Atomistry » Sodium » PDB 3hwe-3ic9 » 3i01
Atomistry »
  Sodium »
    PDB 3hwe-3ic9 »
      3i01 »

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: Mon Oct 7 10:31:08 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy