Atomistry » Sodium » PDB 3qq0-3r57 » 3qvm
Atomistry »
  Sodium »
    PDB 3qq0-3r57 »
      3qvm »

Sodium in PDB 3qvm: The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica

Protein crystallography data

The structure of The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica, PDB code: 3qvm was solved by A.U.Singer, O.Kagan, Y.Kim, A.M.Edwards, A.Joachimiak, A.Savchenko, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.77 / 2.00
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 123.067, 123.067, 49.218, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18.5

Other elements in 3qvm:

The structure of The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica (pdb code 3qvm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica, PDB code: 3qvm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3qvm

Go back to Sodium Binding Sites List in 3qvm
Sodium binding site 1 out of 2 in the The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na285

b:24.0
occ:1.00
CG A:GLN275 3.6 19.2 1.0
CB A:LYS28 3.7 23.1 1.0
CG A:LYS28 3.9 21.8 1.0
CE1 A:PHE54 3.9 20.4 1.0
CA A:GLN275 4.0 19.2 1.0
CB A:GLN275 4.2 20.0 1.0
CD1 A:PHE54 4.4 20.2 1.0
CD A:GLN275 4.7 20.6 1.0
O A:GLN275 4.7 19.9 1.0
NE2 A:GLN275 4.7 22.9 1.0
O A:ILE274 4.7 18.0 1.0
CD A:LYS28 4.8 21.9 1.0
N A:GLN275 4.8 19.6 1.0
C A:GLN275 4.9 19.5 1.0
CZ A:PHE54 5.0 18.5 1.0

Sodium binding site 2 out of 2 in 3qvm

Go back to Sodium Binding Sites List in 3qvm
Sodium binding site 2 out of 2 in the The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of OLEI00960, A Hydrolase From Oleispira Antarctica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na284

b:16.9
occ:1.00
O B:VAL62 3.0 13.8 1.0
OH B:TYR83 3.0 15.0 1.0
OG B:SER64 3.0 13.7 1.0
CE1 B:TYR83 3.5 14.2 1.0
N B:SER64 3.6 13.8 1.0
C B:GLY63 3.7 15.1 1.0
CZ B:TYR83 3.8 15.0 1.0
CD2 B:PHE200 3.8 14.7 1.0
CA B:GLY63 3.9 14.6 1.0
C B:VAL62 3.9 15.5 1.0
CB B:SER64 4.0 13.6 1.0
CE1 B:PHE72 4.1 16.5 1.0
CA B:SER64 4.2 14.3 1.0
CE2 B:PHE200 4.2 15.1 1.0
O B:GLY63 4.3 14.9 1.0
CG B:PHE200 4.3 14.9 1.0
N B:GLY63 4.3 16.1 1.0
CB B:TYR61 4.4 12.8 1.0
O B:TYR61 4.4 13.8 1.0
CB B:VAL196 4.4 17.0 1.0
CB B:PHE200 4.6 13.9 1.0
CD1 B:PHE72 4.6 16.4 1.0
C B:TYR61 4.7 14.3 1.0
CG2 B:VAL196 4.7 19.6 1.0
CD1 B:TYR83 4.8 13.6 1.0
O B:HOH290 4.8 15.0 1.0
CZ B:PHE72 5.0 17.0 1.0

Reference:

M.Kube, T.N.Chernikova, Y.Al-Ramahi, A.Beloqui, N.Lopez-Cortez, M.E.Guazzaroni, H.J.Heipieper, S.Klages, O.R.Kotsyurbenko, I.Langer, T.Y.Nechitaylo, H.Lunsdorf, M.Fernandez, S.Juarez, S.Ciordia, A.Singer, O.Kagan, O.Egorova, P.Alain Petit, P.Stogios, Y.Kim, A.Tchigvintsev, R.Flick, R.Denaro, M.Genovese, J.P.Albar, O.N.Reva, M.Martinez-Gomariz, H.Tran, M.Ferrer, A.Savchenko, A.F.Yakunin, M.M.Yakimov, O.V.Golyshina, R.Reinhardt, P.N.Golyshin. Genome Sequence and Functional Genomic Analysis of the Oil-Degrading Bacterium Oleispira Antarctica. Nat Commun V. 4 2156 2013.
ISSN: ESSN 2041-1723
PubMed: 23877221
DOI: 10.1038/NCOMMS3156
Page generated: Mon Oct 7 12:42:45 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy