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Cobalt in PDB 4jbh: 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum

Enzymatic activity of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum

All present enzymatic activity of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum:
1.1.1.1;

Protein crystallography data

The structure of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum, PDB code: 4jbh was solved by S.Lovell, K.P.Battaile, A.Vitale, N.Throne, X.Hu, M.Shen, S.D'auria, D.S.Auld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.16 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.402, 125.336, 82.943, 90.00, 107.12, 90.00
R / Rfree (%) 15.1 / 19.5

Other elements in 4jbh:

The structure of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum (pdb code 4jbh). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum, PDB code: 4jbh:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 4jbh

Go back to Cobalt Binding Sites List in 4jbh
Cobalt binding site 1 out of 4 in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:39.2
occ:0.50
ZN A:ZN401 0.0 39.3 0.5
SG A:CYS105 2.3 25.1 1.0
SG A:CYS94 2.3 28.1 1.0
SG A:CYS97 2.3 29.6 1.0
SG A:CYS91 2.4 27.4 1.0
CB A:CYS105 3.2 24.8 1.0
CB A:CYS97 3.4 25.2 1.0
CB A:CYS94 3.4 34.7 1.0
N A:CYS91 3.5 30.5 1.0
CB A:CYS91 3.5 26.9 1.0
CA A:CYS105 3.5 25.5 1.0
N A:CYS94 3.8 36.0 1.0
N A:GLY92 3.9 33.9 1.0
CA A:CYS91 4.0 35.0 1.0
N A:GLU106 4.0 29.1 1.0
N A:CYS97 4.1 25.7 1.0
C A:CYS105 4.1 30.1 1.0
CA A:CYS94 4.2 26.8 1.0
CA A:CYS97 4.4 25.8 1.0
C A:CYS91 4.4 35.6 1.0
N A:HIS93 4.4 34.2 1.0
N A:VAL107 4.5 34.6 1.0
C A:TYR90 4.6 29.2 1.0
C A:CYS94 4.8 31.4 1.0
CB A:VAL107 4.8 39.4 1.0
N A:CYS105 4.8 27.4 1.0
CA A:GLY92 4.9 28.7 1.0
CA A:TYR90 4.9 31.6 1.0
O A:CYS94 4.9 28.4 1.0
CG2 A:VAL107 4.9 36.1 1.0
C A:HIS93 5.0 31.7 1.0
CB A:TYR90 5.0 26.0 1.0

Cobalt binding site 2 out of 4 in 4jbh

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Cobalt binding site 2 out of 4 in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co403

b:38.0
occ:0.50
ZN B:ZN402 0.1 38.1 0.5
SG B:CYS91 2.3 28.5 1.0
SG B:CYS97 2.3 26.4 1.0
SG B:CYS105 2.3 27.8 1.0
SG B:CYS94 2.4 26.9 1.0
CB B:CYS105 3.3 29.2 1.0
CB B:CYS97 3.4 25.9 1.0
CB B:CYS91 3.4 29.8 1.0
N B:CYS91 3.4 27.3 1.0
CB B:CYS94 3.6 36.3 1.0
CA B:CYS105 3.7 28.8 1.0
N B:GLY92 3.8 30.6 1.0
CA B:CYS91 3.8 31.4 1.0
N B:CYS94 3.9 34.2 1.0
N B:GLU106 4.1 28.4 1.0
C B:CYS91 4.2 37.1 1.0
N B:CYS97 4.3 26.3 1.0
CA B:CYS94 4.3 33.2 1.0
C B:CYS105 4.3 32.1 1.0
N B:HIS93 4.3 32.2 1.0
CA B:CYS97 4.5 28.6 1.0
N B:VAL107 4.5 34.6 1.0
C B:TYR90 4.6 31.2 1.0
CB B:VAL107 4.7 33.3 1.0
CA B:GLY92 4.8 33.1 1.0
CA B:TYR90 4.8 32.2 1.0
CB B:TYR90 4.9 27.8 1.0
C B:CYS94 4.9 29.3 1.0
C B:HIS93 5.0 37.4 1.0
C B:GLY92 5.0 35.4 1.0
N B:CYS105 5.0 28.1 1.0
O B:CYS94 5.0 26.2 1.0

Cobalt binding site 3 out of 4 in 4jbh

Go back to Cobalt Binding Sites List in 4jbh
Cobalt binding site 3 out of 4 in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co403

b:40.8
occ:0.50
ZN C:ZN402 0.1 40.8 0.5
SG C:CYS105 2.2 27.1 1.0
SG C:CYS97 2.3 32.4 1.0
SG C:CYS91 2.4 31.4 1.0
SG C:CYS94 2.4 28.4 1.0
CB C:CYS105 3.2 30.3 1.0
CB C:CYS97 3.4 34.9 1.0
N C:CYS91 3.5 29.1 1.0
CB C:CYS91 3.5 30.2 1.0
CB C:CYS94 3.6 33.1 1.0
CA C:CYS105 3.6 32.6 1.0
N C:GLY92 3.8 39.6 1.0
CA C:CYS91 3.9 33.7 1.0
N C:CYS94 3.9 40.0 1.0
N C:GLU106 4.1 29.2 1.0
C C:CYS105 4.2 30.4 1.0
N C:CYS97 4.2 28.0 1.0
C C:CYS91 4.3 41.8 1.0
CA C:CYS94 4.3 28.4 1.0
N C:HIS93 4.3 31.9 1.0
CA C:CYS97 4.4 34.6 1.0
N C:VAL107 4.5 32.8 1.0
C C:TYR90 4.6 36.2 1.0
CB C:VAL107 4.7 39.8 1.0
CA C:GLY92 4.7 34.7 1.0
CA C:TYR90 4.8 29.2 1.0
CG2 C:VAL107 4.8 42.0 1.0
CB C:TYR90 4.8 25.4 1.0
N C:CYS105 4.9 29.9 1.0
C C:CYS94 4.9 32.6 1.0
O C:CYS94 4.9 30.1 1.0
C C:GLY92 4.9 36.0 1.0

Cobalt binding site 4 out of 4 in 4jbh

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Cobalt binding site 4 out of 4 in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co403

b:47.2
occ:0.50
ZN D:ZN402 0.1 47.2 0.5
SG D:CYS97 2.3 32.7 1.0
SG D:CYS94 2.3 30.7 1.0
SG D:CYS91 2.3 36.6 1.0
SG D:CYS105 2.4 29.9 1.0
CB D:CYS97 3.3 37.6 1.0
CB D:CYS105 3.4 33.1 1.0
CB D:CYS94 3.4 35.6 1.0
N D:CYS91 3.4 31.6 1.0
CB D:CYS91 3.5 32.0 1.0
CA D:CYS105 3.7 30.9 1.0
N D:GLY92 3.8 34.5 1.0
N D:CYS94 3.8 35.4 1.0
CA D:CYS91 3.9 35.5 1.0
N D:GLU106 4.1 35.4 1.0
CA D:CYS94 4.2 35.5 1.0
N D:CYS97 4.2 31.4 1.0
C D:CYS91 4.2 39.6 1.0
C D:CYS105 4.3 35.8 1.0
N D:HIS93 4.3 34.8 1.0
CA D:CYS97 4.4 34.8 1.0
N D:VAL107 4.6 38.4 1.0
C D:TYR90 4.6 33.6 1.0
CA D:GLY92 4.7 37.8 1.0
CB D:VAL107 4.8 41.9 1.0
C D:CYS94 4.8 34.6 1.0
CA D:TYR90 4.8 33.1 1.0
O D:CYS94 4.9 35.6 1.0
CB D:TYR90 4.9 30.7 1.0
C D:HIS93 4.9 40.8 1.0
C D:GLY92 5.0 37.0 1.0
N D:CYS105 5.0 29.9 1.0

Reference:

A.Vitale, N.Thorne, S.Lovell, K.P.Battaile, X.Hu, M.Shen, S.D'auria, D.S.Auld. Physicochemical Characterization of A Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum. Plos One V. 8 63828 2013.
ISSN: ESSN 1932-6203
PubMed: 23755111
DOI: 10.1371/JOURNAL.PONE.0063828
Page generated: Sun Dec 13 10:44:48 2020

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