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Sodium in PDB 4xn4: Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Methionine

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

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

Protein crystallography data

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Methionine, PDB code: 4xn4 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) 19.58 / 1.99
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.426, 120.426, 170.215, 90.00, 90.00, 120.00
R / Rfree (%) 12.7 / 16.3

Other elements in 4xn4:

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Methionine 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-Methionine (pdb code 4xn4). 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 L-Methionine, PDB code: 4xn4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4xn4

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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 L-Methionine


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-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:47.7
occ:1.00
 O A:HOH1168 2.3 14.5 0.5
O A:HOH1961 2.4 43.9 1.0
O A:HOH1641 2.5 27.0 0.5
O A:PHE774 2.5 19.5 1.0
O A:HIS771 2.6 19.8 1.0
O A:HOH2067 3.3 62.5 1.0
C A:HIS771 3.6 22.8 1.0
C A:PHE774 3.7 22.2 1.0
N A:PHE774 4.0 20.6 1.0
O A:ARG772 4.0 24.2 1.0
C A:ARG772 4.1 23.3 1.0
CA A:ARG772 4.1 26.2 1.0
O A:GLN770 4.2 23.6 1.0
N A:ARG772 4.3 23.4 1.0
CA A:PHE774 4.3 21.5 1.0
C A:GLN770 4.3 26.6 1.0
N A:HIS771 4.5 23.2 1.0
CB A:PHE774 4.7 20.1 1.0
O A:LEU769 4.7 23.2 1.0
N A:THR775 4.7 19.9 1.0
CA A:HIS771 4.7 22.5 1.0
N A:SER773 4.7 21.0 1.0
CA A:THR775 4.8 20.9 1.0
CA A:GLN770 4.9 23.4 1.0
C A:SER773 4.9 21.0 1.0
CB A:THR775 5.0 23.2 1.0

Sodium binding site 2 out of 8 in 4xn4

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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 L-Methionine


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-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:42.6
occ:1.00
 O A:HOH1973 2.5 30.6 1.0
O A:HOH1385 2.6 45.4 1.0
OD1 A:ASN343 2.6 30.5 1.0
OE1 A:GLU615 2.8 29.3 1.0
OE2 A:GLU615 2.8 28.4 1.0
CD A:GLU615 3.3 26.2 1.0
NE A:ARG346 3.4 23.8 1.0
CG A:ASN343 3.6 27.2 1.0
ND2 A:ASN343 3.8 27.0 1.0
O A:HOH1735 3.9 46.7 1.0
CD A:ARG346 4.0 18.8 1.0
CZ A:ARG346 4.1 24.4 1.0
CG2 A:THR618 4.3 21.5 1.0
O A:HOH1971 4.4 40.1 1.0
NH2 A:ARG346 4.4 25.4 1.0
O A:HOH1008 4.4 34.5 1.0
CB A:THR618 4.8 20.0 1.0
CG A:GLU615 4.8 20.3 1.0
NZ A:LYS286 4.9 83.9 1.0
O A:HOH1867 4.9 44.8 1.0
OG1 A:THR618 4.9 19.9 1.0
CB A:ASN343 5.0 21.7 1.0

Sodium binding site 3 out of 8 in 4xn4

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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 L-Methionine


