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

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

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

Protein crystallography data

The structure of Nco- Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True- Atomic Resolution, PDB code: 4udy 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) 33.16 / 1.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.183, 75.008, 71.149, 90.00, 111.22, 90.00
R / Rfree (%) 13.63 / 16.48

Other elements in 4udy:

The structure of Nco- 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 Nco- Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True- Atomic Resolution (pdb code 4udy). 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 Nco- Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True- Atomic Resolution, PDB code: 4udy:

Nickel binding site 1 out of 1 in 4udy

Go back to Nickel Binding Sites List in 4udy
Nickel binding site 1 out of 1 in the Nco- 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 Nco- 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:8.0
occ:0.57
 NI X:WCC1003 0.0 8.0 0.6
C X:0NM1005 1.8 8.4 0.6
FE X:FE21004 2.1 21.2 0.3
SG X:CYS526 2.1 10.5 1.0
S4 X:WCC1003 2.2 8.4 0.7
S1 X:WCC1003 2.3 8.2 0.8
O X:0NM1005 2.7 7.7 0.6
N X:0NM1005 2.8 7.9 0.6
FE3 X:WCC1003 2.8 6.8 0.7
FE X:FE21004 2.9 8.5 0.7
O X:HOH2677 2.9 15.4 0.3
CB X:CYS526 3.3 9.1 1.0
FE1 X:WCC1003 3.4 7.0 0.7
HB3 X:CYS526 3.5 11.0 1.0
HB2 X:CYS526 3.5 11.0 1.0
FE4 X:WCC1003 3.6 7.2 0.7
S3 X:WCC1003 3.8 9.2 0.8
HA2 X:GLY445 3.8 9.1 1.0
HZ3 X:LYS563 4.0 16.3 1.0
SG X:CYS295 4.1 9.1 0.7
HA3 X:GLY475 4.4 9.0 1.0
SG X:CYS295 4.4 12.1 0.3
H X:CYS476 4.4 9.6 1.0
O X:HOH2623 4.6 7.8 1.0
HE3 X:LYS563 4.6 10.6 1.0
HZ2 X:LYS563 4.6 16.3 1.0
NZ X:LYS563 4.6 10.8 1.0
CA X:CYS526 4.7 7.3 1.0
S2 X:WCC1003 4.7 7.2 0.7
CA X:GLY445 4.7 7.5 1.0
SG X:CYS446 4.7 9.8 1.0
HA X:CYS526 4.8 8.8 1.0
H X:CYS526 4.8 8.7 1.0
HB2 X:LYS563 4.8 8.7 1.0
NE2 X:HIS261 4.8 12.5 1.0
H X:GLY445 4.9 8.8 1.0
C X:GLY445 4.9 7.8 1.0
HD13 X:ILE567 4.9 16.5 1.0
HB3 X:ALA564 5.0 14.5 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 19:12:14 2024

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