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Sodium in PDB 3pzs: Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92

Enzymatic activity of Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92

All present enzymatic activity of Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92:
2.7.1.35;

Protein crystallography data

The structure of Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92, PDB code: 3pzs was solved by J.S.Brunzelle, Z.Wawrzak, M.Kudritska, O.Onopriyenko, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.92 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.914, 88.101, 102.917, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92 (pdb code 3pzs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92, PDB code: 3pzs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3pzs

Go back to Sodium Binding Sites List in 3pzs
Sodium binding site 1 out of 2 in the Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na287

b:25.3
occ:1.00
OE2 A:GLU194 2.2 23.0 1.0
O A:HIS189 2.3 28.3 1.0
O A:HOH378 2.3 28.3 1.0
O A:HOH388 2.4 25.1 1.0
O A:CYS192 2.4 27.4 1.0
O A:HOH351 2.5 35.1 1.0
CD A:GLU194 3.2 29.1 1.0
C A:HIS189 3.3 29.4 1.0
C A:CYS192 3.6 28.6 1.0
CG A:GLU194 3.6 25.7 1.0
O A:SER184 3.9 30.5 1.0
N A:HIS189 4.0 23.6 1.0
N A:CYS192 4.1 28.8 1.0
N A:ALA190 4.1 27.7 1.0
CA A:ALA190 4.2 28.9 1.0
CA A:CYS192 4.2 28.8 1.0
CA A:HIS189 4.2 23.4 1.0
O A:HOH397 4.2 32.4 1.0
CA A:GLY187 4.2 27.8 1.0
OE1 A:GLU194 4.2 22.2 1.0
C A:ALA190 4.3 32.8 1.0
CB A:CYS192 4.3 29.9 1.0
O A:ALA190 4.4 32.2 1.0
CB A:GLU194 4.4 20.1 1.0
O A:HOH295 4.5 24.4 1.0
C A:GLY187 4.5 30.8 1.0
N A:PHE193 4.6 24.2 1.0
N A:GLU194 4.7 20.1 1.0
N A:TYR188 4.7 26.0 1.0
CB A:HIS189 4.8 23.9 1.0
CA A:PHE193 4.9 23.2 1.0
N A:GLY187 4.9 27.9 1.0
N A:ASP191 4.9 28.3 0.5
O A:HOH425 4.9 45.2 1.0
N A:ASP191 4.9 28.9 0.5
C A:PHE193 5.0 24.9 1.0

Sodium binding site 2 out of 2 in 3pzs

Go back to Sodium Binding Sites List in 3pzs
Sodium binding site 2 out of 2 in the Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na287

b:31.8
occ:1.00
O B:HOH332 2.2 29.0 1.0
O B:HOH369 2.3 36.7 1.0
O B:HIS189 2.3 42.4 1.0
O B:CYS192 2.4 31.1 1.0
OE2 B:GLU194 2.4 30.6 1.0
O B:HOH425 2.4 35.1 1.0
CD B:GLU194 3.3 32.9 1.0
C B:HIS189 3.3 43.1 1.0
C B:CYS192 3.5 33.6 1.0
CG B:GLU194 3.7 27.1 1.0
O B:SER184 3.9 31.6 1.0
N B:HIS189 4.0 38.1 1.0
N B:CYS192 4.1 40.1 1.0
O B:HOH406 4.2 36.9 1.0
CA B:CYS192 4.2 38.2 1.0
N B:ALA190 4.2 39.5 1.0
CA B:GLY187 4.2 31.1 1.0
CA B:HIS189 4.3 39.2 1.0
CB B:GLU194 4.3 20.1 1.0
O B:HOH343 4.3 27.8 1.0
CB B:CYS192 4.3 40.0 1.0
CA B:ALA190 4.3 39.9 1.0
OE1 B:GLU194 4.4 27.7 1.0
C B:ALA190 4.5 45.8 1.0
N B:GLU194 4.6 20.1 1.0
C B:GLY187 4.6 36.9 1.0
N B:PHE193 4.6 25.4 1.0
N B:TYR188 4.6 34.4 1.0
O B:ALA190 4.7 45.5 1.0
CA B:PHE193 4.8 22.9 1.0
C B:PHE193 4.8 24.4 1.0
N B:GLY187 4.9 30.2 1.0
C B:SER184 5.0 33.4 1.0
CB B:HIS189 5.0 41.1 1.0

Reference:

J.S.Brunzelle, Z.Wawrzak, M.Kudritska, O.Onopriyenko, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of A Pyridoxamine Kinase From Yersinia Pestis CO92 To Be Published.
Page generated: Tue Dec 15 06:22:11 2020

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