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Sodium in PDB 4xmx: Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin

Enzymatic activity of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin

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

Protein crystallography data

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin, PDB code: 4xmx 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) 20.81 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.037, 121.037, 170.658, 90.00, 90.00, 120.00
R / Rfree (%) 14.5 / 19.1

Other elements in 4xmx:

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin 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 Bestatin (pdb code 4xmx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin, PDB code: 4xmx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4xmx

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Sodium binding site 1 out of 5 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin


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 Bestatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:27.0
occ:1.00
 O A:GLY335 2.3 18.9 1.0
O A:HOH1576 2.3 35.2 1.0
O A:HOH1482 2.4 27.9 1.0
O A:SER332 2.5 18.9 1.0
O A:HOH1410 2.6 20.6 1.0
O A:ASP333 2.9 18.8 1.0
C A:GLY335 3.4 19.2 1.0
O A:HOH1253 3.5 46.1 1.0
C A:ASP333 3.5 17.2 1.0
C A:SER332 3.7 18.5 1.0
N A:ARG337 3.9 20.2 1.0
CA A:ASP333 3.9 17.7 1.0
N A:GLY335 4.0 18.7 1.0
O A:HOH1322 4.1 30.3 1.0
N A:SER336 4.2 18.9 1.0
CA A:SER336 4.2 20.3 1.0
N A:ASP333 4.3 18.4 1.0
CA A:GLY335 4.4 18.0 1.0
C A:SER336 4.4 20.9 1.0
N A:LEU334 4.4 16.9 1.0
C A:LEU334 4.4 19.0 1.0
CB A:ARG337 4.6 20.2 1.0
CA A:ARG337 4.7 20.5 1.0
CA A:LEU334 4.8 18.0 1.0
CA A:SER332 4.9 18.4 1.0
O A:LEU334 4.9 21.3 1.0

Sodium binding site 2 out of 5 in 4xmx

Go back to Sodium Binding Sites List in 4xmx
Sodium binding site 2 out of 5 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin


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 Bestatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:36.5
occ:1.00
 O A:HOH1418 2.2 42.4 1.0
O A:ASP452 2.3 23.7 1.0
OD1 A:ASP452 2.4 29.1 1.0
O A:HOH1382 2.6 26.9 1.0
O7 A:MLI926 2.7 76.1 1.0
C2 A:MLI926 3.1 74.2 1.0
O A:HOH1323 3.1 41.5 1.0
C A:ASP452 3.2 26.4 1.0
O6 A:MLI926 3.4 72.4 1.0
CG A:ASP452 3.4 28.4 1.0
O2 A:GOL910 3.6 47.2 1.0
O A:HOH1042 3.7 39.6 1.0
O A:HOH1477 3.8 9.5 0.5
N A:ASP452 3.8 27.8 1.0
CA A:ASP452 3.8 26.9 1.0
C1 A:MLI926 3.9 69.2 1.0
CB A:ASP452 4.1 27.3 1.0
N A:ASP453 4.2 28.6 1.0
OD2 A:ASP452 4.3 28.4 1.0
CA A:ASP453 4.5 28.7 1.0
O3 A:GOL910 4.7 53.0 1.0
C2 A:GOL910 4.9 37.3 1.0

Sodium binding site 3 out of 5 in 4xmx

Go back to Sodium Binding Sites List in 4xmx
Sodium binding site 3 out of 5 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin


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 Bestatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:32.4
occ:1.00
 OD1 A:ASP566 2.5 21.7 1.0
OG A:SER570 2.7 19.1 1.0
O A:HOH1596 2.7 37.4 1.0
O A:HOH1518 2.8 30.4 1.0
O A:ASP566 2.9 20.3 1.0
O9 A:MLI924 3.2 47.5 1.0
CG A:ASP566 3.4 21.6 1.0
NH2 A:ARG349 3.6 24.6 1.0
N A:SER570 3.6 18.1 1.0
CB A:SER570 3.8 19.6 1.0
NH1 A:ARG349 3.9 24.9 1.0
CB A:GLN569 3.9 20.2 1.0
C A:ASP566 3.9 21.9 1.0
OD2 A:ASP566 3.9 23.1 1.0
CZ A:ARG349 4.0 24.6 1.0
C3 A:MLI924 4.0 46.5 1.0
CA A:SER570 4.0 19.3 1.0
O8 A:MLI924 4.2 67.5 1.0
C A:GLN569 4.2 18.7 1.0
CA A:ASP566 4.4 20.9 1.0
O A:HOH1187 4.4 44.6 1.0
CB A:ASP566 4.4 20.2 1.0
O A:HOH1450 4.5 28.2 1.0
CA A:GLN569 4.6 21.2 1.0
O A:GLN569 4.9 20.5 1.0
CG A:GLN569 4.9 20.6 1.0

Sodium binding site 4 out of 5 in 4xmx

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Sodium binding site 4 out of 5 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:24.9
occ:1.00
 OH A:TYR185 2.7 13.1 1.0
OD1 A:ASN306 2.8 21.0 1.0
OE2 A:GLU264 2.8 13.8 1.0
O A:GLY305 3.1 16.5 1.0
C A:GLY305 3.1 18.1 1.0
CA A:GLY305 3.3 17.4 1.0
CD A:LYS319 3.4 13.6 1.0
CG A:GLU264 3.5 13.3 1.0
CZ A:TYR185 3.6 13.6 1.0
CE1 A:TYR185 3.6 13.7 1.0
CD A:GLU264 3.6 13.4 1.0
N A:ASN306 3.8 17.4 1.0
CE A:LYS319 3.8 13.6 1.0
CD2 A:LEU186 3.9 14.4 1.0
CG A:ASN306 4.0 19.5 1.0
NZ A:LYS319 4.0 13.0 1.0
CD1 A:LEU186 4.2 14.6 1.0
ND1 A:HIS301 4.2 16.4 1.0
CA A:ASN306 4.4 18.2 1.0
CG A:LEU186 4.5 14.7 1.0
CG A:HIS301 4.5 15.1 1.0
CB A:HIS301 4.6 14.8 1.0
O A:HIS301 4.7 14.2 1.0
N A:GLY305 4.7 15.4 1.0
CG A:LYS319 4.7 13.5 1.0
CE1 A:HIS301 4.8 17.6 1.0
CB A:ASN306 4.8 18.8 1.0
OE1 A:GLU264 4.8 12.1 1.0
CE2 A:TYR185 4.9 13.2 1.0
OG1 A:THR309 4.9 15.9 1.0
CD1 A:TYR185 4.9 13.8 1.0
ND2 A:ASN306 5.0 20.4 1.0

Sodium binding site 5 out of 5 in 4xmx

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Sodium binding site 5 out of 5 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:29.2
occ:1.00
 O A:HOH1549 2.3 35.7 1.0
OE1 A:GLN19 2.3 22.4 1.0
O A:HOH1356 2.4 19.2 1.0
O A:LEU138 2.4 22.1 1.0
O A:ILE20 2.5 17.8 1.0
N A:LEU138 3.3 19.6 1.0
CD A:GLN19 3.3 20.5 1.0
C A:LEU138 3.4 21.4 1.0
C A:ILE20 3.5 17.2 1.0
CA A:LEU138 3.8 22.8 1.0
O A:HOH1543 3.9 34.7 1.0
N A:ILE20 4.0 19.6 1.0
O A:HOH1526 4.1 44.4 1.0
CB A:GLN19 4.1 20.2 1.0
CG A:GLN19 4.2 21.9 1.0
C A:VAL137 4.2 18.7 1.0
NE2 A:GLN19 4.2 19.6 1.0
N A:THR21 4.3 18.1 1.0
CA A:THR21 4.3 16.7 1.0
CG1 A:VAL137 4.3 17.7 1.0
CA A:VAL137 4.4 17.2 1.0
CB A:LEU138 4.4 24.3 1.0
CA A:ILE20 4.5 18.6 1.0
N A:ALA139 4.5 19.9 1.0
CA A:GLN19 4.8 19.5 1.0
C A:GLN19 4.8 20.4 1.0
CA A:ALA139 4.9 20.2 1.0
CB A:VAL137 4.9 16.6 1.0
CG2 A:THR21 5.0 18.2 1.0

Reference:

A.Addlagatta, R.Gumpena, C.Kishor. Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with Bestatin To Be Published.
Page generated: Mon Oct 7 19:10:40 2024

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