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Sodium in PDB 4xo4: Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine

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

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

Protein crystallography data

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine, PDB code: 4xo4 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) 19.95 / 2.18
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.509, 120.509, 170.283, 90.00, 90.00, 120.00
R / Rfree (%) 13.2 / 17

Other elements in 4xo4:

The structure of Crystal Structure 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 E. Coli Aminopeptidase N in Complex with L- Methionine (pdb code 4xo4). 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 E. Coli Aminopeptidase N in Complex with L- Methionine, PDB code: 4xo4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4xo4

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Sodium binding site 1 out of 7 in the Crystal Structure 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 E. Coli Aminopeptidase N in Complex with L- Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:24.2
occ:1.00
 O A:GLY335 2.3 19.7 1.0
O A:HOH1674 2.3 31.9 1.0
O A:SER332 2.5 20.2 1.0
O A:HOH1573 2.5 23.2 1.0
O A:HOH1515 2.6 23.2 1.0
O A:ASP333 2.7 20.7 1.0
C A:ASP333 3.4 21.1 1.0
C A:GLY335 3.4 21.2 1.0
C A:SER332 3.6 20.5 1.0
O A:HOH1256 3.6 45.5 1.0
CA A:ASP333 3.7 19.5 1.0
N A:GLY335 3.9 21.4 1.0
N A:ARG337 3.9 20.2 1.0
O A:HOH1625 3.9 43.8 1.0
N A:ASP333 4.1 19.1 1.0
O A:HOH1292 4.2 34.7 1.0
C A:LEU334 4.2 21.7 1.0
N A:LEU334 4.3 19.8 1.0
CA A:GLY335 4.3 20.8 1.0
N A:SER336 4.3 22.8 1.0
CA A:SER336 4.4 23.1 1.0
C A:SER336 4.5 22.1 1.0
CB A:ARG337 4.5 21.2 1.0
CA A:ARG337 4.7 21.4 1.0
O A:LEU334 4.7 21.6 1.0
CA A:LEU334 4.7 21.7 1.0
CA A:SER332 4.8 20.3 1.0

Sodium binding site 2 out of 7 in 4xo4

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Sodium binding site 2 out of 7 in the Crystal Structure 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 E. Coli Aminopeptidase N in Complex with L- Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:22.6
occ:1.00
 O A:HOH1668 2.2 33.1 1.0
O A:LEU138 2.3 19.3 1.0
O A:ILE20 2.3 19.6 1.0
O A:HOH1482 2.4 18.2 1.0
OE1 A:GLN19 2.4 20.2 1.0
CD A:GLN19 3.3 20.3 1.0
C A:LEU138 3.4 19.2 1.0
C A:ILE20 3.4 18.6 1.0
N A:LEU138 3.5 18.6 1.0
O A:HOH1715 3.9 42.9 1.0
N A:ILE20 4.0 18.0 1.0
CA A:LEU138 4.0 19.5 1.0
CB A:GLN19 4.1 19.7 1.0
O A:HOH1702 4.1 38.8 1.0
NE2 A:GLN19 4.2 17.5 1.0
N A:THR21 4.2 18.9 1.0
CG A:GLN19 4.2 20.2 1.0
CA A:THR21 4.2 19.3 1.0
C A:VAL137 4.3 18.1 1.0
CA A:ILE20 4.3 18.4 1.0
CG1 A:VAL137 4.4 17.8 1.0
N A:ALA139 4.4 17.8 1.0
CA A:VAL137 4.5 17.3 1.0
CB A:LEU138 4.6 22.1 1.0
CA A:ALA139 4.7 19.1 1.0
CA A:GLN19 4.7 18.5 1.0
C A:GLN19 4.7 19.7 1.0
CG2 A:THR21 4.9 22.5 1.0
CB A:ALA139 5.0 18.7 1.0

Sodium binding site 3 out of 7 in 4xo4

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Sodium binding site 3 out of 7 in the Crystal Structure 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 E. Coli Aminopeptidase N in Complex with L- Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:28.0
occ:1.00
 OE2 A:GLU264 2.7 20.3 1.0
OH A:TYR185 2.7 15.7 1.0
OD1 A:ASN306 2.8 18.0 1.0
O A:GLY305 3.2 16.6 1.0
C A:GLY305 3.2 16.7 1.0
CA A:GLY305 3.3 15.5 1.0
CG A:GLU264 3.4 17.7 1.0
CD A:GLU264 3.4 19.9 1.0
CE1 A:TYR185 3.5 15.5 1.0
CD A:LYS319 3.6 17.0 1.0
CZ A:TYR185 3.6 16.9 1.0
CD2 A:LEU186 3.8 17.2 1.0
CE A:LYS319 3.8 15.8 1.0
N A:ASN306 3.9 16.9 1.0
NZ A:LYS319 4.0 15.6 1.0
CG A:ASN306 4.0 16.8 1.0
CD1 A:LEU186 4.2 19.9 1.0
ND1 A:HIS301 4.2 15.8 1.0
CG A:LEU186 4.4 18.6 1.0
CA A:ASN306 4.5 17.4 1.0
CG A:HIS301 4.5 14.7 1.0
OE1 A:GLU264 4.6 21.7 1.0
O A:HIS301 4.7 15.0 1.0
CB A:HIS301 4.7 14.3 1.0
N A:GLY305 4.7 14.9 1.0
CE1 A:HIS301 4.7 16.3 1.0
CD1 A:TYR185 4.8 15.4 1.0
CE2 A:TYR185 4.9 15.5 1.0
CG A:LYS319 4.9 16.8 1.0
CB A:ASN306 4.9 16.9 1.0
CB A:GLU264 4.9 17.5 1.0
ND2 A:ASN306 4.9 18.0 1.0
OG1 A:THR309 5.0 20.5 1.0

Sodium binding site 4 out of 7 in 4xo4

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Sodium binding site 4 out of 7 in the Crystal Structure 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 E. Coli Aminopeptidase N in Complex with L- Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:48.4
occ:1.00
 OG A:SER570 2.5 24.7 1.0
OD1 A:ASP566 2.6 24.4 1.0
O A:HOH1665 2.7 35.6 1.0
O A:HOH1713 2.7 42.9 1.0
O A:ASP566 2.9 18.4 1.0
CG A:ASP566 3.5 24.0 1.0
O A:HOH1593 3.6 42.6 1.0
N A:SER570 3.6 19.3 1.0
CB A:SER570 3.7 20.5 1.0
NH2 A:ARG349 3.7 31.5 1.0
C A:ASP566 3.8 20.9 1.0
NH1 A:ARG349 3.9 29.0 1.0
CA A:SER570 3.9 20.4 1.0
CB A:GLN569 3.9 25.2 1.0
CZ A:ARG349 4.1 27.2 1.0
OD2 A:ASP566 4.1 31.7 1.0
CA A:ASP566 4.2 19.8 1.0
C A:GLN569 4.3 23.4 1.0
O A:HOH1561 4.3 45.5 1.0
CB A:ASP566 4.4 21.8 1.0
O A:HOH1358 4.4 41.3 1.0
CA A:GLN569 4.7 22.6 1.0
N A:ALA567 4.8 20.1 1.0
CG A:GLN569 5.0 26.7 1.0

Sodium binding site 5 out of 7 in 4xo4

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Sodium binding site 5 out of 7 in the Crystal Structure 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 E. Coli Aminopeptidase N in Complex with L- Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:45.2
occ:1.00
 OD1 A:ASP432 2.3 31.9 1.0
O A:HOH1659 2.5 43.4 1.0
OG A:SER434 2.5 34.7 1.0
O A:HOH1357 2.6 37.3 1.0
OE1 A:GLU426 2.7 25.0 1.0
CD A:GLU426 3.2 31.3 1.0
CG A:ASP432 3.5 30.7 1.0
CB A:SER434 3.7 24.3 1.0
OE2 A:GLU426 3.7 34.3 1.0
O A:HOH1235 3.8 44.4 1.0
N A:SER434 3.8 17.6 1.0
NH1 A:ARG437 4.0 47.1 0.5
N A:LEU433 4.1 21.4 1.0
CA A:SER434 4.1 21.6 1.0
CG A:GLU426 4.2 30.0 1.0
OD2 A:ASP432 4.2 38.1 1.0
CA A:ASP432 4.3 27.9 1.0
CB A:ASP432 4.3 28.7 1.0
NH1 A:ARG437 4.6 12.6 0.5
C A:ASP432 4.6 24.4 1.0
O A:HOH1572 4.6 33.2 1.0
C A:LEU433 4.7 19.6 1.0
CA A:LEU433 5.0 21.1 1.0

Sodium binding site 6 out of 7 in 4xo4

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Sodium binding site 6 out of 7 in the Crystal Structure 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 E. Coli Aminopeptidase N in Complex with L- Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:42.4
occ:1.00
 O A:HOH1474 2.1 27.5 1.0
OD1 A:ASP452 2.4 29.0 1.0
O A:HOH1669 2.5 30.9 1.0
O A:ASP452 2.8 22.7 1.0
O A:HOH1316 2.9 31.9 1.0
O A:HOH1496 3.3 39.3 1.0
CG A:ASP452 3.6 26.2 1.0
C A:ASP452 3.6 23.5 1.0
O A:HOH1035 3.6 38.6 1.0
N A:ASP452 3.7 24.6 1.0
CA A:MET903 3.9 45.0 1.0
CB A:MET903 4.0 40.9 1.0
N A:MET903 4.0 44.3 1.0
CA A:ASP452 4.0 23.5 1.0
O A:HOH1757 4.4 33.8 1.0
CB A:ASP452 4.4 25.1 1.0
OD2 A:ASP452 4.5 23.9 1.0
N A:ASP453 4.8 25.3 1.0
C A:LYS451 4.8 27.1 1.0
O A:HOH1345 4.9 23.2 1.0
O A:HOH1397 5.0 34.9 1.0

Sodium binding site 7 out of 7 in 4xo4

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Sodium binding site 7 out of 7 in the Crystal Structure 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 E. Coli Aminopeptidase N in Complex with L- Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na911

b:51.6
occ:1.00
 O A:HOH1647 2.5 35.8 1.0
OD1 A:ASN343 2.6 29.7 1.0
O A:HOH1603 2.8 50.9 1.0
OE1 A:GLU615 2.9 32.6 1.0
OE2 A:GLU615 2.9 37.3 1.0
CD A:GLU615 3.3 29.1 1.0
CG A:ASN343 3.5 26.0 1.0
ND2 A:ASN343 3.8 29.8 1.0
NE A:ARG346 3.8 25.4 1.0
CD A:ARG346 4.3 24.0 1.0
CG2 A:THR618 4.5 31.0 1.0
CZ A:ARG346 4.5 29.5 1.0
NH2 A:ARG346 4.7 30.3 1.0
CG A:GLU615 4.8 25.6 1.0
CB A:THR618 4.9 30.3 1.0
CB A:ASN343 4.9 24.5 1.0
OG1 A:THR618 5.0 29.8 1.0

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Methionine To Be Published.
Page generated: Mon Oct 7 19:19:04 2024

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