Atomistry » Sodium » PDB 2xjr-2xzi » 2xvy
Atomistry »
  Sodium »
    PDB 2xjr-2xzi »
      2xvy »

Sodium in PDB 2xvy: Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc)

Enzymatic activity of Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc)

All present enzymatic activity of Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc):
4.99.1.3;

Protein crystallography data

The structure of Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc), PDB code: 2xvy was solved by C.V.Romao, S.A.L.Lobo, M.A.Carrondo, L.M.Saraiva, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.44 / 1.70
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 120.810, 120.810, 119.710, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 18.8

Other elements in 2xvy:

The structure of Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc) also contains other interesting chemical elements:

Cobalt (Co) 1 atom
Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc) (pdb code 2xvy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc), PDB code: 2xvy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2xvy

Go back to Sodium Binding Sites List in 2xvy
Sodium binding site 1 out of 2 in the Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1286

b:20.0
occ:1.00
 O A:LEU209 2.5 19.9 0.5
OH A:TYR164 2.9 19.8 1.0
O2 A:SO41272 3.1 26.8 0.5
N A:HIS154 3.1 17.5 1.0
CB A:THR89 3.6 20.6 1.0
CA A:GLY153 3.7 17.1 1.0
C A:LEU209 3.7 18.6 0.5
OG1 A:THR89 3.7 24.6 1.0
CE1 A:TYR164 3.8 17.8 1.0
CZ A:TYR164 3.8 20.0 1.0
C A:GLY153 3.8 18.9 1.0
CB A:HIS154 4.0 20.2 1.0
CG2 A:THR89 4.0 19.5 1.0
CA A:HIS154 4.1 19.5 1.0
CA A:MET210 4.3 20.1 1.0
S A:SO41272 4.3 25.2 0.5
N A:MET210 4.3 19.1 1.0
CB A:LEU209 4.5 18.7 0.5
C A:LEU209 4.5 19.1 0.5
CB A:MET210 4.6 20.8 1.0
O1 A:SO41272 4.6 21.6 0.5
CG A:LEU209 4.6 21.2 0.5
CG A:LEU209 4.7 20.2 0.5
SD A:MET210 4.8 39.5 1.0
O4 A:SO41272 4.8 25.2 0.5
O A:HOH2223 4.8 27.1 1.0
CB A:LEU209 4.9 17.1 0.5
O A:LEU209 4.9 19.2 0.5
CA A:LEU209 4.9 18.2 0.5
O A:MET152 4.9 18.3 1.0
CG A:MET210 4.9 21.4 1.0
CE A:MET210 5.0 40.0 1.0
N A:GLY153 5.0 17.2 1.0

Sodium binding site 2 out of 2 in 2xvy

Go back to Sodium Binding Sites List in 2xvy
Sodium binding site 2 out of 2 in the Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cobalt Chelatase Cbik (Periplasmic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallised with Cobalt and Shc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1287

b:48.7
occ:1.00
 O3 A:GOL1282 2.5 63.9 1.0
O A:HOH2165 3.3 29.9 1.0
N A:HIS216 3.3 23.2 1.0
N A:ASP215 3.5 25.9 1.0
CD2 A:HIS216 3.6 26.8 1.0
C3 A:GOL1282 3.7 62.0 1.0
CE A:MET210 3.9 40.0 1.0
CB A:HIS216 3.9 22.3 1.0
CG A:HIS216 3.9 23.6 1.0
CB A:ASP215 4.0 29.4 1.0
C A:GLY214 4.1 25.4 1.0
CA A:ASP215 4.1 27.2 1.0
C A:ASP215 4.2 24.8 1.0
CA A:GLY214 4.2 25.8 1.0
CA A:HIS216 4.2 22.8 1.0
O A:HOH2222 4.3 27.8 0.8
NE2 A:HIS216 4.7 25.9 1.0
C2 A:GOL1282 4.8 60.8 1.0
N A:GLY214 4.8 23.5 1.0
O2 A:GOL1282 4.8 59.4 1.0
SD A:MET210 4.9 39.5 1.0
OD2 A:ASP215 4.9 48.2 1.0
CG A:ASP215 4.9 36.8 1.0
O A:GLY214 5.0 24.2 1.0

Reference:

S.A.Lobo, M.A.Videira, I.Pacheco, M.N.Wass, M.J.Warren, M.Teixeira, P.M.Matias, C.V.Romao, L.M.Saraiva. Desulfovibrio Vulgaris Cbik(P) Cobaltochelatase: Evolution of A Haem Binding Protein Orchestrated By the Incorporation of Two Histidine Residues. Environ. Microbiol. V. 19 106 2017.
ISSN: ESSN 1462-2920
PubMed: 27486032
DOI: 10.1111/1462-2920.13479
Page generated: Mon Oct 7 05:15:51 2024

Last articles

Ca in 5KLG
Ca in 5KJ8
Ca in 5KLB
Ca in 5KJ4
Ca in 5KL4
Ca in 5KK7
Ca in 5KIQ
Ca in 5KIS
Ca in 5KIX
Ca in 5KIA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy