Atomistry » Nickel » PDB 3hy4-3kvb » 3i04
Atomistry »
  Nickel »
    PDB 3hy4-3kvb »
      3i04 »

Nickel in PDB 3i04: Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster

Enzymatic activity of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster

All present enzymatic activity of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster:
1.2.7.4; 1.2.99.2; 2.3.1.169;

Protein crystallography data

The structure of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster, PDB code: 3i04 was solved by Y.Kung, T.I.Doukov, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.39 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.830, 136.768, 141.611, 101.23, 109.18, 103.87
R / Rfree (%) 17.2 / 22.1

Other elements in 3i04:

The structure of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster also contains other interesting chemical elements:

Iron (Fe) 56 atoms
Copper (Cu) 4 atoms
Sodium (Na) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster (pdb code 3i04). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster, PDB code: 3i04:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 3i04

Go back to Nickel Binding Sites List in 3i04
Nickel binding site 1 out of 8 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni800

b:26.9
occ:1.00
 NI A:XCC800 0.0 26.9 1.0
C A:CYN900 2.1 31.2 1.0
SG A:CYS550 2.1 24.0 1.0
S1 A:XCC800 2.3 22.9 1.0
S4 A:XCC800 2.3 24.9 1.0
N A:CYN900 2.7 32.2 1.0
FE3 A:XCC800 2.8 21.9 1.0
FE2 A:XCC800 3.1 25.6 1.0
O A:HOH2513 3.1 24.7 1.0
CB A:CYS550 3.3 19.5 1.0
FE1 A:XCC800 3.7 21.2 1.0
FE4 A:XCC800 3.8 22.6 1.0
S3 A:XCC800 4.0 22.7 1.0
O A:HOH676 4.2 16.5 1.0
SG A:CYS317 4.5 23.4 1.0
SG A:CYS470 4.6 19.1 1.0
CA A:CYS550 4.7 20.7 1.0
OG A:SER585 4.7 14.8 1.0
S2 A:XCC800 4.7 21.8 1.0
CA A:GLY469 4.7 20.4 1.0
NZ A:LYS587 4.7 14.0 1.0
C A:GLY469 4.9 20.3 1.0
NE2 A:HIS283 5.0 15.9 1.0

Nickel binding site 2 out of 8 in 3i04

Go back to Nickel Binding Sites List in 3i04
Nickel binding site 2 out of 8 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni800

b:24.6
occ:1.00
 NI B:XCC800 0.0 24.6 1.0
C B:CYN900 2.0 25.5 1.0
S4 B:XCC800 2.2 20.9 1.0
SG B:CYS550 2.2 21.3 1.0
S1 B:XCC800 2.4 19.6 1.0
N B:CYN900 2.7 25.3 1.0
FE3 B:XCC800 2.8 19.0 1.0
FE2 B:XCC800 3.2 26.1 1.0
O B:HOH2514 3.2 24.7 1.0
CB B:CYS550 3.4 17.0 1.0
FE1 B:XCC800 3.6 18.1 1.0
FE4 B:XCC800 3.8 20.9 1.0
S3 B:XCC800 4.0 19.0 1.0
O B:HOH690 4.2 20.7 1.0
SG B:CYS470 4.5 16.3 1.0
CA B:GLY469 4.6 21.1 1.0
SG B:CYS317 4.6 20.8 1.0
S2 B:XCC800 4.7 18.9 1.0
CA B:CYS550 4.7 17.7 1.0
OG B:SER585 4.7 15.7 1.0
NZ B:LYS587 4.8 14.8 1.0
C B:GLY469 4.9 21.6 1.0
NE2 B:HIS283 5.0 16.3 1.0
N B:CYS470 5.0 20.4 1.0

Nickel binding site 3 out of 8 in 3i04

Go back to Nickel Binding Sites List in 3i04
Nickel binding site 3 out of 8 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni800

b:28.2
occ:1.00
 NI C:XCC800 0.0 28.2 1.0
SG C:CYS550 2.1 24.0 1.0
S4 C:XCC800 2.2 26.0 1.0
C C:CYN900 2.3 33.8 1.0
S1 C:XCC800 2.4 19.4 1.0
N C:CYN900 2.7 31.9 1.0
FE3 C:XCC800 2.9 25.3 1.0
FE2 C:XCC800 3.1 31.3 1.0
O C:HOH2515 3.2 32.0 1.0
CB C:CYS550 3.2 20.7 1.0
FE1 C:XCC800 3.7 25.4 1.0
FE4 C:XCC800 3.7 23.4 1.0
S3 C:XCC800 4.0 26.4 1.0
O C:HOH693 4.2 22.9 1.0
SG C:CYS317 4.6 24.0 1.0
CA C:GLY469 4.6 23.2 1.0
SG C:CYS470 4.6 24.1 1.0
CA C:CYS550 4.6 21.6 1.0
OG C:SER585 4.7 20.9 1.0
NZ C:LYS587 4.7 20.2 1.0
S2 C:XCC800 4.8 23.1 1.0
C C:GLY469 5.0 22.5 1.0

Nickel binding site 4 out of 8 in 3i04

Go back to Nickel Binding Sites List in 3i04
Nickel binding site 4 out of 8 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni800

b:36.4
occ:1.00
 NI D:XCC800 0.0 36.4 1.0
C D:CYN900 2.1 42.6 1.0
S4 D:XCC800 2.2 31.0 1.0
SG D:CYS550 2.3 28.8 1.0
S1 D:XCC800 2.3 29.0 1.0
FE3 D:XCC800 2.7 27.4 1.0
N D:CYN900 2.9 43.7 1.0
O D:HOH2516 3.2 37.7 1.0
FE2 D:XCC800 3.3 36.6 1.0
CB D:CYS550 3.4 25.5 1.0
FE1 D:XCC800 3.6 30.5 1.0
FE4 D:XCC800 3.7 29.2 1.0
S3 D:XCC800 3.9 31.1 1.0
O D:HOH678 4.2 23.5 1.0
SG D:CYS470 4.5 24.9 1.0
S2 D:XCC800 4.6 30.4 1.0
SG D:CYS317 4.7 30.2 1.0
CA D:GLY469 4.7 26.3 1.0
OG D:SER585 4.7 25.8 1.0
CA D:CYS550 4.8 24.5 1.0
C D:GLY469 4.9 26.9 1.0
NZ D:LYS587 4.9 25.8 1.0
NE2 D:HIS283 5.0 20.6 1.0

Nickel binding site 5 out of 8 in 3i04

Go back to Nickel Binding Sites List in 3i04
Nickel binding site 5 out of 8 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni951

b:24.4
occ:1.00
 N M:CYS597 1.8 21.9 1.0
N M:GLY596 2.0 22.8 1.0
SG M:CYS595 2.2 23.7 1.0
SG M:CYS597 2.3 23.4 1.0
C M:GLY596 2.7 21.1 1.0
CA M:GLY596 2.8 20.9 1.0
CA M:CYS597 2.9 23.2 1.0
CB M:CYS597 3.0 23.7 1.0
CU M:CU1950 3.0 35.4 1.0
C M:CYS595 3.1 22.9 1.0
CB M:CYS595 3.2 23.7 1.0
CA M:CYS595 3.5 23.6 1.0
C M:ACT953 3.5 56.3 1.0
N M:PHE598 3.6 25.8 1.0
C M:CYS597 3.6 24.5 1.0
N M:CYS595 3.8 24.0 1.0
O M:ACT953 3.8 56.7 1.0
CD1 M:LEU527 3.9 28.1 1.0
O M:GLY596 3.9 20.6 1.0
O M:CYS595 4.2 21.5 1.0
CH3 M:ACT953 4.5 56.0 1.0
CD2 M:PHE598 4.6 22.6 1.0
O M:CYS597 4.7 25.5 1.0
CD1 M:PHE229 4.8 33.6 1.0
S3 M:SF4900 4.8 22.7 1.0
CE1 M:PHE229 4.9 34.2 1.0
CA M:PHE598 4.9 25.0 1.0
CE2 M:PHE598 5.0 22.7 1.0

Nickel binding site 6 out of 8 in 3i04

Go back to Nickel Binding Sites List in 3i04
Nickel binding site 6 out of 8 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ni951

b:24.4
occ:1.00
 N N:CYS597 2.0 22.6 1.0
N N:GLY596 2.0 24.1 1.0
SG N:CYS595 2.2 25.2 1.0
SG N:CYS597 2.3 23.2 1.0
C N:GLY596 2.8 22.8 1.0
CA N:GLY596 2.9 23.3 1.0
CA N:CYS597 3.0 21.9 1.0
CB N:CYS597 3.0 22.2 1.0
CU N:CU1950 3.0 34.0 1.0
C N:CYS595 3.1 24.5 1.0
CB N:CYS595 3.1 25.2 1.0
CA N:CYS595 3.4 24.6 1.0
C N:CYS597 3.6 22.0 1.0
N N:PHE598 3.6 22.1 1.0
C N:ACT953 3.7 71.2 1.0
N N:CYS595 3.7 24.0 1.0
CD1 N:LEU527 3.7 23.4 1.0
O N:GLY596 4.0 22.8 1.0
O N:CYS595 4.2 24.5 1.0
O N:ACT953 4.3 71.2 1.0
CH3 N:ACT953 4.3 71.2 1.0
CD2 N:PHE598 4.5 19.6 1.0
CD1 N:PHE229 4.6 35.2 1.0
CE1 N:PHE229 4.6 36.1 1.0
O N:CYS597 4.6 23.9 1.0
CE2 N:PHE598 4.7 18.9 1.0
S3 N:SF4900 4.8 20.9 1.0
CA N:PHE598 4.9 21.5 1.0
C N:SER594 5.0 24.4 1.0

