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Calcium in PDB 9g7i: Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum

Enzymatic activity of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum

All present enzymatic activity of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum:
1.2.7.4; 2.3.1.169;

Protein crystallography data

The structure of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum, PDB code: 9g7i was solved by O.N.Lemaire, M.D.Yin, B.J.Murphy, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.68 / 2.93
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 298.077, 298.077, 127.526, 90, 90, 90
R / Rfree (%) 19 / 22

Other elements in 9g7i:

The structure of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum also contains other interesting chemical elements:

Iron (Fe) 28 atoms
Nickel (Ni) 6 atoms
Chlorine (Cl) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum (pdb code 9g7i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum, PDB code: 9g7i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 9g7i

Go back to Calcium Binding Sites List in 9g7i
Calcium binding site 1 out of 10 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca809

b:125.2
occ:1.00
 OD1 A:ASP39 3.0 105.5 1.0
O A:HOH902 3.0 88.8 1.0
CG A:ASP39 3.5 100.3 1.0
OD2 A:ASP39 3.6 101.6 1.0
CB A:ASP39 4.8 88.8 1.0

Calcium binding site 2 out of 10 in 9g7i

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Calcium binding site 2 out of 10 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca810

b:136.7
occ:1.00
 OE2 A:GLU174 2.8 87.4 0.5
CD A:GLU174 3.9 89.0 0.5
OE2 A:GLU146 4.2 98.1 1.0
CG A:GLU174 4.4 83.8 0.5
OG A:SER145 4.6 87.3 1.0
OE1 A:GLU174 5.0 94.6 0.5

Calcium binding site 3 out of 10 in 9g7i

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Calcium binding site 3 out of 10 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca811

b:118.2
occ:1.00
 OE1 A:GLU141 3.5 98.0 1.0
CD A:PRO237 4.1 54.6 1.0
CD A:GLU141 4.1 94.1 1.0
CG A:GLU141 4.3 69.9 1.0
CB A:GLU141 4.3 62.7 1.0
O A:CYS142 4.3 64.4 1.0
O A:GLU141 4.5 69.7 1.0
CA A:GLY236 4.7 56.0 1.0
C A:GLU141 4.9 62.7 1.0
O5 A:PE4805 4.9 106.6 1.0
C A:CYS142 4.9 65.4 1.0

Calcium binding site 4 out of 10 in 9g7i

Go back to Calcium Binding Sites List in 9g7i
Calcium binding site 4 out of 10 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca812

b:124.4
occ:1.00
 OE1 A:GLU75 3.2 93.2 1.0
OE2 A:GLU75 3.8 76.3 1.0
CD A:GLU75 3.9 78.2 1.0
NZ A:LYS80 4.1 84.3 1.0
CE A:LYS80 4.2 53.5 1.0

Calcium binding site 5 out of 10 in 9g7i

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Calcium binding site 5 out of 10 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca708

b:122.3
occ:1.00
 OE2 B:GLU226 2.6 117.7 1.0
CD B:GLU226 3.7 97.8 1.0
CG2 B:VAL124 4.2 62.3 1.0
OG B:SER127 4.3 92.5 1.0
CG B:GLU226 4.5 75.6 1.0
OE1 B:GLU226 4.5 70.2 1.0
CD B:PRO163 4.7 57.0 1.0
CA B:VAL124 4.8 59.9 1.0
CE1 B:PHE222 4.9 54.9 1.0
O B:HOH802 4.9 60.0 1.0

Calcium binding site 6 out of 10 in 9g7i

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Calcium binding site 6 out of 10 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca705

b:103.1
occ:1.00
 O C:GLU365 3.0 82.4 1.0
OG C:SER374 3.1 77.5 1.0
O C:SER374 4.0 89.3 1.0
CB C:SER374 4.2 70.1 1.0
C C:GLU365 4.2 75.0 1.0
CA C:SER374 4.2 76.3 1.0
CG1 C:ILE378 4.4 72.4 1.0
CD1 C:ILE378 4.4 75.6 1.0
CB C:LYS377 4.5 76.5 1.0
C C:MET364 4.5 75.8 1.0
CB C:MET364 4.5 73.1 1.0
C C:SER374 4.6 84.6 1.0
N C:GLU365 4.6 80.5 1.0
O C:MET364 4.7 76.5 1.0
CD C:LYS377 4.7 106.4 1.0
CA C:MET364 4.8 73.8 1.0
N C:ASP367 5.0 77.4 1.0

Calcium binding site 7 out of 10 in 9g7i

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Calcium binding site 7 out of 10 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca706

b:123.1
occ:1.00
 OD1 C:ASP239 3.0 114.5 1.0
CG C:ASP239 3.7 94.5 1.0
OD2 C:ASP239 3.8 99.4 1.0
CD1 C:ILE404 4.4 98.8 1.0
O C:SER237 4.4 87.8 1.0
CG2 C:ILE404 4.4 69.6 1.0
C C:SER237 4.5 80.4 1.0
CG1 C:ILE404 4.5 78.1 1.0
CB C:SER237 4.5 71.3 1.0
N C:ILE238 4.6 76.7 1.0
C C:ILE238 4.7 75.8 1.0
CA C:ILE238 4.8 77.7 1.0
N C:ASP239 4.8 77.5 1.0
OG C:SER237 4.9 107.8 1.0

Calcium binding site 8 out of 10 in 9g7i

Go back to Calcium Binding Sites List in 9g7i
Calcium binding site 8 out of 10 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca707

b:123.5
occ:1.00
 OE1 C:GLU226 2.8 102.7 1.0
CD C:GLU226 3.9 95.7 1.0
CE2 C:PHE128 4.0 82.3 1.0
CZ C:PHE128 4.0 78.3 1.0
CD1 C:PHE222 4.1 65.0 1.0
OE2 C:GLU226 4.3 88.9 1.0
OG C:SER127 4.3 106.4 1.0
CG C:PRO162 4.4 62.2 1.0
CA C:PRO162 4.5 53.0 1.0
CG C:MET223 4.6 69.3 1.0
N C:PRO162 4.6 63.2 1.0
CB C:PRO162 4.6 57.7 1.0
CE1 C:PHE222 4.6 65.8 1.0
CG C:PHE222 4.8 60.4 1.0
CB C:PHE222 4.9 58.9 1.0
C C:LEU161 5.0 66.5 1.0
CD2 C:PHE128 5.0 77.8 1.0
CD C:PRO162 5.0 73.2 1.0

Calcium binding site 9 out of 10 in 9g7i

Go back to Calcium Binding Sites List in 9g7i
Calcium binding site 9 out of 10 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca808

b:126.8
occ:1.00
 OD1 D:ASP705 2.7 142.9 1.0
O D:PRO706 3.3 117.1 1.0
CG D:ASP705 3.5 143.3 1.0
NH2 D:ARG645 3.6 84.5 1.0
O D:ASP705 3.9 116.6 1.0
OD2 D:ASP705 4.2 151.4 1.0
CB D:ASP705 4.2 120.4 1.0
C D:PRO706 4.2 101.7 1.0
CA D:ILE707 4.2 96.9 1.0
C D:ASP705 4.3 113.6 1.0
O D:ILE707 4.4 105.3 1.0
O D:GLU640 4.4 106.8 1.0
N D:ILE707 4.6 85.0 1.0
C D:ILE707 4.7 100.2 1.0
CZ D:ARG645 4.8 90.2 1.0
CA D:GLU640 4.9 86.8 1.0
CA D:ASP705 4.9 111.7 1.0
C D:GLU640 4.9 99.9 1.0
N D:PRO706 5.0 110.9 1.0

Calcium binding site 10 out of 10 in 9g7i

Go back to Calcium Binding Sites List in 9g7i
Calcium binding site 10 out of 10 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca809

b:163.4
occ:1.00
 O D:SER490 2.7 116.4 1.0
OD2 D:ASP182 3.3 157.1 1.0
OD1 D:ASP182 3.5 125.0 1.0
CG D:ASP182 3.6 127.2 1.0
O D:PHE491 3.8 112.0 1.0
C D:SER490 3.9 100.8 1.0
CA D:PHE491 4.2 89.0 1.0
C D:PHE491 4.4 94.5 1.0
N D:PHE491 4.5 99.6 1.0
CB D:ASP182 5.0 101.0 1.0

Reference:

M.D.Yin, O.N.Lemaire, J.G.Rosas Jimenez, M.Belhamri, A.Shevchenko, G.Hummer, T.Wagner, B.J.Murphy. Conformational Dynamics of A Multienzyme Complex in Anaerobic Carbon Fixation. Science V. 387 498 2025.
ISSN: ESSN 1095-9203
PubMed: 39883773
DOI: 10.1126/SCIENCE.ADR9672
Page generated: Tue Feb 25 08:41:51 2025

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