Atomistry » Sodium » PDB 6myw-6nfx » 6n6c
Atomistry »
  Sodium »
    PDB 6myw-6nfx »
      6n6c »

Sodium in PDB 6n6c: Vibrio Cholerae Oligoribonuclease Bound to Paa

Protein crystallography data

The structure of Vibrio Cholerae Oligoribonuclease Bound to Paa, PDB code: 6n6c was solved by J.D.Lormand, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.75 / 1.62
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.375, 89.375, 59.451, 90.00, 90.00, 120.00
R / Rfree (%) 14.6 / 15.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Vibrio Cholerae Oligoribonuclease Bound to Paa (pdb code 6n6c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Vibrio Cholerae Oligoribonuclease Bound to Paa, PDB code: 6n6c:

Sodium binding site 1 out of 1 in 6n6c

Go back to Sodium Binding Sites List in 6n6c
Sodium binding site 1 out of 1 in the Vibrio Cholerae Oligoribonuclease Bound to Paa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Vibrio Cholerae Oligoribonuclease Bound to Paa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na701

b:24.6
occ:1.00
O A:HOH221 2.3 25.7 1.0
O A:HOH383 2.3 30.5 1.0
O A:HOH252 2.4 22.8 1.0
OD1 A:ASP12 2.4 27.4 1.0
OP1 D:A604 2.5 24.0 0.9
O3' D:A603 2.6 22.9 0.9
P D:A604 3.1 24.2 0.9
CG A:ASP12 3.5 27.4 1.0
O A:HOH205 3.8 29.8 1.0
C3' D:A603 3.8 22.3 0.9
O2' D:A603 3.9 25.4 0.9
OD2 A:ASP12 4.1 36.0 1.0
O A:HOH340 4.1 26.4 1.0
OD2 A:ASP112 4.1 24.0 1.0
C4' D:A603 4.1 21.7 0.9
O A:LEU13 4.2 22.6 1.0
O5' D:A604 4.2 22.5 0.9
C5' D:A604 4.2 21.3 0.9
O A:HOH301 4.2 28.0 1.0
OP2 D:A604 4.3 24.5 0.9
OD1 A:ASP112 4.3 25.1 1.0
O A:ASN107 4.4 24.9 1.0
C2' D:A603 4.5 22.8 0.9
CG A:ASP112 4.6 23.7 1.0
O D:HOH804 4.7 28.0 1.0
CB A:ASP12 4.7 18.8 1.0
C5' D:A603 4.7 21.1 0.9
N A:LEU13 4.9 22.7 1.0

Reference:

S.K.Kim, J.D.Lormand, C.A.Weiss, K.A.Eger, H.Turdiev, A.Turdiev, W.C.Winkler, H.Sondermann, V.T.Lee. A Dedicated Diribonucleotidase Resolves A Key Bottleneck For the Terminal Step of Rna Degradation. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31225796
DOI: 10.7554/ELIFE.46313
Page generated: Tue Oct 8 12:09:12 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy