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Sodium in PDB 4xmw: Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Aspartic Acid

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

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

Protein crystallography data

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Aspartic Acid, PDB code: 4xmw 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) 19.94 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.214, 120.214, 170.546, 90.00, 90.00, 120.00
R / Rfree (%) 14.8 / 20.5

Other elements in 4xmw:

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

Sodium binding site 1 out of 7 in 4xmw

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Sodium binding site 1 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Aspartic 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 L-Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:39.7
occ:1.00
 O A:HOH1742 2.1 40.3 1.0
O A:GLY335 2.3 24.2 1.0
O A:HOH1670 2.3 37.8 1.0
O A:SER332 2.5 22.9 1.0
O A:HOH1476 2.5 29.9 1.0
O A:ASP333 3.0 23.9 1.0
C A:GLY335 3.4 24.1 1.0
C A:ASP333 3.6 25.6 1.0
C A:SER332 3.6 24.5 1.0
CA A:ASP333 3.9 25.8 1.0
N A:ARG337 3.9 25.9 1.0
N A:GLY335 4.0 23.1 1.0
O A:HOH1358 4.1 38.7 1.0
N A:ASP333 4.2 25.3 1.0
O A:HOH1842 4.2 41.6 1.0
O A:HOH1516 4.3 52.0 1.0
CA A:GLY335 4.3 22.5 1.0
C A:LEU334 4.3 25.0 1.0
N A:SER336 4.3 24.2 1.0
N A:LEU334 4.4 23.5 1.0
CA A:SER336 4.5 26.9 1.0
O A:HOH1947 4.5 45.6 1.0
C A:SER336 4.5 27.2 1.0
CB A:ARG337 4.5 29.5 1.0
CA A:ARG337 4.6 29.1 1.0
O A:HOH1564 4.6 42.9 1.0
CA A:SER332 4.8 24.1 1.0
O A:LEU334 4.8 24.4 1.0
CA A:LEU334 4.9 24.2 1.0

Sodium binding site 2 out of 7 in 4xmw

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Sodium binding site 2 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Aspartic 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 L-Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:40.3
occ:1.00
 O A:HOH1894 2.4 48.5 1.0
O A:HOH1166 2.7 36.1 1.0
O A:ASN623 2.8 24.1 1.0
O A:HOH1370 2.8 43.1 1.0
O A:GLY350 3.0 29.6 1.0
O A:HOH1728 3.6 54.3 1.0
N A:GLU627 3.7 28.8 1.0
C A:ASN623 3.7 27.4 1.0
CB A:ALA626 3.8 29.4 1.0
CB A:ALA354 3.8 27.5 1.0
C A:GLY350 3.9 31.9 1.0
CB A:GLU627 4.0 36.4 0.5
CA A:GLU627 4.1 32.4 0.5
CA A:GLU627 4.1 26.6 0.5
O A:HOH1792 4.1 28.1 1.0
CB A:GLU627 4.2 23.4 0.5
CA A:ASN623 4.2 29.3 1.0
C A:ALA626 4.2 28.9 1.0
CA A:GLY350 4.4 27.7 1.0
CB A:ASN623 4.4 32.0 1.0
CA A:ALA626 4.5 28.6 1.0
O A:HOH1475 4.5 48.6 1.0
O A:ARG349 4.7 32.6 1.0
O A:HOH1788 4.7 37.5 1.0
CA A:ALA354 4.8 28.8 1.0
N A:GLU624 4.8 25.6 1.0
N A:LEU351 4.9 28.4 1.0
O A:ALA626 5.0 27.2 1.0
N A:ALA626 5.0 27.2 1.0
N A:ALA354 5.0 25.7 1.0

Sodium binding site 3 out of 7 in 4xmw

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Sodium binding site 3 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Aspartic 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 L-Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:31.0
occ:1.00
 OH A:TYR185 2.6 19.8 1.0
OD1 A:ASN306 2.7 23.6 1.0
OE2 A:GLU264 2.9 22.0 1.0
O A:GLY305 2.9 21.3 1.0
C A:GLY305 3.0 23.3 1.0
CA A:GLY305 3.2 21.8 1.0
CD A:LYS319 3.4 20.5 1.0
CZ A:TYR185 3.5 20.4 1.0
CE1 A:TYR185 3.5 21.4 1.0
CG A:GLU264 3.7 21.8 1.0
N A:ASN306 3.7 22.2 1.0
CD A:GLU264 3.7 22.9 1.0
CE A:LYS319 3.8 19.9 1.0
CD2 A:LEU186 3.8 20.0 1.0
CG A:ASN306 3.9 23.2 1.0
NZ A:LYS319 4.2 21.1 1.0
CA A:ASN306 4.3 22.8 1.0
CD1 A:LEU186 4.3 22.2 1.0
ND1 A:HIS301 4.3 22.7 1.0
CG A:LEU186 4.4 20.8 1.0
N A:GLY305 4.6 21.9 1.0
O A:HIS301 4.6 20.8 1.0
CG A:HIS301 4.7 22.2 1.0
OG1 A:THR309 4.7 21.4 1.0
CB A:ASN306 4.7 21.8 1.0
CE2 A:TYR185 4.8 19.8 1.0
CG A:LYS319 4.8 20.4 1.0
CB A:HIS301 4.8 20.1 1.0
CD1 A:TYR185 4.8 20.6 1.0
CE1 A:HIS301 4.9 21.7 1.0
ND2 A:ASN306 4.9 23.3 1.0
OE1 A:GLU264 4.9 22.8 1.0

Sodium binding site 4 out of 7 in 4xmw

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Sodium binding site 4 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Aspartic 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 L-Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:65.0
occ:1.00
 O A:HOH1800 2.3 49.3 1.0
O A:HOH1689 2.4 43.8 1.0
O A:HOH1009 2.5 40.0 1.0
OE1 A:GLN821 2.6 36.6 1.0
OD1 A:ASN373 2.8 38.3 1.0
O A:HOH1655 2.9 35.2 1.0
CG A:ASN373 3.5 35.6 1.0
CD A:GLN821 3.5 35.3 1.0
O A:GLU121 3.5 20.5 1.0
O A:HOH1114 3.7 36.5 1.0
NE2 A:GLN821 4.0 35.3 1.0
ND2 A:ASN373 4.1 35.8 1.0
OE2 A:GLU107 4.1 52.3 1.0
O A:HOH1303 4.3 31.6 1.0
CB A:ASN373 4.3 32.1 1.0
O A:HOH1139 4.4 35.6 1.0
C A:GLU121 4.4 20.7 1.0
N A:ALA122 4.5 22.3 1.0
CG A:GLN821 4.8 33.8 1.0
CA A:ASN373 4.9 26.3 1.0
NE2 A:GLN119 4.9 25.0 1.0

Sodium binding site 5 out of 7 in 4xmw

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Sodium binding site 5 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Aspartic 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 L-Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:48.9
occ:1.00
 OD1 A:ASP561 2.6 37.6 1.0
O A:HOH1573 2.7 39.3 1.0
O A:ALA558 3.1 32.6 1.0
O A:ARG559 3.1 35.4 1.0
NE A:ARG564 3.2 37.1 1.0
N A:ASP561 3.6 26.7 1.0
C A:ARG559 3.7 36.4 1.0
CG A:ASP561 3.7 40.0 1.0
CD A:ARG564 3.8 30.3 1.0
C A:ASN560 3.8 30.8 1.0
CA A:ASP561 3.8 31.5 1.0
CZ A:ARG564 3.8 43.9 1.0
NH2 A:ARG564 3.9 38.1 1.0
O A:HOH1760 4.0 49.1 1.0
O A:ASN560 4.2 31.7 1.0
CG A:ARG564 4.2 27.8 1.0
C A:ALA558 4.2 32.5 1.0
N A:ASN560 4.3 32.1 1.0
CA A:ASN560 4.4 35.2 1.0
O A:HOH1542 4.4 31.7 1.0
CB A:ASP561 4.4 35.3 1.0
CA A:ARG559 4.5 41.7 1.0
OD2 A:ASP561 4.7 46.8 1.0
N A:ARG559 4.8 36.2 1.0
CD2 A:LEU612 4.8 28.0 1.0
NH1 A:ARG564 4.9 44.1 1.0
O A:HOH1528 4.9 36.6 1.0

