Atomistry » Sodium » PDB 6s08-6sez » 6s5x
Atomistry »
  Sodium »
    PDB 6s08-6sez »
      6s5x »

Sodium in PDB 6s5x: Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae

Protein crystallography data

The structure of Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae, PDB code: 6s5x was solved by F.Whelan, J.P.Turkenburg, S.C.Griffiths, A.Bateman, J.R.Potts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.31 / 1.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 48.880, 48.880, 144.573, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae (pdb code 6s5x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae, PDB code: 6s5x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6s5x

Go back to Sodium Binding Sites List in 6s5x
Sodium binding site 1 out of 2 in the Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:16.7
occ:1.00
O A:ASN234 2.3 12.0 1.0
O A:HOH551 2.3 19.2 1.0
OD2 A:ASP295 2.3 13.0 1.0
O A:HOH578 2.3 22.6 1.0
O A:ALA231 2.4 11.9 1.0
OD1 A:ASP295 2.7 17.2 1.0
CG A:ASP295 2.9 16.7 1.0
O A:HOH586 3.4 26.5 1.0
C A:ALA231 3.4 12.5 1.0
HA A:ASP235 3.5 9.6 1.0
C A:ASN234 3.5 13.1 1.0
H A:ASN234 3.7 8.7 1.0
HB1 A:ALA231 3.7 14.0 1.0
HD2 A:PRO236 3.7 15.2 1.0
HA A:ALA231 3.7 10.3 1.0
HH A:TYR289 4.0 12.2 1.0
CA A:ALA231 4.0 8.6 1.0
HD3 A:PRO236 4.1 15.2 1.0
O A:HOH613 4.2 31.3 1.0
CA A:ASP235 4.3 8.0 1.0
N A:ASP235 4.3 10.3 1.0
CB A:ASP295 4.3 12.6 1.0
CB A:ALA231 4.4 11.7 1.0
N A:ASN234 4.4 7.2 1.0
CD A:PRO236 4.4 12.7 1.0
HA A:ASP232 4.5 14.5 1.0
CA A:ASN234 4.5 9.2 1.0
OH A:TYR289 4.5 10.2 1.0
N A:ASP232 4.5 9.7 1.0
HB2 A:ASN234 4.5 13.2 1.0
HB3 A:ASP295 4.6 15.1 1.0
O A:HOH504 4.6 43.1 1.0
HE2 A:TYR289 4.7 11.1 1.0
HB2 A:ASP295 4.7 15.1 1.0
OD1 A:ASP235 4.7 17.6 1.0
HB2 A:ASP235 4.7 12.2 1.0
CA A:ASP232 4.8 12.1 1.0
C A:ASP232 4.9 16.4 1.0
HB3 A:ALA231 4.9 14.0 1.0
CB A:ASN234 5.0 11.0 1.0

Sodium binding site 2 out of 2 in 6s5x

Go back to Sodium Binding Sites List in 6s5x
Sodium binding site 2 out of 2 in the Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:12.4
occ:1.00
O B:ASN234 2.3 12.9 1.0
O B:ALA231 2.3 11.6 1.0
OD2 B:ASP295 2.3 11.7 1.0
O B:HOH600 2.4 27.3 1.0
O B:HOH627 2.4 15.3 1.0
O B:HOH520 2.8 28.6 1.0
OD1 B:ASP295 2.8 16.6 1.0
CG B:ASP295 2.9 11.6 1.0
C B:ALA231 3.4 8.4 1.0
HD2 B:PRO236 3.4 13.2 1.0
C B:ASN234 3.5 12.9 1.0
HA B:ASP235 3.5 14.5 1.0
HA B:ALA231 3.7 9.6 1.0
H B:ASN234 3.7 10.9 1.0
HH B:TYR289 3.7 11.4 1.0
HB1 B:ALA231 3.7 9.9 1.0
HD3 B:PRO236 3.9 13.2 1.0
CA B:ALA231 4.0 8.0 1.0
CD B:PRO236 4.1 11.0 1.0
OD1 B:ASP235 4.1 29.9 1.0
HA B:ASP232 4.2 16.1 1.0
O B:HOH515 4.3 42.0 1.0
N B:ASP235 4.3 8.5 1.0
CA B:ASP235 4.3 12.1 1.0
CB B:ASP295 4.3 7.2 1.0
OH B:TYR289 4.3 9.5 1.0
N B:ASN234 4.4 9.1 1.0
CB B:ALA231 4.4 8.3 1.0
N B:ASP232 4.4 8.7 1.0
CA B:ASN234 4.4 7.8 1.0
HB2 B:ASN234 4.4 8.5 1.0
HE2 B:TYR289 4.5 9.3 1.0
HB3 B:ASP295 4.5 8.6 1.0
HB2 B:ASP295 4.6 8.6 1.0
CA B:ASP232 4.7 13.4 1.0
O B:HOH563 4.7 28.2 1.0
CG B:ASP235 4.8 97.2 1.0
C B:ASP232 4.8 11.1 1.0
O B:HOH637 4.9 24.6 1.0
HB3 B:ALA231 4.9 9.9 1.0
CB B:ASN234 4.9 7.1 1.0

Reference:

F.Whelan, A.Lafita, S.C.Griffiths, R.E.M.Cooper, J.L.Whittingham, J.P.Turkenburg, I.W.Manfield, A.N.St John, E.Paci, A.Bateman, J.R.Potts. Defining the Remarkable Structural Malleability of A Bacterial Surface Protein Rib Domain Implicated in Infection. Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
PubMed: 31818940
DOI: 10.1073/PNAS.1911776116
Page generated: Tue Oct 8 13:22:55 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy