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Nickel in PDB 8x9d: Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration

Enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration

All present enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration, PDB code: 8x9d was solved by H.H.Lee, Y.Heo, H.J.Yoon, S.M.Kim, S.Y.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.02 / 2.11
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.045, 74.552, 71.309, 90, 111.53, 90
R / Rfree (%) 16.5 / 21.9

Other elements in 8x9d:

The structure of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration also contains other interesting chemical elements:

Iron (Fe) 11 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration (pdb code 8x9d). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration, PDB code: 8x9d:

Nickel binding site 1 out of 1 in 8x9d

Go back to Nickel Binding Sites List in 8x9d
Nickel binding site 1 out of 1 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni703

b:28.1
occ:0.70
 NI A:XCC703 0.0 28.1 0.7
SG A:CYS526 2.0 25.2 0.5
SG A:CYS526 2.0 27.7 0.5
S1 A:XCC703 2.2 26.2 0.7
O A:HOH829 2.4 37.9 1.0
S4 A:XCC703 2.4 25.7 0.7
FE2 A:XCC703 2.8 28.8 0.7
FE3 A:XCC703 2.9 25.6 0.7
CB A:CYS526 3.2 24.5 0.5
CB A:CYS526 3.3 24.7 0.5
FE4 A:XCC703 3.6 26.2 0.7
FE1 A:XCC703 4.0 25.5 0.6
NE2 A:HIS261 4.2 27.1 1.0
S3 A:XCC703 4.2 27.4 0.7
NZ A:LYS563 4.2 25.9 1.0
O A:HOH946 4.3 22.8 1.0
CA A:GLY445 4.5 22.3 1.0
CA A:CYS526 4.5 23.6 0.5
CA A:CYS526 4.5 22.8 0.5
SG A:CYS446 4.5 24.4 1.0
C A:GLY445 4.7 23.5 1.0
SG A:CYS295 4.8 25.7 1.0
CE A:LYS563 4.9 24.1 1.0
S2 A:XCC703 4.9 26.2 0.7
CE1 A:HIS261 4.9 26.9 1.0
CD1 A:ILE567 4.9 20.9 1.0
CB A:LYS563 5.0 20.5 1.0

Reference:

S.M.Kim, S.H.Kang, J.Lee, Y.Heo, E.G.Poloniataki, J.Kang, H.J.Yoon, S.Y.Kong, Y.Yun, H.Kim, J.Ryu, H.H.Lee, Y.H.Kim. Identifying A Key Spot For Electron Mediator-Interaction to Tailor Co Dehydrogenase'S Affinity Nat Commun V. 15 2732 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-46909-1
Page generated: Thu Oct 10 09:48:48 2024

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