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Sodium in PDB 4dq9: Crystal Structure of the Minor Pseudopilin Epsh From the Type II Secretion System of Vibrio Cholerae

Protein crystallography data

The structure of Crystal Structure of the Minor Pseudopilin Epsh From the Type II Secretion System of Vibrio Cholerae, PDB code: 4dq9 was solved by K.Raghunathan, F.S.Vago, D.Grindem, T.Ball, W.J.Wedemeyer, D.N.Arvidson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.94 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.391, 71.110, 84.646, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.9

Other elements in 4dq9:

The structure of Crystal Structure of the Minor Pseudopilin Epsh From the Type II Secretion System of Vibrio Cholerae also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Minor Pseudopilin Epsh From the Type II Secretion System of Vibrio Cholerae (pdb code 4dq9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Minor Pseudopilin Epsh From the Type II Secretion System of Vibrio Cholerae, PDB code: 4dq9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4dq9

Go back to Sodium Binding Sites List in 4dq9
Sodium binding site 1 out of 2 in the Crystal Structure of the Minor Pseudopilin Epsh From the Type II Secretion System of Vibrio Cholerae


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 the Minor Pseudopilin Epsh From the Type II Secretion System of Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:25.0
occ:1.00
OG1 A:THR69 2.6 20.5 1.0
OD2 A:ASP62 2.7 28.5 1.0
O A:ARG60 3.0 16.9 1.0
N A:THR69 3.2 18.3 1.0
O A:ARG67 3.2 19.3 1.0
CG A:ASP62 3.3 27.1 1.0
CB A:THR69 3.5 20.2 1.0
C A:ARG67 3.5 17.5 1.0
C A:LEU68 3.5 17.8 1.0
CA A:LEU68 3.7 16.9 1.0
N A:LEU68 3.7 16.8 1.0
C A:ARG60 3.7 17.0 1.0
NH2 A:ARG60 3.8 37.1 1.0
CB A:ARG67 3.8 18.1 1.0
CG A:ARG67 3.9 26.4 1.0
NE A:ARG60 3.9 31.8 1.0
CB A:ASP62 3.9 20.4 1.0
CA A:THR69 3.9 17.6 1.0
N A:ASP62 4.0 16.8 1.0
CZ A:ARG60 4.2 33.5 1.0
OD1 A:ASP62 4.2 32.4 1.0
CB A:ARG60 4.2 18.1 1.0
CA A:ARG67 4.3 17.2 1.0
O A:LEU68 4.4 17.9 1.0
C A:ILE61 4.4 18.5 1.0
CG A:ARG60 4.4 24.2 1.0
CA A:ILE61 4.5 16.6 1.0
N A:ILE61 4.5 16.2 1.0
CD A:ARG67 4.5 37.1 1.0
CA A:ARG60 4.6 17.1 1.0
CA A:ASP62 4.6 19.6 1.0
OE1 A:GLN90 4.7 31.6 1.0
CG2 A:THR69 4.9 19.8 1.0
CD A:ARG60 4.9 30.0 1.0

Sodium binding site 2 out of 2 in 4dq9

Go back to Sodium Binding Sites List in 4dq9
Sodium binding site 2 out of 2 in the Crystal Structure of the Minor Pseudopilin Epsh From the Type II Secretion System of Vibrio Cholerae


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 the Minor Pseudopilin Epsh From the Type II Secretion System of Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:28.4
occ:1.00
OE1 A:GLN80 2.7 29.8 1.0
O A:HOH401 2.8 30.6 1.0
N A:LYS81 2.8 16.6 1.0
OE2 A:GLU136 2.9 54.7 1.0
CA A:GLN80 3.5 17.1 1.0
CG A:LYS81 3.6 21.0 1.0
C A:GLN80 3.6 14.6 1.0
CB A:GLN80 3.7 19.9 1.0
CB A:LYS81 3.7 18.8 1.0
CD A:GLU136 3.7 53.6 1.0
CD A:GLN80 3.8 28.4 1.0
CA A:LYS81 3.8 16.5 1.0
CG A:GLU136 4.0 54.5 1.0
O A:HOH317 4.1 20.6 1.0
CD A:LYS81 4.3 23.7 1.0
CB A:GLU136 4.3 56.8 1.0
CG A:GLN80 4.3 23.0 1.0
O A:LYS81 4.8 18.8 1.0
NE2 A:GLN80 4.8 33.1 1.0
CE A:LYS81 4.8 31.8 1.0
OE1 A:GLU136 4.8 43.8 1.0
O A:GLN80 4.8 17.6 1.0
C A:LYS81 4.8 17.0 1.0
O A:TRP79 4.9 19.6 1.0
N A:GLN80 4.9 16.9 1.0
O A:HOH425 4.9 22.4 1.0

Reference:

K.Raghunathan, F.S.Vago, D.Grindem, T.Ball, W.J.Wedemeyer, M.Bagdasarian, D.N.Arvidson. The 1.59 Angstrom Resolution Structure of the Minor Pseudopilin Epsh of Vibrio Cholerae Reveals A Long Flexible Loop. Biochim.Biophys.Acta V.1844 406 2013.
ISSN: ISSN 0006-3002
PubMed: 24316251
DOI: 10.1016/J.BBAPAP.2013.11.013
Page generated: Tue Dec 15 06:37:09 2020

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