Nickel binding site 7 out of 8 in 3i04

Go back to Nickel Binding Sites List in 3i04
Nickel binding site 7 out of 8 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ni951

b:66.9
occ:1.00
 N O:CYS597 1.9 60.5 1.0
N O:GLY596 2.3 62.0 1.0
SG O:CYS597 2.5 61.3 1.0
SG O:CYS595 2.7 63.1 1.0
C O:GLY596 2.8 60.9 1.0
CA O:GLY596 2.9 61.4 1.0
CA O:CYS597 2.9 59.4 1.0
CB O:CYS597 3.1 59.5 1.0
CU O:CU1950 3.1 73.3 1.0
C O:CYS595 3.3 62.2 1.0
C O:ACT953 3.4 0.1 1.0
CB O:CYS595 3.5 62.5 1.0
CD1 O:LEU527 3.6 56.8 1.0
N O:PHE598 3.7 57.6 1.0
C O:CYS597 3.7 58.6 1.0
CA O:CYS595 3.7 62.5 1.0
N O:CYS595 3.9 62.7 1.0
O O:GLY596 4.0 61.1 1.0
CH3 O:ACT953 4.1 0.2 1.0
O O:ACT953 4.1 0.1 1.0
O O:CYS595 4.4 62.0 1.0
CD2 O:PHE598 4.6 55.3 1.0
O O:CYS597 4.7 58.2 1.0
CD1 O:PHE229 4.9 48.6 1.0
S3 O:SF4900 4.9 59.2 1.0
SG O:CYS509 4.9 54.4 1.0
CA O:PHE598 4.9 57.0 1.0
CE1 O:PHE229 4.9 50.4 1.0

Nickel binding site 8 out of 8 in 3i04

Go back to Nickel Binding Sites List in 3i04
Nickel binding site 8 out of 8 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ni951

b:41.2
occ:1.00
 N P:CYS597 2.0 37.8 1.0
N P:GLY596 2.1 41.3 1.0
SG P:CYS595 2.4 41.8 1.0
SG P:CYS597 2.4 37.9 1.0
C P:GLY596 2.9 38.4 1.0
CA P:CYS597 2.9 38.0 1.0
CB P:CYS597 3.0 37.7 1.0
CA P:GLY596 3.0 38.7 1.0
CB P:CYS595 3.1 42.2 1.0
C P:CYS595 3.1 41.4 1.0
CU P:CU1950 3.1 49.3 1.0
CA P:CYS595 3.4 41.9 1.0
C P:ACT953 3.5 76.1 1.0
N P:CYS595 3.7 42.2 1.0
C P:CYS597 3.7 37.4 1.0
N P:PHE598 3.8 36.6 1.0
CD1 P:LEU527 3.8 37.8 1.0
O P:GLY596 4.1 36.5 1.0
O P:CYS595 4.2 42.4 1.0
CH3 P:ACT953 4.3 75.8 1.0
O P:ACT953 4.4 76.3 1.0
CD2 P:PHE598 4.5 30.0 1.0
CD1 P:PHE229 4.5 38.5 1.0
CE1 P:PHE229 4.6 40.3 1.0
O P:CYS597 4.8 37.7 1.0
S3 P:SF4900 4.8 39.0 1.0
CE2 P:PHE598 4.8 32.8 1.0
C P:SER594 5.0 43.0 1.0
CA P:PHE598 5.0 35.5 1.0

Reference:

Y.Kung, T.I.Doukov, J.Seravalli, S.W.Ragsdale, C.L.Drennan. Crystallographic Snapshots of Cyanide- and Water-Bound C-Clusters From Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase. Biochemistry V. 48 7432 2009.
ISSN: ISSN 0006-2960
PubMed: 19583207
DOI: 10.1021/BI900574H
Page generated: Wed Dec 16 01:24:32 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy