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Sodium in PDB 4lw9: Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg

Protein crystallography data

The structure of Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg, PDB code: 4lw9 was solved by F.S.Vago, K.Raghunathan, J.C.Jens, W.J.Wedemeyer, M.Bagdasarian, J.S.Brunzelle, D.N.Arvidson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.54 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.610, 70.015, 131.544, 90.00, 103.29, 90.00
R / Rfree (%) 20.2 / 24.5

Other elements in 4lw9:

The structure of Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg also contains other interesting chemical elements:

Zinc (Zn) 32 atoms
Platinum (Pt) 12 atoms
Calcium (Ca) 14 atoms
Chlorine (Cl) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg (pdb code 4lw9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg, PDB code: 4lw9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4lw9

Go back to Sodium Binding Sites List in 4lw9
Sodium binding site 1 out of 6 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:41.1
occ:1.00
 OD1 A:ASP109 2.6 33.7 1.0
O A:ILE108 2.8 26.7 1.0
O A:HOH344 2.8 40.8 1.0
OD1 A:ASN130 3.1 22.1 1.0
N A:GLY106 3.3 37.4 1.0
ND2 A:ASN130 3.4 23.0 1.0
CG A:ASN130 3.5 22.7 1.0
CB A:TRP131 3.6 26.5 1.0
CE3 A:TRP131 3.6 26.8 1.0
CG A:ASP109 3.6 31.8 1.0
CB A:LYS105 3.7 41.1 1.0
C A:LYS105 3.7 39.7 1.0
C A:ILE108 3.8 28.8 1.0
CA A:ASP109 3.8 28.7 1.0
CA A:GLY106 3.8 35.5 1.0
N A:TRP131 4.0 26.5 1.0
N A:ASP109 4.2 28.8 1.0
CA A:TRP131 4.2 27.6 1.0
CB A:ASP109 4.2 30.1 1.0
O A:LYS105 4.2 39.4 1.0
CA A:LYS105 4.2 39.1 1.0
CD2 A:TRP131 4.3 27.0 1.0
C A:GLY106 4.3 34.3 1.0
CG A:TRP131 4.4 26.7 1.0
O A:HOH327 4.5 38.0 1.0
O A:GLY106 4.6 34.2 1.0
CZ3 A:TRP131 4.6 26.3 1.0
OD2 A:ASP109 4.7 35.0 1.0
N A:LYS105 4.7 37.7 1.0
C A:ASN130 4.7 25.5 1.0
CB A:ASN130 4.8 23.8 1.0
N A:ILE108 5.0 29.5 1.0
C A:ASP109 5.0 27.9 1.0

Sodium binding site 2 out of 6 in 4lw9

Go back to Sodium Binding Sites List in 4lw9
Sodium binding site 2 out of 6 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:38.2
occ:1.00
 OE1 A:GLU65 2.2 35.5 1.0
CD A:GLU65 3.1 33.7 1.0
OE2 A:GLU65 3.3 35.8 1.0
CG A:GLU65 4.5 31.0 1.0
CB A:GLU65 4.8 26.9 1.0
O A:HOH314 4.9 27.9 1.0

Sodium binding site 3 out of 6 in 4lw9

Go back to Sodium Binding Sites List in 4lw9
Sodium binding site 3 out of 6 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:33.8
occ:1.00
 O I:LYS86 2.7 21.7 1.0
O B:HOH305 2.7 31.6 1.0
N B:ASP61 3.1 21.9 1.0
CA I:LYS86 3.4 27.3 1.0
C I:LYS86 3.4 24.1 1.0
CB B:ASP61 3.5 26.1 1.0
N B:THR60 3.5 19.1 1.0
CB B:THR59 3.5 19.8 1.0
OG1 B:THR59 3.6 17.9 1.0
CB B:THR60 3.7 21.2 1.0
CD I:LYS86 3.9 37.6 1.0
CA B:THR60 3.9 20.1 1.0
CA B:ASP61 3.9 23.7 1.0
CB I:LYS86 3.9 31.6 1.0
C B:THR60 3.9 20.9 1.0
O B:HOH304 4.0 28.4 1.0
C B:THR59 4.1 19.6 1.0
CA B:THR59 4.4 19.2 1.0
OG1 B:THR60 4.4 21.2 1.0
CG I:LYS86 4.5 35.2 1.0
O B:SER101 4.5 22.4 1.0
CG2 B:THR59 4.6 19.6 1.0
O I:ILE85 4.6 21.6 1.0
N I:LYS86 4.7 24.6 1.0
O I:HOH350 4.7 43.6 1.0
CG2 B:THR60 4.7 20.4 1.0
N I:ARG87 4.7 22.7 1.0
CG B:ASP61 4.8 28.8 1.0
CE I:LYS86 4.9 38.7 1.0
NZ I:LYS86 4.9 39.5 1.0
O B:THR59 5.0 19.2 1.0

Sodium binding site 4 out of 6 in 4lw9

Go back to Sodium Binding Sites List in 4lw9
Sodium binding site 4 out of 6 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:37.8
occ:1.00
 OD1 B:ASP109 2.6 24.5 1.0
O B:ILE108 2.8 24.6 1.0
OD1 B:ASN130 3.2 20.2 1.0
N B:GLY106 3.5 31.9 1.0
CB B:TRP131 3.6 24.2 1.0
ND2 B:ASN130 3.6 20.0 1.0
CG B:ASP109 3.6 23.8 1.0
CG B:ASN130 3.6 21.1 1.0
C B:LYS105 3.6 34.1 1.0
CE3 B:TRP131 3.7 24.0 1.0
CA B:GLY106 3.7 31.2 1.0
CA B:ASP109 3.7 22.1 1.0
C B:ILE108 3.8 23.3 1.0
CB B:LYS105 3.9 35.9 1.0
O B:LYS105 3.9 36.2 1.0
N B:TRP131 4.1 23.0 1.0
N B:ASP109 4.1 22.6 1.0
CB B:ASP109 4.1 23.1 1.0
CA B:TRP131 4.2 24.9 1.0
CA B:LYS105 4.3 34.4 1.0
C B:GLY106 4.3 30.1 1.0
CD2 B:TRP131 4.3 24.2 1.0
CG B:TRP131 4.4 23.7 1.0
OD2 B:ASP109 4.6 27.4 1.0
O B:GLY106 4.7 28.6 1.0
CZ3 B:TRP131 4.7 23.7 1.0
N B:LYS105 4.7 32.8 1.0
C B:ASN130 4.8 23.0 1.0
CB B:ASN130 4.9 21.6 1.0
N B:ILE108 4.9 24.8 1.0
N B:THR107 4.9 29.6 1.0
C B:ASP109 5.0 21.2 1.0

Sodium binding site 5 out of 6 in 4lw9

Go back to Sodium Binding Sites List in 4lw9
Sodium binding site 5 out of 6 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:27.3
occ:1.00
 CD2 B:HIS143 4.5 43.0 1.0
NE2 B:HIS143 4.7 43.4 1.0
CE1 A:HIS143 4.7 38.9 1.0

Sodium binding site 6 out of 6 in 4lw9

Go back to Sodium Binding Sites List in 4lw9
Sodium binding site 6 out of 6 in the Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg


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 Vibrio Cholera Major Pseudopilin Epsg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na204

b:43.0
occ:1.00
 O D:ILE108 2.8 27.7 1.0
OD1 D:ASP109 2.9 28.9 1.0
OD1 D:ASN130 3.2 19.9 1.0
N D:GLY106 3.3 32.3 1.0
ND2 D:ASN130 3.3 21.4 1.0
CG D:ASN130 3.5 19.7 1.0
CA D:GLY106 3.5 32.5 1.0
C D:LYS105 3.7 35.0 1.0
CB D:TRP131 3.7 24.0 1.0
C D:ILE108 3.8 26.1 1.0
CG D:ASP109 3.9 28.1 1.0
CA D:ASP109 3.9 25.6 1.0
CB D:LYS105 3.9 36.3 1.0
CE3 D:TRP131 3.9 25.7 1.0
N D:TRP131 4.1 22.4 1.0
O D:LYS105 4.1 35.6 1.0
C D:GLY106 4.2 31.9 1.0
CA D:TRP131 4.2 23.4 1.0
N D:ASP109 4.3 25.6 1.0
CA D:LYS105 4.3 34.5 1.0
CB D:ASP109 4.3 26.8 1.0
CG D:TRP131 4.5 24.5 1.0
CD2 D:TRP131 4.6 25.7 1.0
O D:GLY106 4.6 30.2 1.0
C D:ASN130 4.8 21.8 1.0
CB D:ASN130 4.8 19.8 1.0
N D:LYS105 4.8 33.7 1.0
N D:THR107 4.9 31.0 1.0
OD2 D:ASP109 4.9 29.3 1.0
O D:HOH365 4.9 39.4 1.0
CZ3 D:TRP131 4.9 25.1 1.0
N D:ILE108 5.0 26.4 1.0

Reference:

F.S.Vago, K.Raghunathan, J.C.Jens, W.J.Wedemeyer, M.Bagdasarian, J.S.Brunzelle, D.N.Arvidson. Crystal Structure of Vibrio Cholera Major Pseudopilin Epsg To Be Published.
Page generated: Mon Oct 7 16:52:01 2024

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