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-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:23.6
occ:1.00
 O A:HOH1949 2.2 31.0 1.0
O A:GLY335 2.3 18.0 1.0
O A:HOH1812 2.3 26.6 1.0
O A:SER332 2.4 16.9 1.0
O A:HOH1665 2.5 21.4 1.0
O A:ASP333 2.7 16.9 1.0
C A:GLY335 3.4 17.9 1.0
O A:HOH1125 3.4 51.9 1.0
C A:ASP333 3.4 17.8 1.0
C A:SER332 3.6 17.9 1.0
N A:GLY335 3.8 15.7 1.0
CA A:ASP333 3.8 18.3 1.0
N A:ARG337 4.0 17.6 1.0
N A:ASP333 4.2 17.0 1.0
CA A:GLY335 4.2 17.6 1.0
C A:LEU334 4.2 18.9 1.0
O A:HOH1606 4.2 27.3 1.0
N A:LEU334 4.3 16.7 1.0
N A:SER336 4.3 17.4 1.0
O A:HOH1993 4.3 33.4 1.0
O A:HOH1549 4.3 29.1 1.0
O A:HOH2193 4.4 41.8 1.0
CA A:SER336 4.4 17.7 1.0
C A:SER336 4.5 17.4 1.0
CB A:ARG337 4.6 18.2 1.0
O A:LEU334 4.7 16.1 1.0
CA A:ARG337 4.7 19.2 1.0
O A:HOH1895 4.7 48.6 1.0
CA A:LEU334 4.8 17.0 1.0
CA A:SER332 4.8 17.4 1.0

Sodium binding site 4 out of 8 in 4xn4

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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 L-Methionine


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-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:36.9
occ:0.80
 O A:HOH1522 1.8 47.9 1.0
O A:HOH1946 2.3 45.0 1.0
O A:HOH2032 2.3 25.5 0.5
O A:TYR544 2.6 21.4 1.0
O A:HOH1459 2.6 37.6 1.0
O A:HOH2124 2.9 50.8 1.0
O A:HOH1849 3.3 45.1 1.0
C A:TYR544 3.5 20.6 1.0
O A:HOH1405 3.8 27.1 0.8
CA A:LYS545 4.1 23.9 1.0
N A:TYR544 4.1 18.3 1.0
O A:HOH1323 4.1 56.1 1.0
N A:LYS545 4.2 22.6 1.0
O A:HOH1923 4.3 48.6 1.0
O A:HOH1416 4.3 38.1 1.0
N A:TRP546 4.4 20.7 1.0
CA A:TYR544 4.5 18.6 1.0
O A:HOH2005 4.6 36.4 1.0
O A:HOH1554 4.6 36.8 1.0
CD1 A:TRP546 4.6 26.6 1.0
OE1 A:GLU543 4.7 51.3 1.0
C A:LYS545 4.8 23.5 1.0

Sodium binding site 5 out of 8 in 4xn4

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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 L-Methionine


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-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:49.6
occ:0.80
 O A:HOH2224 2.0 52.5 1.0
O A:HOH2155 2.1 50.3 1.0
O A:HOH1620 2.2 43.9 1.0
O A:HOH2043 2.5 38.8 1.0
O A:HOH2151 2.6 28.7 1.0
O A:HOH1304 3.9 17.4 1.0
O A:HOH1536 4.2 35.6 1.0
O A:HOH2222 4.5 48.6 1.0
CE A:LYS235 4.6 30.1 1.0
O A:THR202 4.6 19.0 1.0
O A:HOH1538 4.7 27.5 1.0
O A:HOH1955 4.9 35.9 1.0

Sodium binding site 6 out of 8 in 4xn4

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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 L-Methionine


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-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na911

b:29.8
occ:1.00
 O A:HOH2049 2.4 36.5 1.0
O A:HOH1794 2.4 30.1 1.0
O A:LEU138 2.4 16.2 1.0
OE1 A:GLN19 2.6 20.9 1.0
O A:ILE20 2.6 21.5 1.0
CD A:GLN19 3.4 20.7 1.0
C A:LEU138 3.4 16.8 1.0
N A:LEU138 3.5 16.3 1.0
C A:ILE20 3.6 19.3 1.0
CB A:GLN19 4.0 19.0 1.0
CA A:LEU138 4.0 16.1 1.0
N A:ILE20 4.1 17.7 1.0
O A:HOH2075 4.1 31.5 1.0
CA A:THR21 4.2 17.8 1.0
CG A:GLN19 4.2 18.7 1.0
N A:THR21 4.2 17.2 1.0
NE2 A:GLN19 4.3 18.7 1.0
C A:VAL137 4.4 16.9 1.0
O A:HOH1403 4.4 34.0 1.0
CB A:LEU138 4.5 19.6 1.0
N A:ALA139 4.5 15.2 1.0
CA A:ILE20 4.5 18.1 1.0
CA A:VAL137 4.6 16.4 1.0
CG2 A:THR21 4.6 21.1 1.0
CG1 A:VAL137 4.6 17.8 1.0
O A:HOH1979 4.7 36.6 1.0
CA A:GLN19 4.7 17.3 1.0
C A:GLN19 4.8 19.2 1.0
O A:HOH2089 4.8 35.7 1.0
CA A:ALA139 4.8 15.8 1.0
CB A:THR21 5.0 21.1 1.0

Sodium binding site 7 out of 8 in 4xn4

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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 L-Methionine


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-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na912

b:43.7
occ:1.00
 O A:HOH1036 1.9 35.8 1.0
O A:HOH2027 2.5 42.5 1.0
OD1 A:ASP453 2.5 29.0 1.0
O A:TYR454 2.8 21.9 1.0
O A:MET903 2.8 29.5 1.0
CG A:ASP453 3.5 30.4 1.0
O A:HOH1113 3.5 24.8 0.5
O A:HOH1218 3.6 42.0 1.0
C A:TYR454 3.8 23.5 1.0
C A:MET903 3.9 41.5 1.0
OD2 A:ASP453 3.9 32.9 1.0
N A:TYR454 3.9 20.2 1.0
O A:HOH1651 4.1 45.9 1.0
O A:HOH1755 4.1 54.7 1.0
OXT A:MET903 4.3 34.7 1.0
CA A:TYR454 4.5 21.5 1.0
N A:ASN455 4.7 22.5 1.0
CB A:ASP453 4.7 23.4 1.0
C A:ASP453 4.7 21.9 1.0
CA A:ASP453 4.7 21.1 1.0
CA A:ASN455 4.8 22.5 1.0
CD A:PRO456 5.0 27.1 1.0

Sodium binding site 8 out of 8 in 4xn4

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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 L-Methionine


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 L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na913

b:28.4
occ:1.00
 OD1 A:ASP24 2.7 40.7 1.0
O A:HOH2078 2.8 36.9 1.0
OG1 A:THR26 2.8 18.7 1.0
O A:ASP24 2.9 16.3 1.0
O A:THR37 3.1 20.5 1.0
N A:THR26 3.3 16.8 1.0
C A:ASP24 3.5 18.4 1.0
C A:LEU25 3.5 19.3 1.0
CB A:THR26 3.5 19.5 1.0
CA A:LEU25 3.8 17.0 1.0
N A:LEU25 3.8 16.1 1.0
CG A:ASP24 3.8 31.5 1.0
C A:THR37 3.9 19.7 1.0
CG2 A:THR37 4.0 22.9 1.0
CA A:THR26 4.0 17.3 1.0
CG2 A:VAL39 4.0 20.6 1.0
O A:LEU25 4.0 18.4 1.0
CB A:THR37 4.1 19.6 1.0
CB A:ASP24 4.2 21.3 1.0
O A:HOH1338 4.3 44.5 1.0
N A:VAL39 4.4 16.0 1.0
N A:ALA38 4.5 17.2 1.0
CA A:ASP24 4.5 18.5 1.0
O A:HOH1583 4.6 23.5 1.0
CA A:ALA38 4.6 18.2 1.0
CA A:THR37 4.7 18.1 1.0
CB A:VAL39 4.7 17.6 1.0
O A:HOH1982 4.9 43.8 1.0
C A:ALA38 4.9 19.6 1.0
CG2 A:THR26 4.9 22.5 1.0
OD2 A:ASP24 5.0 39.3 1.0

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-Methionine To Be Published.
Page generated: Mon Oct 7 19:13:52 2024

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