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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

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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

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