Atomistry » Magnesium » PDB 8f90-8fl8 » 8fdb
Atomistry »
  Magnesium »
    PDB 8f90-8fl8 »
      8fdb »

Magnesium in PDB 8fdb: Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution.

Protein crystallography data

The structure of Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution., PDB code: 8fdb was solved by A.Rodriguez-Romero, A.Rodriguez-Hernandez, J.Marcos-Viquez, I.Bustos-Jaimes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.95 / 3.06
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 71.885, 113.142, 171.008, 90, 90, 90
R / Rfree (%) 20.6 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution. (pdb code 8fdb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution., PDB code: 8fdb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8fdb

Go back to Magnesium Binding Sites List in 8fdb
Magnesium binding site 1 out of 2 in the Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution.


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 Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:31.1
occ:1.00
O A:ILE96 2.8 27.5 1.0
O2P A:AGP501 2.8 32.0 1.0
N A:ARG49 3.1 32.1 1.0
CA A:GLY48 3.3 25.9 1.0
CB A:SER97 3.5 30.4 1.0
C A:GLY48 3.6 32.6 1.0
O A:ARG49 3.6 33.7 1.0
CB A:SER52 3.6 25.4 1.0
CA A:SER97 3.7 31.3 1.0
OG A:SER97 3.7 30.7 1.0
O1P A:AGP501 3.9 37.9 1.0
P A:AGP501 3.9 46.7 1.0
C A:ILE96 3.9 23.1 1.0
OG A:SER52 3.9 19.8 1.0
CG1 A:ILE105 4.0 41.8 1.0
CA A:ARG49 4.0 37.4 1.0
CB A:ARG49 4.1 41.6 1.0
C6 A:AGP501 4.2 37.5 1.0
C A:ARG49 4.3 34.7 1.0
N A:SER97 4.3 26.3 1.0
N A:GLY48 4.5 33.0 1.0
O6 A:AGP501 4.6 46.5 1.0
CD1 A:ILE105 4.6 43.3 1.0
O A:VAL47 4.6 25.5 1.0
O A:GLY48 4.7 36.6 1.0
CB A:ILE105 4.8 37.9 1.0
CG2 A:ILE105 4.9 37.8 1.0
C A:VAL47 5.0 25.1 1.0

Magnesium binding site 2 out of 2 in 8fdb

Go back to Magnesium Binding Sites List in 8fdb
Magnesium binding site 2 out of 2 in the Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:29.7
occ:1.00
O1P B:AGP702 2.6 34.0 1.0
OH A:TYR61 2.9 25.2 1.0
CB A:TYR215 3.0 23.0 1.0
N A:GLY212 3.2 25.2 1.0
CG A:TYR215 3.2 26.9 1.0
CD2 A:TYR215 3.2 27.1 1.0
CB A:SER237 3.4 23.4 1.0
P B:AGP702 3.6 38.4 1.0
O3P B:AGP702 3.7 38.9 1.0
CA A:ARG211 3.8 23.8 1.0
CZ A:TYR61 3.8 26.1 1.0
C A:ARG211 3.9 25.0 1.0
C6 B:AGP702 4.0 44.3 1.0
CA A:GLY212 4.0 20.4 1.0
CA A:SER237 4.1 20.8 1.0
CD1 A:TYR215 4.1 27.1 1.0
CE2 A:TYR215 4.1 26.6 1.0
O A:GLY210 4.1 24.9 1.0
O A:GLY212 4.2 21.8 1.0
O6 B:AGP702 4.3 42.1 1.0
CE2 A:TYR61 4.4 28.6 1.0
CG A:ARG211 4.4 23.6 1.0
NH1 A:ARG211 4.5 36.5 1.0
CA A:TYR215 4.5 23.0 1.0
CE1 A:TYR61 4.5 26.9 1.0
OG A:SER237 4.6 36.8 1.0
N A:ARG211 4.6 27.8 1.0
C A:GLY212 4.6 26.2 1.0
C A:GLY210 4.7 25.7 1.0
CB A:ARG211 4.7 20.6 1.0
OG B:SER77 4.8 37.1 1.0
CE1 A:TYR215 4.8 28.0 1.0
CZ A:TYR215 4.8 29.0 1.0
O4 B:AGP702 4.9 55.5 1.0
N A:SER237 4.9 21.8 1.0
O2P B:AGP702 4.9 32.6 1.0
N A:TYR215 5.0 22.5 1.0

Reference:

J.Marcos-Viquez, A.Rodriguez-Hernandez, L.I.Alvarez-Anorve, A.Medina-Garcia, J.Plumbridge, M.L.Calcagno, A.Rodriguez-Romero, I.Bustos-Jaimes. Substrate Binding in the Allosteric Site Mimics Homotropic Cooperativity in the Sis-Fold Glucosamine-6-Phosphate Deaminases. Protein Sci. E4651 2023.
ISSN: ESSN 1469-896X
PubMed: 37145875
DOI: 10.1002/PRO.4651
Page generated: Fri Oct 4 02:29:13 2024

Last articles

Zn in 1MC5
Zn in 1MFM
Zn in 1MA0
Zn in 1MED
Zn in 1MEA
Zn in 1MBX
Zn in 1MA3
Zn in 1M9O
Zn in 1M9R
Zn in 1M9Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy