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Sodium 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:

Nickel (Ni) 8 atoms
Iron (Fe) 56 atoms
Copper (Cu) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3i04

Go back to Sodium Binding Sites List in 3i04
Sodium binding site 1 out of 4 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 Sodium with other atoms in the Na 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
M:Na1

b:28.8
occ:1.00
O M:HOH730 2.2 34.2 1.0
O M:ASN412 2.3 30.6 1.0
O M:GLY414 2.4 28.9 1.0
O M:LEU417 2.4 35.3 1.0
OE1 M:GLU331 2.5 41.8 1.0
O M:PHE328 2.7 29.8 1.0
C M:ASN412 3.3 29.6 1.0
C M:PHE328 3.5 30.6 1.0
C M:GLY414 3.6 29.2 1.0
C M:LEU417 3.6 36.4 1.0
CD M:GLU331 3.7 43.7 1.0
CA M:ASN412 3.8 29.9 1.0
CB M:PHE328 3.8 29.6 1.0
CB M:GLU331 3.8 39.4 1.0
N M:LEU417 4.0 35.0 1.0
CA M:PHE328 4.2 30.4 1.0
N M:GLY414 4.2 29.4 1.0
CG M:GLU331 4.3 42.0 1.0
N M:GLY416 4.3 33.8 1.0
CA M:LEU417 4.4 35.1 1.0
N M:GLU329 4.4 31.1 1.0
N M:TYR413 4.4 29.0 1.0
CA M:GLY414 4.5 29.4 1.0
C M:TYR413 4.5 29.4 1.0
N M:GLU415 4.5 30.8 1.0
CB M:ASN412 4.5 29.8 1.0
CA M:GLU329 4.5 32.2 1.0
OD1 M:ASN412 4.5 31.5 1.0
CA M:GLU415 4.5 32.8 1.0
O M:ILE411 4.5 29.4 1.0
N M:TRP418 4.6 37.2 1.0
OE2 M:GLU331 4.7 47.2 1.0
O M:GLU329 4.7 33.2 1.0
CB M:LEU417 4.8 34.5 1.0
CA M:TRP418 4.8 38.3 1.0
CA M:TYR413 4.8 29.5 1.0
C M:GLU329 4.8 32.8 1.0
C M:GLU415 4.9 33.0 1.0
N M:ASN412 5.0 29.9 1.0
O M:TYR413 5.0 31.0 1.0

Sodium binding site 2 out of 4 in 3i04

Go back to Sodium Binding Sites List in 3i04
Sodium binding site 2 out of 4 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 Sodium with other atoms in the Na 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
N:Na730

b:26.8
occ:1.00
O N:HOH732 2.0 27.0 1.0
O N:LEU417 2.3 33.3 1.0
O N:ASN412 2.4 30.9 1.0
O N:GLY414 2.6 29.8 1.0
O N:PHE328 2.6 28.9 1.0
OE2 N:GLU331 2.6 37.1 1.0
C N:ASN412 3.4 30.2 1.0
C N:LEU417 3.5 33.2 1.0
C N:PHE328 3.6 28.4 1.0
CD N:GLU331 3.6 39.7 1.0
C N:GLY414 3.8 29.9 1.0
CA N:ASN412 3.8 30.5 1.0
N N:LEU417 3.9 32.7 1.0
CG N:GLU331 3.9 37.7 1.0
CB N:PHE328 4.0 28.3 1.0
CA N:LEU417 4.2 32.5 1.0
N N:GLY416 4.2 31.8 1.0
CB N:GLU331 4.3 35.8 1.0
N N:GLY414 4.3 30.0 1.0
OD1 N:ASN412 4.3 30.8 1.0
CA N:PHE328 4.3 28.7 1.0
N N:GLU329 4.5 28.5 1.0
N N:TYR413 4.5 29.6 1.0
C N:TYR413 4.5 30.1 1.0
N N:TRP418 4.5 33.3 1.0
CA N:GLU329 4.6 29.6 1.0
CA N:GLY414 4.6 29.3 1.0
CB N:ASN412 4.6 28.8 1.0
O N:ILE411 4.6 31.0 1.0
CA N:TRP418 4.7 33.6 1.0
CB N:LEU417 4.7 31.9 1.0
N N:GLU415 4.7 30.6 1.0
O N:GLU329 4.7 28.3 1.0
CA N:GLU415 4.8 31.7 1.0
OE1 N:GLU331 4.8 43.3 1.0
C N:GLY416 4.8 33.1 1.0
CA N:TYR413 4.8 29.2 1.0
C N:GLU329 4.8 29.2 1.0
C N:GLU415 4.9 31.9 1.0
CG N:ASN412 4.9 30.7 1.0
O N:TYR413 5.0 31.0 1.0
N N:ASN412 5.0 30.8 1.0
CA N:GLY416 5.0 32.1 1.0

Sodium binding site 3 out of 4 in 3i04

Go back to Sodium Binding Sites List in 3i04
Sodium binding site 3 out of 4 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 Sodium with other atoms in the Na 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
O:Na730

b:65.0
occ:1.00
O O:HOH731 2.4 44.9 1.0
O O:LEU417 2.4 66.9 1.0
O O:PHE328 2.5 55.2 1.0
O O:ASN412 2.7 58.4 1.0
O O:GLY414 2.8 58.6 1.0
OE2 O:GLU331 2.8 76.9 1.0
C O:LEU417 3.6 67.3 1.0
C O:PHE328 3.7 54.8 1.0
C O:ASN412 3.7 57.9 1.0
N O:LEU417 3.9 66.2 1.0
C O:GLY414 3.9 59.4 1.0
CD O:GLU331 3.9 74.9 1.0
CA O:ASN412 4.1 58.6 1.0
CB O:GLU331 4.2 70.6 1.0
CA O:LEU417 4.2 66.5 1.0
N O:GLY416 4.3 63.3 1.0
OD1 O:ASN412 4.3 60.1 1.0
CG O:GLU331 4.3 72.0 1.0
CB O:PHE328 4.5 52.8 1.0
CA O:GLU329 4.5 59.0 1.0
N O:GLU329 4.5 56.6 1.0
O O:GLU329 4.6 60.5 1.0
CA O:PHE328 4.6 53.1 1.0
CA O:GLU415 4.6 61.6 1.0
N O:GLY414 4.6 57.8 1.0
C O:GLU329 4.7 60.5 1.0
N O:TRP418 4.7 68.3 1.0
N O:GLU415 4.7 60.4 1.0
CB O:LEU417 4.7 66.1 1.0
CB O:ASN412 4.7 58.2 1.0
C O:GLY416 4.8 65.6 1.0
C O:GLU415 4.8 62.4 1.0
N O:GLU331 4.9 68.9 1.0
N O:TYR413 4.9 57.0 1.0
CA O:GLY414 4.9 58.5 1.0
CA O:TRP418 4.9 69.6 1.0
CG O:ASN412 4.9 58.8 1.0

Sodium binding site 4 out of 4 in 3i04

Go back to Sodium Binding Sites List in 3i04
Sodium binding site 4 out of 4 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 Sodium with other atoms in the Na 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
P:Na730

b:35.7
occ:1.00
O P:ASN412 2.3 33.6 1.0
O P:LEU417 2.4 44.4 1.0
O P:PHE328 2.6 37.0 1.0
O P:HOH731 2.6 31.3 1.0
O P:GLY414 2.6 37.6 1.0
OE2 P:GLU331 3.1 50.0 1.0
C P:ASN412 3.3 35.0 1.0
C P:PHE328 3.5 36.7 1.0
C P:LEU417 3.6 45.5 1.0
C P:GLY414 3.7 37.6 1.0
CA P:ASN412 3.8 36.6 1.0
N P:LEU417 4.0 41.4 1.0
CD P:GLU331 4.0 54.0 1.0
CG P:GLU331 4.0 52.9 1.0
CB P:PHE328 4.2 33.4 1.0
N P:GLY414 4.2 34.9 1.0
N P:GLU329 4.3 38.5 1.0
CA P:GLU329 4.3 41.2 1.0
CA P:LEU417 4.3 43.4 1.0
OD1 P:ASN412 4.4 38.1 1.0
N P:GLY416 4.4 39.3 1.0
N P:TYR413 4.4 33.8 1.0
CA P:PHE328 4.5 34.8 1.0
CB P:ASN412 4.5 36.9 1.0
N P:GLU415 4.5 37.8 1.0
C P:TYR413 4.5 34.1 1.0
CA P:GLY414 4.5 36.2 1.0
CA P:GLU415 4.6 39.6 1.0
O P:ILE411 4.6 39.0 1.0
N P:TRP418 4.7 48.3 1.0
C P:GLU329 4.7 42.7 1.0
CB P:LEU417 4.8 42.3 1.0
O P:GLU329 4.8 42.8 1.0
CA P:TYR413 4.9 34.1 1.0
C P:GLU415 4.9 40.2 1.0
CA P:TRP418 4.9 51.8 1.0
CG P:ASN412 4.9 37.4 1.0
C P:GLY416 5.0 40.4 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: Tue Dec 15 06:13:55 2020

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