at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1417

b:31.6
occ:1.00
 O3B A:LA81419 1.8 27.6 1.0
O1A A:LA81419 1.9 22.2 1.0
OD2 A:ASP374 2.0 30.3 1.0
O A:HOH2112 2.0 21.9 1.0
F3 A:ALF1420 2.2 21.6 1.0
O A:HOH2115 2.2 19.5 1.0
PB A:LA81419 3.0 25.3 1.0
CG A:ASP374 3.1 31.8 1.0
PA A:LA81419 3.1 25.0 1.0
O3A A:LA81419 3.5 27.1 1.0
CB A:ASP374 3.6 31.4 1.0
F1 A:ALF1420 3.6 22.1 1.0
O1B A:LA81419 3.7 26.4 1.0
AL A:ALF1420 3.7 23.6 1.0
N A:ASP374 3.7 32.1 1.0
O5' A:LA81419 3.8 28.3 1.0
O A:HOH2113 4.0 42.4 1.0
NZ A:LYS215 4.0 26.0 1.0
O1 A:3PG1421 4.1 18.8 1.0
OD1 A:ASP374 4.1 30.6 1.0
C5' A:LA81419 4.2 30.6 1.0
O A:HOH2095 4.2 41.4 1.0
CA A:ASP374 4.3 31.6 1.0
O2B A:LA81419 4.3 29.6 1.0
O2A A:LA81419 4.4 29.4 1.0
CE A:LYS215 4.4 27.3 1.0
O A:HOH2008 4.5 34.4 1.0
F4 A:ALF1420 4.5 25.7 1.0
O A:HOH2096 4.6 25.6 1.0
O2 A:3PG1421 4.6 22.0 1.0
N A:GLY373 4.6 28.3 1.0
C A:GLY373 4.7 31.9 1.0
CA A:GLY373 4.7 31.2 1.0
C1 A:3PG1421 4.8 18.9 1.0
CD A:LYS215 4.9 29.0 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: Sun Aug 10 16:40:37 2025

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