Sodium binding site 6 out of 7 in 4xmw

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Sodium binding site 6 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Aspartic 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 L-Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:46.1
occ:1.00
 O A:HOH1764 2.6 44.7 1.0
O A:LEU138 2.7 24.6 1.0
OE1 A:GLN19 2.7 29.1 1.0
O A:HOH1918 2.8 32.1 1.0
O A:ILE20 3.1 26.5 1.0
CD A:GLN19 3.5 27.5 1.0
C A:LEU138 3.6 22.0 1.0
N A:LEU138 3.8 23.9 1.0
C A:ILE20 3.8 27.5 1.0
CB A:GLN19 3.9 24.9 1.0
CA A:THR21 4.0 24.2 1.0
CG A:GLN19 4.1 26.5 1.0
O A:HOH1893 4.1 40.6 1.0
CA A:LEU138 4.1 24.9 1.0
O A:HOH1315 4.2 31.3 1.0
N A:ILE20 4.2 26.8 1.0
CG2 A:THR21 4.2 23.5 1.0
N A:THR21 4.3 25.9 1.0
NE2 A:GLN19 4.4 28.2 1.0
O A:HOH1871 4.5 38.3 1.0
CB A:LEU138 4.5 27.1 1.0
O A:HOH1966 4.6 45.4 1.0
N A:ALA139 4.7 22.8 1.0
CA A:ILE20 4.7 26.5 1.0
CB A:THR21 4.7 25.3 1.0
CA A:GLN19 4.7 23.6 1.0
C A:VAL137 4.8 24.4 1.0
O A:HOH1808 4.8 42.1 1.0
C A:GLN19 4.8 25.3 1.0
O A:HOH1172 4.9 25.8 1.0
CA A:VAL137 5.0 23.1 1.0

Sodium binding site 7 out of 7 in 4xmw

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Sodium binding site 7 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Aspartic 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 L-Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:32.1
occ:1.00
 OE1 A:GLU121 2.6 26.2 1.0
OE1 A:GLU264 2.6 22.8 1.0
CG A:ASP902 2.7 32.2 0.5
OD1 A:ASP902 2.9 29.6 0.5
OE2 A:GLU320 3.0 21.0 1.0
OD1 A:ASP902 3.0 26.0 0.5
CG A:ASP902 3.0 30.9 0.5
CB A:ASP902 3.0 35.7 0.5
OE2 A:GLU264 3.1 22.0 1.0
OD2 A:ASP902 3.1 31.9 0.5
NZ A:LYS319 3.2 21.1 1.0
OD2 A:ASP902 3.2 30.2 0.5
CD A:GLU264 3.2 22.9 1.0
CD A:GLU121 3.5 24.3 1.0
OE2 A:GLU121 3.7 22.9 1.0
ZN A:ZN901 3.7 24.0 1.0
CB A:ASP902 3.7 37.0 0.5
SD A:MET263 3.9 24.3 1.0
O A:HOH1139 4.0 35.6 1.0
NE2 A:HIS301 4.0 22.3 1.0
CD A:GLU320 4.1 21.7 1.0
OH A:TYR381 4.1 22.8 1.0
O A:ASP902 4.2 39.9 0.5
CE A:MET263 4.3 22.4 1.0
CA A:ASP902 4.4 42.9 0.5
CD2 A:HIS301 4.5 19.7 1.0
OE1 A:GLU320 4.6 18.9 1.0
CE A:LYS319 4.7 19.9 1.0
N A:ASP902 4.7 43.8 0.5
CE2 A:TYR376 4.7 24.8 1.0
CE1 A:HIS301 4.7 21.7 1.0
CA A:ASP902 4.7 44.3 0.5
CG A:GLU264 4.8 21.8 1.0
C A:ASP902 4.8 43.7 0.5
CG A:GLU121 4.9 22.4 1.0

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Aspartic Acid To Be Published.
Page generated: Mon Oct 7 19:10:35 2024

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