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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: Tue Dec 15 05:59:46 2020

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