Atomistry » Sodium » PDB 4xea-4xn0 » 4xmz
Atomistry »
  Sodium »
    PDB 4xea-4xn0 »
      4xmz »

Sodium in PDB 4xmz: Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid

Enzymatic activity of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid

All present enzymatic activity of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid:
3.4.11.2;

Protein crystallography data

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid, PDB code: 4xmz was solved by A.Addlagatta, R.Gumpena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 2.15
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.638, 120.638, 171.304, 90.00, 90.00, 120.00
R / Rfree (%) 14.3 / 18.1

Other elements in 4xmz:

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid 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 2,4-Diaminobutyric Acid (pdb code 4xmz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid, PDB code: 4xmz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4xmz

Go back to Sodium Binding Sites List in 4xmz
Sodium binding site 1 out of 8 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid


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 2,4-Diaminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na902

b:25.2
occ:1.00
 O A:HOH1878 2.3 30.8 1.0
O A:GLY335 2.3 16.4 1.0
O A:HOH1767 2.3 26.1 1.0
O A:SER332 2.5 15.1 1.0
O A:HOH1602 2.6 21.1 1.0
O A:ASP333 2.9 16.4 1.0
C A:GLY335 3.4 15.0 1.0
C A:ASP333 3.4 16.4 1.0
C A:SER332 3.6 14.5 1.0
CA A:ASP333 3.8 16.0 1.0
N A:GLY335 3.9 14.6 1.0
N A:ARG337 4.0 18.1 1.0
O A:HOH1548 4.1 28.9 1.0
N A:ASP333 4.1 15.5 1.0
C A:LEU334 4.2 15.8 1.0
CA A:GLY335 4.2 14.6 1.0
N A:LEU334 4.3 15.0 1.0
N A:SER336 4.4 14.7 1.0
O A:HOH1962 4.5 24.6 1.0
O A:HOH1376 4.5 20.7 1.0
CA A:SER336 4.5 16.7 1.0
O A:HOH2075 4.6 41.0 1.0
C A:SER336 4.6 17.9 1.0
CB A:ARG337 4.6 18.5 1.0
O A:LEU334 4.7 15.4 1.0
O A:HOH1790 4.7 41.9 1.0
CA A:ARG337 4.7 18.8 1.0
CA A:LEU334 4.8 15.9 1.0
CA A:SER332 4.8 13.0 1.0

Sodium binding site 2 out of 8 in 4xmz

Go back to Sodium Binding Sites List in 4xmz
Sodium binding site 2 out of 8 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid


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 2,4-Diaminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:35.7
occ:1.00
 O A:HOH1866 2.3 32.3 1.0
O A:ASN623 2.7 21.0 1.0
O A:HOH1322 2.7 23.6 1.0
O A:HOH1009 2.7 33.3 1.0
O A:GLY350 2.8 26.1 1.0
N A:GLU627 3.6 17.9 1.0
C A:ASN623 3.7 21.2 1.0
CB A:ALA354 3.8 16.0 1.0
C A:GLY350 3.8 21.3 1.0
CB A:GLU627 3.8 20.3 0.5
CB A:ALA626 3.8 18.5 1.0
OE2 A:GLU627 3.9 18.2 0.5
CA A:GLU627 4.1 19.2 0.5
CA A:GLU627 4.1 18.4 0.5
CA A:ASN623 4.1 23.9 1.0
CB A:GLU627 4.1 18.0 0.5
C A:ALA626 4.2 18.0 1.0
CA A:GLY350 4.3 19.6 1.0
O A:HOH1750 4.4 30.6 1.0
CB A:ASN623 4.5 26.1 1.0
CA A:ALA626 4.5 17.4 1.0
CA A:ALA354 4.7 16.6 1.0
CG A:GLU627 4.7 21.3 0.5
O A:ARG349 4.7 23.0 1.0
CD A:GLU627 4.7 21.9 0.5
N A:GLU624 4.7 19.4 1.0
O A:HOH1834 4.7 18.5 1.0
N A:LEU351 4.8 18.6 1.0
N A:ALA354 4.8 15.4 1.0
N A:ALA626 4.9 16.9 1.0
O A:ALA626 5.0 19.7 1.0

Sodium binding site 3 out of 8 in 4xmz

Go back to Sodium Binding Sites List in 4xmz
Sodium binding site 3 out of 8 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid


