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Sodium in PDB 4xmv: Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine

Enzymatic activity of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine

All present enzymatic activity of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine:
3.4.11.2;

Protein crystallography data

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine, PDB code: 4xmv was solved by A.Addlagatta, R.Gumpena, C.Kishor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.92
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.812, 120.812, 170.279, 90.00, 90.00, 120.00
R / Rfree (%) 14.8 / 21.6

Other elements in 4xmv:

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine (pdb code 4xmv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine, PDB code: 4xmv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4xmv

Go back to Sodium Binding Sites List in 4xmv
Sodium binding site 1 out of 3 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine


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 MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:28.1
occ:1.00
O A:HOH1030 2.4 34.4 1.0
O A:GLY335 2.4 19.3 1.0
O A:SER332 2.7 28.3 1.0
O A:HOH1164 2.9 23.1 1.0
O A:ASP333 3.2 27.0 1.0
C A:GLY335 3.7 20.1 1.0
N A:ARG337 3.7 22.7 1.0
C A:SER332 3.9 26.6 1.0
C A:ASP333 4.0 23.8 1.0
CB A:ARG337 4.3 22.0 1.0
CA A:ASP333 4.3 24.3 1.0
CA A:SER336 4.4 21.4 1.0
C A:SER336 4.4 23.1 1.0
N A:SER336 4.5 20.7 1.0
CA A:ARG337 4.5 22.3 1.0
N A:ASP333 4.6 25.2 1.0
N A:GLY335 4.7 20.3 1.0
CA A:GLY335 4.8 20.2 1.0

Sodium binding site 2 out of 3 in 4xmv

Go back to Sodium Binding Sites List in 4xmv
Sodium binding site 2 out of 3 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine


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 MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:23.5
occ:1.00
OH A:TYR299 2.6 19.1 1.0
O A:LEU243 2.8 24.2 1.0
O A:HOH1040 2.8 32.9 1.0
O A:MET234 2.9 21.7 1.0
CZ A:TYR299 3.5 18.9 1.0
CA A:GLU244 3.7 23.6 1.0
CE2 A:TYR299 3.7 19.2 1.0
C A:MET234 3.7 22.1 1.0
C A:LEU243 3.7 23.2 1.0
CB A:ASP237 3.8 22.9 1.0
CA A:MET234 3.8 22.9 1.0
N A:GLU238 3.9 26.4 1.0
N A:TYR245 3.9 21.8 1.0
CG A:GLU238 4.0 29.4 1.0
N A:GLU244 4.1 23.2 1.0
C A:GLU244 4.1 22.9 1.0
OE2 A:GLU238 4.2 29.4 1.0
CB A:MET234 4.2 24.0 1.0
CD A:GLU238 4.3 30.4 1.0
O A:HOH1076 4.4 12.4 1.0
C A:ASP237 4.4 24.6 1.0
CB A:GLU238 4.4 29.0 1.0
CA A:GLU238 4.5 28.5 1.0
CA A:ASP237 4.5 22.6 1.0
CG A:MET234 4.7 24.8 1.0
CG A:ASP237 4.8 22.6 1.0
CE1 A:TYR299 4.8 19.1 1.0
O A:SER233 4.8 23.5 1.0
N A:ASP237 4.8 20.2 1.0
CB A:GLU244 4.9 25.5 1.0
OD2 A:ASP237 4.9 23.3 1.0
CA A:TYR245 4.9 21.8 1.0
N A:LYS235 4.9 22.1 1.0
CA A:LEU243 5.0 22.9 1.0

Sodium binding site 3 out of 3 in 4xmv

Go back to Sodium Binding Sites List in 4xmv
Sodium binding site 3 out of 3 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:31.9
occ:1.00
OE1 A:GLN19 2.3 22.1 1.0
O A:LEU138 2.5 23.9 1.0
O A:HOH1160 2.5 10.9 1.0
O A:ILE20 2.5 25.6 1.0
CD A:GLN19 3.3 22.8 1.0
C A:ILE20 3.5 23.9 1.0
O A:HOH1145 3.6 27.1 1.0
C A:LEU138 3.6 23.3 1.0
N A:LEU138 3.8 22.2 1.0
N A:ILE20 4.0 25.0 1.0
CG A:GLN19 4.0 22.8 1.0
CB A:GLN19 4.1 23.3 1.0
O A:HOH1197 4.2 14.4 1.0
NE2 A:GLN19 4.2 21.8 1.0
CA A:THR21 4.2 21.8 1.0
CA A:LEU138 4.2 22.4 1.0
N A:THR21 4.3 21.8 1.0
CA A:ILE20 4.5 25.2 1.0
CG1 A:VAL137 4.5 18.2 1.0
C A:VAL137 4.6 20.4 1.0
N A:ALA139 4.7 24.3 1.0
CG2 A:THR21 4.7 20.4 1.0
CB A:LEU138 4.7 23.0 1.0
CA A:VAL137 4.8 18.9 1.0
C A:GLN19 4.8 24.1 1.0
CA A:GLN19 4.8 23.7 1.0

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Arginine To Be Published.
Page generated: Mon Oct 7 19:10:07 2024

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