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Sodium in PDB 6a82: Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli

Protein crystallography data

The structure of Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli, PDB code: 6a82 was solved by Y.Q.Zhao, Y.J.Gu, W.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.83 / 2.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 85.060, 85.060, 121.340, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 20.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli (pdb code 6a82). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli, PDB code: 6a82:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6a82

Go back to Sodium Binding Sites List in 6a82
Sodium binding site 1 out of 3 in the Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli


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 C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:23.1
occ:1.00
 O A:ALA518 2.3 22.9 1.0
O A:ALA299 2.3 20.7 1.0
O A:GLN294 2.4 21.9 1.0
O A:THR297 2.4 21.8 1.0
O A:HOH788 2.5 17.7 1.0
O A:HOH745 2.5 20.2 1.0
C A:THR297 3.4 23.0 1.0
C A:ALA299 3.4 23.5 1.0
C A:PHE298 3.4 21.7 1.0
C A:GLN294 3.4 22.9 1.0
C A:ALA518 3.5 21.3 1.0
N A:ALA299 3.6 22.1 1.0
CA A:PHE298 3.7 21.1 1.0
O A:PHE298 3.8 20.3 1.0
N A:PHE298 4.0 21.6 1.0
CA A:ALA299 4.1 22.9 1.0
CA A:GLN294 4.2 21.6 1.0
CA A:GLU519 4.3 21.3 1.0
N A:GLU519 4.4 20.1 1.0
CG2 A:ILE521 4.4 20.2 1.0
N A:ALA295 4.4 21.4 1.0
N A:ASN300 4.5 20.9 1.0
N A:THR297 4.5 20.6 1.0
CA A:ALA518 4.5 19.0 1.0
CA A:THR297 4.6 22.4 1.0
CB A:GLN294 4.6 21.4 1.0
CA A:ALA295 4.6 22.6 1.0
O A:ALA295 4.6 22.8 1.0
OE1 A:GLU519 4.6 24.1 1.0
C A:ALA295 4.7 20.9 1.0
OG1 A:THR297 4.7 22.5 1.0
CB A:ASN300 4.8 21.3 1.0
CA A:ASN300 4.8 23.6 1.0
C A:GLU519 4.9 21.0 1.0

Sodium binding site 2 out of 3 in 6a82

Go back to Sodium Binding Sites List in 6a82
Sodium binding site 2 out of 3 in the Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli


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 C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:23.8
occ:1.00
 O B:GLN294 2.3 20.1 1.0
O B:ALA518 2.4 22.6 1.0
O B:ALA299 2.4 26.4 1.0
O B:THR297 2.4 19.1 1.0
O B:HOH757 2.4 19.4 1.0
O B:HOH747 2.6 19.6 1.0
C B:THR297 3.4 20.3 1.0
C B:GLN294 3.4 19.8 1.0
C B:PHE298 3.4 21.9 1.0
C B:ALA299 3.5 25.9 1.0
N B:ALA299 3.6 24.2 1.0
C B:ALA518 3.6 20.6 1.0
CA B:PHE298 3.7 22.2 1.0
O B:PHE298 3.8 24.3 1.0
N B:PHE298 3.9 22.8 1.0
CA B:GLN294 4.1 21.3 1.0
CA B:ALA299 4.1 26.8 1.0
CG2 B:ILE521 4.4 19.8 1.0
CA B:GLU519 4.4 20.0 1.0
N B:ALA295 4.4 19.9 1.0
N B:GLU519 4.4 19.6 1.0
N B:THR297 4.4 19.6 1.0
CA B:ALA518 4.5 21.7 1.0
CA B:THR297 4.5 22.2 1.0
N B:ASN300 4.5 24.0 1.0
CB B:GLN294 4.5 18.4 1.0
CA B:ALA295 4.6 21.5 1.0
OG1 B:THR297 4.6 21.3 1.0
O B:ALA295 4.6 19.8 1.0
C B:ALA295 4.6 20.0 1.0
OE1 B:GLU519 4.7 26.7 1.0
CB B:ASN300 4.8 25.0 1.0
CA B:ASN300 4.8 24.3 1.0
C B:GLU519 4.9 21.0 1.0

Sodium binding site 3 out of 3 in 6a82

Go back to Sodium Binding Sites List in 6a82
Sodium binding site 3 out of 3 in the Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli


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 the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:21.6
occ:1.00
 O C:GLN294 2.3 19.5 1.0
O C:ALA518 2.4 24.5 1.0
O C:THR297 2.4 21.9 1.0
O C:ALA299 2.4 21.0 1.0
O C:HOH832 2.4 21.2 1.0
O C:HOH740 2.7 19.7 1.0
C C:THR297 3.4 22.7 1.0
C C:GLN294 3.4 20.1 1.0
C C:PHE298 3.4 20.6 1.0
C C:ALA299 3.5 22.0 1.0
C C:ALA518 3.6 24.6 1.0
N C:ALA299 3.6 21.9 1.0
CA C:PHE298 3.7 21.5 1.0
O C:PHE298 3.8 23.0 1.0
N C:PHE298 3.9 19.5 1.0
CA C:ALA299 4.1 22.0 1.0
CA C:GLN294 4.1 20.0 1.0
CG2 C:ILE521 4.4 19.8 1.0
N C:ALA295 4.4 20.7 1.0
CA C:GLU519 4.4 24.2 1.0
N C:GLU519 4.4 21.4 1.0
N C:THR297 4.5 19.6 1.0
CA C:ALA518 4.5 24.7 1.0
N C:ASN300 4.5 22.6 1.0
CA C:THR297 4.5 22.8 1.0
CA C:ALA295 4.6 22.2 1.0
CB C:GLN294 4.6 20.2 1.0
O C:ALA295 4.6 21.6 1.0
C C:ALA295 4.6 20.9 1.0
OG1 C:THR297 4.7 21.9 1.0
OE1 C:GLU519 4.8 25.1 1.0
CB C:ASN300 4.8 21.6 1.0
CA C:ASN300 4.8 22.5 1.0
C C:GLU519 4.9 22.1 1.0
CB C:ILE521 5.0 21.2 1.0

Reference:

Y.Zhao, Q.Meng, Y.Lai, L.Wang, D.Zhou, C.Dou, Y.Gu, C.Nie, Y.Wei, W.Cheng. Structural and Mechanistic Insights Into Polymyxin Resistance Mediated By Eptc Originating From Escherichia Coli. Febs J. V. 286 750 2019.
ISSN: ISSN 1742-4658
PubMed: 30537137
DOI: 10.1111/FEBS.14719
Page generated: Tue Oct 8 01:44:55 2024

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