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 2,4-Diaminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:34.6
occ:1.00
 O A:HOH1883 2.6 33.2 1.0
O A:LEU138 2.6 15.9 1.0
OE1 A:GLN19 2.7 21.0 1.0
O A:HOH2044 2.8 29.9 1.0
O A:ILE20 3.0 19.3 1.0
CD A:GLN19 3.5 18.1 1.0
C A:LEU138 3.6 15.5 1.0
N A:LEU138 3.7 14.6 1.0
C A:ILE20 3.8 18.0 1.0
O A:HOH1979 4.0 30.2 1.0
CB A:GLN19 4.0 17.2 1.0
CG A:GLN19 4.0 17.2 1.0
CA A:THR21 4.1 17.7 1.0
CA A:LEU138 4.1 16.2 1.0
O A:HOH1319 4.2 21.7 1.0
N A:THR21 4.3 16.7 1.0
CG2 A:THR21 4.3 17.6 1.0
N A:ILE20 4.3 17.4 1.0
NE2 A:GLN19 4.3 18.1 1.0
CB A:LEU138 4.5 17.8 1.0
O A:HOH1935 4.5 12.2 0.5
O A:HOH1951 4.6 31.4 1.0
C A:VAL137 4.6 14.9 1.0
N A:ALA139 4.7 15.2 1.0
CA A:ILE20 4.8 17.3 1.0
CB A:THR21 4.8 17.9 1.0
CA A:VAL137 4.8 14.4 1.0
O A:HOH2102 4.9 35.0 1.0
CA A:GLN19 4.9 17.3 1.0
O A:HOH1333 4.9 15.2 1.0
C A:GLN19 5.0 17.4 1.0

Sodium binding site 4 out of 8 in 4xmz

Go back to Sodium Binding Sites List in 4xmz
Sodium binding site 4 out of 8 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid


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 2,4-Diaminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:23.8
occ:1.00
 OH A:TYR185 2.7 10.7 1.0
OE2 A:GLU264 2.8 17.3 1.0
OD1 A:ASN306 2.8 15.9 1.0
O A:GLY305 3.1 14.0 1.0
C A:GLY305 3.2 14.2 1.0
CA A:GLY305 3.4 13.4 1.0
CD A:LYS319 3.4 12.8 1.0
CG A:GLU264 3.5 14.6 1.0
CE1 A:TYR185 3.5 12.3 1.0
CZ A:TYR185 3.5 12.3 1.0
CD A:GLU264 3.6 15.9 1.0
CE A:LYS319 3.7 12.9 1.0
CD2 A:LEU186 3.8 13.7 1.0
N A:ASN306 3.9 12.8 1.0
CG A:ASN306 4.0 13.7 1.0
NZ A:LYS319 4.0 12.4 1.0
ND1 A:HIS301 4.1 11.9 1.0
CD1 A:LEU186 4.3 14.6 1.0
CA A:ASN306 4.4 12.9 1.0
CG A:LEU186 4.5 13.8 1.0
CG A:HIS301 4.5 12.8 1.0
CB A:HIS301 4.7 12.2 1.0
O A:HIS301 4.7 12.2 1.0
CE1 A:HIS301 4.7 12.9 1.0
N A:GLY305 4.7 13.5 1.0
CG A:LYS319 4.7 13.2 1.0
OE1 A:GLU264 4.8 15.2 1.0
CB A:ASN306 4.8 13.9 1.0
CD1 A:TYR185 4.9 12.8 1.0
CE2 A:TYR185 4.9 12.2 1.0
ND2 A:ASN306 4.9 14.1 1.0
CB A:GLU264 4.9 13.8 1.0
OG1 A:THR309 4.9 15.1 1.0

Sodium binding site 5 out of 8 in 4xmz

Go back to Sodium Binding Sites List in 4xmz
Sodium binding site 5 out of 8 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid


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 2,4-Diaminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:33.6
occ:1.00
 OG1 A:THR26 2.7 16.0 1.0
O A:HOH1982 2.8 38.2 1.0
OD1 A:ASP24 2.9 40.7 1.0
O A:ASP24 3.0 17.4 1.0
O A:THR37 3.1 19.7 1.0
N A:THR26 3.3 15.2 1.0
C A:LEU25 3.4 16.7 1.0
C A:ASP24 3.5 17.4 1.0
CB A:THR26 3.6 17.8 1.0
CA A:LEU25 3.7 15.7 1.0
N A:LEU25 3.8 14.2 1.0
C A:THR37 3.9 18.5 1.0
O A:LEU25 3.9 16.6 1.0
CG2 A:VAL39 4.0 17.4 1.0
CG2 A:THR37 4.0 20.8 1.0
CG A:ASP24 4.0 32.5 1.0
CA A:THR26 4.0 16.2 1.0
CB A:THR37 4.2 18.3 1.0
CB A:ASP24 4.4 24.9 1.0
N A:VAL39 4.4 13.7 1.0
N A:ALA38 4.5 15.7 1.0
CA A:ASP24 4.5 17.9 1.0
CA A:ALA38 4.6 16.3 1.0
O A:HOH1554 4.6 21.2 1.0
CA A:THR37 4.7 16.8 1.0
CB A:VAL39 4.7 17.9 1.0
O A:HOH1895 4.8 39.3 1.0
CG2 A:THR26 4.9 19.4 1.0
C A:ALA38 4.9 15.5 1.0

Sodium binding site 6 out of 8 in 4xmz

Go back to Sodium Binding Sites List in 4xmz
Sodium binding site 6 out of 8 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:35.8
occ:1.00
 O A:HOH1837 2.6 34.8 1.0
OH A:TYR130 2.7 26.9 1.0
O A:HOH1411 2.8 28.5 1.0
O A:ALA80 3.0 16.4 1.0
O A:GLU77 3.0 23.6 1.0
N A:ALA80 3.6 19.3 1.0
CZ A:TYR130 3.7 22.0 1.0
O A:HOH1545 3.7 28.0 1.0
C A:ALA80 3.8 18.5 1.0
CE1 A:TYR130 3.8 19.8 1.0
CB A:GLU76 3.9 25.8 1.0
OE2 A:GLU76 3.9 27.3 1.0
CG A:GLU76 4.0 24.7 1.0
C A:GLU77 4.1 26.5 1.0
N A:GLU77 4.1 26.7 1.0
CD A:GLU76 4.2 25.1 1.0
CA A:ALA80 4.2 18.3 1.0
N A:GLY79 4.3 23.4 1.0
C A:GLY79 4.4 21.1 1.0
CA A:GLU76 4.4 25.5 1.0
CA A:GLY79 4.6 24.2 1.0
C A:GLU76 4.6 27.1 1.0
O A:GLY56 4.7 17.7 1.0
N A:LEU81 4.8 16.8 1.0
CA A:GLU77 4.8 27.0 1.0

Sodium binding site 7 out of 8 in 4xmz

Go back to Sodium Binding Sites List in 4xmz
Sodium binding site 7 out of 8 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:31.5
occ:1.00
 OD1 A:ASP566 2.6 17.0 1.0
OG A:SER570 2.7 16.0 1.0
O A:HOH1955 2.8 28.5 1.0
O A:HOH2005 3.0 29.3 1.0
O A:ASP566 3.2 16.0 1.0
CG A:ASP566 3.4 18.1 1.0
NH2 A:ARG349 3.6 26.4 1.0
NH1 A:ARG349 3.7 27.9 1.0
N A:SER570 3.7 14.5 1.0
O A:HOH1581 3.8 31.2 1.0
CZ A:ARG349 3.9 25.6 1.0
CB A:SER570 3.9 15.0 1.0
CB A:GLN569 4.0 16.9 1.0
OD2 A:ASP566 4.0 22.2 1.0
CA A:SER570 4.1 15.2 1.0
C A:ASP566 4.1 16.9 1.0
C A:GLN569 4.3 16.6 1.0
O A:HOH1031 4.3 32.5 1.0
O A:HOH1564 4.4 39.2 1.0
CA A:ASP566 4.4 15.8 1.0
O A:HOH2061 4.5 30.4 1.0
CB A:ASP566 4.5 16.1 1.0
CA A:GLN569 4.7 16.3 1.0
NE A:ARG349 4.8 24.8 1.0
CG A:GLN569 4.9 17.0 1.0
O A:GLN569 5.0 15.2 1.0

Sodium binding site 8 out of 8 in 4xmz

Go back to Sodium Binding Sites List in 4xmz
Sodium binding site 8 out of 8 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:19.8
occ:1.00
 OH A:TYR299 2.6 14.3 1.0
O A:HOH1479 2.7 19.1 1.0
O A:LEU243 2.7 15.2 1.0
O A:MET234 2.8 14.4 1.0
CZ A:TYR299 3.4 15.0 1.0
CE2 A:TYR299 3.5 14.5 1.0
C A:MET234 3.6 14.1 1.0
CA A:MET234 3.6 15.0 1.0
CA A:GLU244 3.6 14.4 1.0
CG A:GLU238 3.6 16.8 1.0
C A:LEU243 3.7 15.2 1.0
CB A:ASP237 3.8 13.6 1.0
N A:TYR245 3.8 13.1 1.0
C A:GLU244 4.0 13.4 1.0
N A:GLU238 4.0 14.8 1.0
CB A:MET234 4.0 16.4 1.0
N A:GLU244 4.1 14.1 1.0
O A:HOH1414 4.4 14.2 1.0
C A:ASP237 4.4 14.5 1.0
OE2 A:GLU238 4.5 20.3 1.0
CD A:GLU238 4.5 18.6 1.0
CA A:ASP237 4.5 13.1 1.0
CB A:GLU238 4.6 16.6 1.0
CA A:GLU238 4.6 14.9 1.0
CE1 A:TYR299 4.7 13.4 1.0
CG A:MET234 4.8 17.9 1.0
O A:SER233 4.8 15.1 1.0
N A:LYS235 4.8 14.6 1.0
CD2 A:TYR299 4.8 13.5 1.0
CG A:ASP237 4.8 14.4 1.0
N A:ASP237 4.8 12.7 1.0
CA A:TYR245 4.9 13.9 1.0
OD2 A:ASP237 4.9 13.7 1.0
O A:GLU244 4.9 12.5 1.0
CB A:GLU244 4.9 15.6 1.0
N A:MET234 5.0 15.1 1.0
CA A:LEU243 5.0 14.7 1.0

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with 2,4-Diaminobutyric Acid To Be Published.
Page generated: Mon Oct 7 19:11:31 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy