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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

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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

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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

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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

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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

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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

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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

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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

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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

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