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Sodium in PDB 3i01: Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.

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

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

Protein crystallography data

The structure of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster., PDB code: 3i01 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) 36.96 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.651, 136.870, 140.864, 101.26, 109.11, 104.08
R / Rfree (%) 18.6 / 24.2

Other elements in 3i01:

The structure of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-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 Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. (pdb code 3i01). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster., PDB code: 3i01:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3i01

Go back to Sodium Binding Sites List in 3i01
Sodium binding site 1 out of 4 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-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 Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na730

b:29.8
occ:1.00
 O M:ASN412 2.1 31.4 1.0
O M:GLY414 2.3 31.8 1.0
O M:LEU417 2.4 36.0 1.0
O M:HOH1431 2.5 32.4 1.0
OE1 M:GLU331 2.5 43.7 1.0
O M:PHE328 2.8 34.8 1.0
C M:ASN412 3.1 32.2 1.0
CD M:GLU331 3.4 42.3 1.0
C M:GLY414 3.4 33.0 1.0
C M:LEU417 3.6 36.2 1.0
CG M:GLU331 3.6 41.4 1.0
C M:PHE328 3.6 34.0 1.0
CA M:ASN412 3.6 31.9 1.0
N M:GLY414 3.9 33.5 1.0
N M:LEU417 3.9 35.3 1.0
CB M:PHE328 4.0 33.1 1.0
CA M:LEU417 4.2 35.5 1.0
N M:TYR413 4.3 32.3 1.0
N M:GLY416 4.3 34.8 1.0
CA M:GLY414 4.3 32.3 1.0
C M:TYR413 4.3 33.0 1.0
CB M:ASN412 4.4 31.5 1.0
CA M:PHE328 4.4 33.7 1.0
N M:GLU415 4.4 33.1 1.0
N M:GLU329 4.5 34.0 1.0
O M:ILE411 4.5 33.1 1.0
CA M:GLU415 4.5 34.9 1.0
OD1 M:ASN412 4.5 30.9 1.0
CA M:GLU329 4.5 35.1 1.0
O M:GLU329 4.5 37.6 1.0
N M:TRP418 4.6 36.3 1.0
OE2 M:GLU331 4.6 42.7 1.0
CB M:LEU417 4.6 34.5 1.0
CA M:TYR413 4.6 33.0 1.0
CB M:GLU331 4.8 39.7 1.0
C M:GLU329 4.8 36.2 1.0
CA M:TRP418 4.8 38.3 1.0
N M:ASN412 4.8 33.1 1.0
C M:GLU415 4.8 34.9 1.0
C M:GLY416 4.9 35.5 1.0
CG M:ASN412 4.9 30.9 1.0

Sodium binding site 2 out of 4 in 3i01

Go back to Sodium Binding Sites List in 3i01
Sodium binding site 2 out of 4 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-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 Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na730

b:28.1
occ:1.00
 O N:HOH1432 2.1 23.0 1.0
O N:LEU417 2.3 36.4 1.0
O N:ASN412 2.3 32.3 1.0
OE2 N:GLU331 2.5 39.5 1.0
O N:GLY414 2.5 32.7 1.0
O N:PHE328 2.6 27.6 1.0
C N:ASN412 3.4 31.9 1.0
CD N:GLU331 3.5 40.2 1.0
C N:LEU417 3.5 35.5 1.0
C N:PHE328 3.5 26.2 1.0
C N:GLY414 3.7 33.2 1.0
CG N:GLU331 3.7 38.2 1.0
CB N:PHE328 3.9 24.9 1.0
CA N:ASN412 3.9 32.7 1.0
N N:LEU417 4.0 34.8 1.0
N N:GLY414 4.2 32.8 1.0
CA N:PHE328 4.2 26.3 1.0
CA N:LEU417 4.2 35.3 1.0
N N:GLY416 4.2 33.5 1.0
N N:TYR413 4.4 31.9 1.0
C N:TYR413 4.5 32.8 1.0
O N:ILE411 4.5 32.8 1.0
OD1 N:ASN412 4.5 32.9 1.0
N N:GLU329 4.5 27.8 1.0
CB N:GLU331 4.5 37.4 1.0
N N:TRP418 4.5 36.0 1.0
CA N:GLY414 4.5 32.7 1.0
OE1 N:GLU331 4.6 45.3 1.0
N N:GLU415 4.6 33.5 1.0
CA N:GLU415 4.7 33.8 1.0
CA N:GLU329 4.7 29.2 1.0
CB N:ASN412 4.7 31.2 1.0
CA N:TRP418 4.7 36.7 1.0
CB N:LEU417 4.7 33.9 1.0
CA N:TYR413 4.8 30.6 1.0
C N:GLY416 4.8 35.0 1.0
O N:GLU329 4.9 29.9 1.0
C N:GLU415 4.9 33.6 1.0
C N:GLU329 5.0 30.4 1.0
N N:ASN412 5.0 34.0 1.0

Sodium binding site 3 out of 4 in 3i01

Go back to Sodium Binding Sites List in 3i01
Sodium binding site 3 out of 4 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-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 Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na730

b:70.2
occ:1.00
 O O:PHE328 2.4 56.9 1.0
O O:LEU417 2.5 67.9 1.0
O O:GLY414 2.6 58.6 1.0
O O:HOH1433 2.7 49.4 1.0
O O:ASN412 2.7 58.2 1.0
OE2 O:GLU331 3.2 77.8 1.0
C O:PHE328 3.6 56.4 1.0
N O:GLY416 3.6 63.0 1.0
N O:LEU417 3.6 66.7 1.0
C O:LEU417 3.7 68.2 1.0
C O:GLY414 3.7 59.0 1.0
C O:ASN412 3.7 57.6 1.0
CD O:GLU331 3.9 76.6 1.0
CG O:GLU331 3.9 73.0 1.0
CA O:LEU417 4.2 66.8 1.0
CA O:ASN412 4.3 58.3 1.0
CB O:PHE328 4.3 54.6 1.0
CA O:GLU415 4.3 61.1 1.0
C O:GLU415 4.3 61.6 1.0
CA O:GLY416 4.3 64.6 1.0
N O:GLU415 4.4 60.0 1.0
C O:GLY416 4.4 66.0 1.0
N O:GLU329 4.4 58.2 1.0
CA O:PHE328 4.5 54.9 1.0
OD1 O:ASN412 4.5 62.8 1.0
N O:GLY414 4.5 57.2 1.0
CA O:GLU329 4.5 60.2 1.0
O O:GLU329 4.6 61.0 1.0
CB O:LEU417 4.7 66.2 1.0
C O:GLU329 4.7 61.5 1.0
CA O:GLY414 4.7 57.9 1.0
N O:TYR413 4.8 56.6 1.0
N O:TRP418 4.8 69.6 1.0
C O:TYR413 4.8 56.5 1.0
CB O:ASN412 4.9 57.7 1.0

Sodium binding site 4 out of 4 in 3i01

Go back to Sodium Binding Sites List in 3i01
Sodium binding site 4 out of 4 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-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 Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na730

b:35.9
occ:1.00
 O P:LEU417 2.3 46.5 1.0
O P:ASN412 2.3 35.0 1.0
O P:GLY414 2.5 37.5 1.0
O P:PHE328 2.6 40.1 1.0
O P:HOH1434 2.6 35.2 1.0
OE2 P:GLU331 2.8 58.2 1.0
C P:ASN412 3.3 36.1 1.0
C P:LEU417 3.4 46.7 1.0
C P:GLY414 3.5 38.2 1.0
C P:PHE328 3.7 39.3 1.0
CD P:GLU331 3.7 61.3 1.0
CA P:ASN412 3.7 37.7 1.0
N P:LEU417 3.8 43.4 1.0
N P:GLY414 4.1 36.5 1.0
CA P:LEU417 4.1 45.0 1.0
CG P:GLU331 4.2 58.5 1.0
N P:GLY416 4.3 41.9 1.0
N P:GLU415 4.3 39.0 1.0
CA P:GLY414 4.4 37.5 1.0
N P:TYR413 4.4 36.1 1.0
C P:TYR413 4.4 35.8 1.0
CA P:GLU415 4.4 41.0 1.0
CB P:PHE328 4.4 35.6 1.0
OD1 P:ASN412 4.5 36.3 1.0
O P:ILE411 4.5 40.9 1.0
CB P:ASN412 4.5 38.0 1.0
N P:GLU329 4.5 40.6 1.0
CB P:LEU417 4.5 43.6 1.0
CA P:GLU329 4.5 42.5 1.0
N P:TRP418 4.5 49.1 1.0
CA P:PHE328 4.7 37.0 1.0
OE1 P:GLU331 4.7 59.8 1.0
O P:GLU329 4.8 44.5 1.0
C P:GLU415 4.8 41.9 1.0
CA P:TRP418 4.8 51.5 1.0
CA P:TYR413 4.8 36.2 1.0
C P:GLY416 4.9 43.3 1.0
C P:GLU329 4.9 44.4 1.0
O P:TYR413 4.9 35.9 1.0
N P:ASN412 4.9 39.6 1.0
CG P:ASN412 5.0 38.7 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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