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Nickel in PDB 4udx: CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution

Enzymatic activity of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution

All present enzymatic activity of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution:
1.2.99.2;

Protein crystallography data

The structure of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution, PDB code: 4udx was solved by J.Fesseler, J.-H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.03
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.516, 74.870, 71.075, 90.00, 111.26, 90.00
R / Rfree (%) 13.2 / 15.65

Other elements in 4udx:

The structure of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution also contains other interesting chemical elements:

Iron (Fe) 11 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution (pdb code 4udx). 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 CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution, PDB code: 4udx:

Nickel binding site 1 out of 1 in 4udx

Go back to Nickel Binding Sites List in 4udx
Nickel binding site 1 out of 1 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ni1003

b:8.5
occ:0.57
 NI X:WCC1003 0.0 8.5 0.6
C X:CO21005 1.8 8.4 0.6
FE X:FE21004 2.1 19.0 0.4
SG X:CYS526 2.1 9.3 0.9
S4 X:WCC1003 2.2 7.8 0.7
S1 X:WCC1003 2.3 7.7 0.7
O2 X:CO21005 2.7 8.4 0.6
O1 X:CO21005 2.8 9.8 0.6
FE3 X:WCC1003 2.8 7.0 0.7
FE X:FE21004 2.8 8.8 0.6
SG X:CYS526 2.9 9.5 0.1
O X:HOH2702 3.0 27.3 1.0
HB2 X:CYS526 3.0 11.5 0.1
CB X:CYS526 3.3 8.0 0.9
FE1 X:WCC1003 3.3 6.8 0.7
HB3 X:CYS526 3.5 9.6 0.9
HB2 X:CYS526 3.5 9.6 0.9
CB X:CYS526 3.5 9.6 0.1
FE4 X:WCC1003 3.6 7.5 0.7
S3 X:WCC1003 3.7 9.1 0.8
HA2 X:GLY445 3.8 9.3 1.0
HB3 X:CYS526 4.1 11.5 0.1
SG X:CYS295 4.2 9.4 0.7
HA3 X:GLY475 4.4 9.0 1.0
H X:CYS476 4.4 10.0 1.0
SG X:CYS295 4.5 11.9 0.3
HA X:CYS526 4.5 9.4 0.1
O X:HOH2643 4.5 8.0 1.0
NZ X:LYS563 4.6 10.2 1.0
HE3 X:LYS563 4.6 10.3 1.0
CA X:CYS526 4.6 7.8 0.1
S2 X:WCC1003 4.6 7.6 0.7
CA X:GLY445 4.7 7.7 1.0
SG X:CYS446 4.7 8.9 1.0
CA X:CYS526 4.7 7.9 0.9
NE2 X:HIS261 4.8 14.1 1.0
HB2 X:LYS563 4.8 8.8 1.0
H X:CYS526 4.8 8.6 1.0
HA X:CYS526 4.8 9.5 0.9
HB3 X:LYS563 4.8 8.8 1.0
H X:GLY445 4.9 9.1 1.0
C X:GLY445 4.9 7.8 1.0
HB3 X:ALA564 4.9 13.5 1.0
HD13 X:ILE567 5.0 15.9 1.0
HD2 X:LYS563 5.0 9.8 1.0

Reference:

J.Fesseler, J.H.Jeoung, H.Dobbek. How the [NIFE4 S4 ] Cluster of Co Dehydrogenase Activates CO2 and Nco(.) Angew.Chem.Int.Ed.Engl. 2015.
ISSN: ESSN 1521-3773
PubMed: 25926100
DOI: 10.1002/ANIE.201501778
Page generated: Wed Oct 9 19:12:09 2024

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