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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

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

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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

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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

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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

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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

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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

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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

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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

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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: Fri Sep 25 08:24:14 2020
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