Atomistry » Magnesium » PDB 5zki-6a1d » 5zwb
Atomistry »
  Magnesium »
    PDB 5zki-6a1d »
      5zwb »

Magnesium in PDB 5zwb: Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base

Enzymatic activity of Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base

All present enzymatic activity of Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base:
2.7.1.35;

Protein crystallography data

The structure of Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base, PDB code: 5zwb was solved by G.Deka, J.F.Benazir, J.N.Kalyani, H.S.Savithri, M.R.N.Murthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.90 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.700, 73.700, 248.310, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base (pdb code 5zwb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base, PDB code: 5zwb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5zwb

Go back to Magnesium Binding Sites List in 5zwb
Magnesium binding site 1 out of 3 in the Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base


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 Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:27.9
occ:1.00
 O A:HOH404 1.9 25.7 1.0
O3B A:ADP304 2.0 39.1 1.0
O A:HOH421 2.0 32.0 1.0
O A:HOH406 2.1 24.7 1.0
O A:HOH431 2.2 32.6 1.0
PB A:ADP304 3.3 40.5 1.0
O2B A:ADP304 3.7 39.7 1.0
MG A:MG312 3.9 20.9 1.0
OE2 A:GLU167 3.9 26.6 1.0
OD1 A:ASP130 4.1 27.0 1.0
OD2 A:ASP130 4.1 26.7 1.0
CA A:GLY236 4.1 25.4 1.0
O1B A:ADP304 4.2 40.3 1.0
O3A A:ADP304 4.3 40.9 1.0
OE1 A:GLU167 4.3 25.7 1.0
CG2 A:VAL132 4.4 27.6 1.0
OH A:TYR141 4.4 36.5 1.0
OD1 A:ASP237 4.4 23.8 1.0
C5A A:JLP233 4.5 34.9 1.0
OP4 A:JLP233 4.5 34.6 0.7
O A:HOH475 4.5 30.8 1.0
CG A:ASP130 4.5 26.5 1.0
CD A:GLU167 4.6 26.3 1.0
C A:GLY236 4.6 24.8 1.0
O A:HOH408 4.7 38.7 1.0
ND2 A:ASN164 4.7 28.0 1.0
N A:ASP237 4.8 24.3 1.0
N A:GLY236 4.8 25.7 1.0
CG1 A:VAL132 4.9 27.8 1.0

Magnesium binding site 2 out of 3 in 5zwb

Go back to Magnesium Binding Sites List in 5zwb
Magnesium binding site 2 out of 3 in the Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base


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 Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg312

b:20.9
occ:1.00
 O A:THR162 2.7 26.2 1.0
OG1 A:THR200 2.7 27.6 1.0
O A:HOH475 2.8 30.8 1.0
O3B A:ADP304 3.0 39.1 1.0
O A:HOH406 3.1 24.7 1.0
CG2 A:THR200 3.4 28.1 1.0
N A:ASN164 3.5 26.9 1.0
O3A A:ADP304 3.6 40.9 1.0
C A:PRO163 3.6 26.7 1.0
CB A:THR200 3.6 28.1 1.0
C A:THR162 3.7 25.9 1.0
MG A:MG301 3.9 27.9 1.0
PB A:ADP304 3.9 40.5 1.0
O A:PRO163 3.9 26.7 1.0
OD1 A:ASP130 4.0 27.0 1.0
CA A:ASN164 4.1 27.2 1.0
OE1 A:GLU167 4.1 25.7 1.0
CA A:PRO163 4.1 26.5 1.0
CB A:ASN164 4.2 27.2 1.0
O A:HOH404 4.3 25.7 1.0
N A:PRO163 4.4 26.0 1.0
CA A:GLY236 4.6 25.4 1.0
O1B A:ADP304 4.6 40.3 1.0
OG1 A:THR162 4.6 25.7 1.0
CB A:THR162 4.6 26.2 1.0
CG A:ASP130 4.8 26.5 1.0
OD2 A:ASP130 4.8 26.7 1.0
CA A:THR162 4.8 25.9 1.0
O2A A:ADP304 4.8 41.6 1.0
PA A:ADP304 4.9 41.7 1.0
CA A:THR200 4.9 28.6 1.0
CG A:ASN164 4.9 27.4 1.0
N A:THR200 5.0 28.2 1.0

Magnesium binding site 3 out of 3 in 5zwb

Go back to Magnesium Binding Sites List in 5zwb
Magnesium binding site 3 out of 3 in the Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via A Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:46.2
occ:1.00
 O B:HOH446 2.0 38.9 1.0
O B:HOH447 2.0 41.5 1.0
O B:HOH558 2.2 40.8 1.0
O B:HOH417 2.3 35.8 1.0
NE2 B:GLN143 3.0 41.7 1.0
CD B:GLN143 4.1 40.9 1.0
OE2 B:GLU145 4.3 30.5 1.0
OE1 B:GLU145 4.4 31.3 1.0
CG B:GLN143 4.7 39.3 1.0
CD B:GLU145 4.8 30.6 1.0

Reference:

G.Deka, J.F.Benazir, J.N.Kalyani, H.S.Savithri, M.R.N.Murthy. Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium To Be Published.
Page generated: Mon Sep 30 18:44:15 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy