Magnesium in PDB 5zwa: Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via Schiff Base in Protomer A and the Product (Plp) in Protomer B

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

All present enzymatic activity of Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via Schiff Base in Protomer A and the Product (Plp) in Protomer B:
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 Schiff Base in Protomer A and the Product (Plp) in Protomer B, PDB code: 5zwa 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) 62.23 / 2.45
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.260, 72.260, 244.880, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 23.5

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 Schiff Base in Protomer A and the Product (Plp) in Protomer B (pdb code 5zwa). 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 Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via Schiff Base in Protomer A and the Product (Plp) in Protomer B, PDB code: 5zwa:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5zwa

Go back to Magnesium Binding Sites List in 5zwa
Magnesium binding site 1 out of 2 in the Crystal Structure of Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium in Complex with Adp, Pl-Linked to LYS233 Via Schiff Base in Protomer A and the Product (Plp) in Protomer B


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 Schiff Base in Protomer A and the Product (Plp) in Protomer B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:24.3
occ:1.00
 O3B A:ADP309 2.0 17.9 0.8
O A:HOH424 2.0 12.4 1.0
O A:HOH419 2.2 14.7 1.0
O A:HOH410 2.2 13.3 1.0
PB A:ADP309 3.2 18.1 0.8
OE2 A:GLU167 3.6 21.3 1.0
O2B A:ADP309 3.7 18.1 0.8
MG A:MG311 3.9 11.4 1.0
O1B A:ADP309 4.0 18.5 0.8
OH A:TYR141 4.1 23.1 1.0
CA A:GLY236 4.2 21.2 1.0
CG2 A:VAL132 4.2 21.4 1.0
OE1 A:GLU167 4.2 21.3 1.0
ND2 A:ASN164 4.3 19.9 1.0
CD A:GLU167 4.3 21.2 1.0
OD1 A:ASP130 4.3 19.7 1.0
O3A A:ADP309 4.3 18.7 0.8
C5A A:JLP233 4.4 28.9 1.0
OD1 A:ASP237 4.5 21.0 1.0
OD2 A:ASP130 4.5 19.7 1.0
OP4 A:JLP233 4.5 28.7 1.0
CG1 A:VAL132 4.7 21.3 1.0
C A:GLY236 4.7 20.9 1.0
O A:HOH426 4.8 14.6 1.0
CB A:VAL132 4.8 21.4 1.0
CG A:ASP130 4.8 20.1 1.0
N A:GLY236 4.8 21.8 1.0
CA A:VAL132 4.8 21.4 1.0
N A:ASP237 4.9 20.8 1.0
O A:HOH403 4.9 26.7 1.0

Magnesium binding site 2 out of 2 in 5zwa

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


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 Schiff Base in Protomer A and the Product (Plp) in Protomer B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg311

b:11.4
occ:1.00
 OG1 A:THR200 2.6 22.2 1.0
O A:HOH426 2.6 14.6 1.0
O A:HOH410 2.8 13.3 1.0
O3B A:ADP309 2.8 17.9 0.8
O A:THR162 2.9 19.3 1.0
CG2 A:THR200 3.3 22.7 1.0
O3A A:ADP309 3.4 18.7 0.8
CB A:THR200 3.5 22.7 1.0
N A:ASN164 3.6 19.6 1.0
PB A:ADP309 3.7 18.1 0.8
C A:PRO163 3.9 19.6 1.0
MG A:MG310 3.9 24.3 1.0
C A:THR162 4.0 19.8 1.0
OD1 A:ASP130 4.0 19.7 1.0
O A:HOH424 4.1 12.4 1.0
CA A:GLY236 4.1 21.2 1.0
CB A:ASN164 4.2 19.9 1.0
OE1 A:GLU167 4.2 21.3 1.0
CA A:ASN164 4.2 19.9 1.0
O A:PRO163 4.2 19.2 1.0
CA A:PRO163 4.4 19.6 1.0
O1B A:ADP309 4.4 18.5 0.8
PA A:ADP309 4.6 19.1 0.8
N A:PRO163 4.6 19.6 1.0
CB A:THR162 4.7 20.0 1.0
OG1 A:THR162 4.7 19.6 1.0
O1A A:ADP309 4.7 19.8 0.8
O5' A:ADP309 4.8 19.7 0.8
CA A:THR200 4.8 22.9 1.0
CG A:ASP130 4.8 20.1 1.0
O A:GLY236 4.8 20.6 1.0
OD2 A:ASP130 4.8 19.7 1.0
C A:GLY236 4.9 20.9 1.0
CG A:ASN164 4.9 19.9 1.0
ND2 A:ASN164 4.9 19.9 1.0
CA A:THR162 5.0 19.9 1.0
O2B A:ADP309 5.0 18.1 0.8

Reference:

G.Deka, J.F.Benazir, J.N.Kalyani, H.S.Savithri, M.R.N.Murthy. Structural and Functional Studies on Pyridoxal Kinase (Pdxk) From Salmonella Typhimurium To Be Published.
Page generated: Mon Dec 14 22:18:22 2020

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