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Zinc in PDB 1rjw: Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R

Enzymatic activity of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R

All present enzymatic activity of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R:
1.1.1.1;

Protein crystallography data

The structure of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R, PDB code: 1rjw was solved by C.Ceccarelli, B.J.Bahnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.44 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.322, 138.222, 158.680, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.2

Other elements in 1rjw:

The structure of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R also contains other interesting chemical elements:

Fluorine (F) 39 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R (pdb code 1rjw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R, PDB code: 1rjw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1rjw

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Zinc binding site 1 out of 8 in the Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:29.8
occ:1.00
 SG A:CYS92 2.3 27.1 1.0
SG A:CYS95 2.3 26.6 1.0
SG A:CYS106 2.3 31.4 1.0
SG A:CYS98 2.4 36.0 1.0
CB A:CYS106 3.2 32.8 1.0
CB A:CYS95 3.4 28.9 1.0
CB A:CYS98 3.5 35.3 1.0
CB A:CYS92 3.5 29.7 1.0
N A:CYS92 3.6 29.1 1.0
N A:GLY93 3.7 32.4 1.0
N A:CYS95 3.8 31.9 1.0
CA A:CYS92 3.9 29.8 1.0
O A:HOH1032 4.0 25.3 1.0
CA A:CYS106 4.1 31.6 1.0
CA A:CYS95 4.2 29.7 1.0
C A:CYS92 4.2 31.6 1.0
N A:HIS94 4.3 34.5 1.0
N A:CYS98 4.4 34.6 1.0
CA A:CYS98 4.5 36.4 1.0
ND1 A:HIS108 4.6 43.3 1.0
CB A:ALA91 4.6 26.4 1.0
CA A:GLY93 4.7 33.5 1.0
C A:ALA91 4.7 29.5 1.0
C A:CYS95 4.9 29.7 1.0
C A:CYS106 4.9 32.9 1.0
O A:CYS95 4.9 29.0 1.0
C A:HIS94 5.0 32.9 1.0
C A:GLY93 5.0 34.9 1.0

Zinc binding site 2 out of 8 in 1rjw

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Zinc binding site 2 out of 8 in the Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:56.2
occ:1.00
 NE2 A:HIS61 2.1 30.1 1.0
O A:ETF501 2.2 75.7 1.0
SG A:CYS38 2.2 39.7 1.0
SG A:CYS148 2.4 35.0 1.0
C2 A:ETF501 3.0 76.0 1.0
CE1 A:HIS61 3.0 30.3 1.0
CD2 A:HIS61 3.1 27.6 1.0
CB A:CYS38 3.3 35.8 1.0
OG1 A:THR40 3.5 35.1 1.0
CB A:CYS148 3.6 28.7 1.0
CB A:THR40 3.9 34.5 1.0
ND1 A:HIS61 4.1 30.4 1.0
CG A:HIS61 4.2 29.9 1.0
C1 A:ETF501 4.4 77.1 1.0
CA A:CYS38 4.7 36.3 1.0
F2 A:ETF501 4.7 77.9 1.0
CG2 A:THR40 4.7 32.4 1.0
N A:THR40 4.9 36.5 1.0

Zinc binding site 3 out of 8 in 1rjw

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Zinc binding site 3 out of 8 in the Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:22.3
occ:1.00
 SG B:CYS92 2.2 27.9 1.0
SG B:CYS98 2.2 27.9 1.0
SG B:CYS106 2.4 27.3 1.0
SG B:CYS95 2.4 23.1 1.0
CB B:CYS106 3.1 27.8 1.0
CB B:CYS95 3.3 25.9 1.0
CB B:CYS98 3.4 32.9 1.0
CB B:CYS92 3.4 29.9 1.0
N B:CYS92 3.6 28.0 1.0
N B:GLY93 3.7 31.4 1.0
N B:CYS95 3.8 28.8 1.0
CA B:CYS92 3.9 29.4 1.0
CA B:CYS106 4.0 29.5 1.0
CA B:CYS95 4.2 27.5 1.0
N B:CYS98 4.2 31.7 1.0
N B:HIS94 4.2 31.6 1.0
C B:CYS92 4.2 30.7 1.0
CA B:CYS98 4.4 33.7 1.0
CA B:GLY93 4.6 31.4 1.0
CB B:ALA91 4.6 23.6 1.0
C B:ALA91 4.7 26.7 1.0
C B:CYS95 4.8 28.5 1.0
C B:CYS106 4.9 30.3 1.0
O B:CYS95 4.9 26.9 1.0
C B:GLY93 4.9 32.3 1.0
C B:HIS94 5.0 31.5 1.0

Zinc binding site 4 out of 8 in 1rjw

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Zinc binding site 4 out of 8 in the Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:29.4
occ:1.00
 NE2 B:HIS61 2.0 23.3 1.0
O B:ETF501 2.2 53.8 1.0
SG B:CYS38 2.3 29.2 1.0
SG B:CYS148 2.4 28.0 1.0
CE1 B:HIS61 2.9 21.3 1.0
CD2 B:HIS61 3.1 21.2 1.0
C2 B:ETF501 3.2 56.9 1.0
CB B:CYS38 3.3 27.2 1.0
CB B:CYS148 3.4 27.7 1.0
OG1 B:THR40 3.9 30.5 1.0
ND1 B:HIS61 4.0 20.3 1.0
CB B:THR40 4.1 30.8 1.0
CG B:HIS61 4.2 23.6 1.0
C1 B:ETF501 4.6 58.6 1.0
F2 B:ETF501 4.7 61.2 1.0
CA B:CYS38 4.7 27.8 1.0
CA B:CYS148 4.8 26.1 1.0
CG2 B:THR40 5.0 29.5 1.0

Zinc binding site 5 out of 8 in 1rjw

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Zinc binding site 5 out of 8 in the Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:25.6
occ:1.00
 SG C:CYS98 2.2 24.9 1.0
SG C:CYS92 2.2 30.4 1.0
SG C:CYS95 2.4 26.5 1.0
SG C:CYS106 2.4 25.5 1.0
CB C:CYS106 3.2 26.3 1.0
CB C:CYS98 3.4 32.6 1.0
CB C:CYS95 3.4 28.4 1.0
CB C:CYS92 3.4 29.4 1.0
N C:CYS92 3.5 29.1 1.0
N C:GLY93 3.6 32.8 1.0
N C:CYS95 3.8 30.9 1.0
CA C:CYS92 3.8 31.1 1.0
O C:HOH1011 4.1 20.7 1.0
CA C:CYS106 4.1 29.3 1.0
C C:CYS92 4.2 32.3 1.0
CA C:CYS95 4.2 30.5 1.0
N C:CYS98 4.3 33.3 1.0
N C:HIS94 4.3 34.5 1.0
CA C:CYS98 4.4 33.3 1.0
CB C:ALA91 4.6 25.3 1.0
C C:ALA91 4.6 29.7 1.0
CA C:GLY93 4.6 33.3 1.0
C C:CYS95 4.8 30.6 1.0
O C:CYS95 4.8 30.5 1.0
C C:HIS94 5.0 32.9 1.0
C C:GLY93 5.0 35.4 1.0
C C:CYS106 5.0 30.8 1.0

Zinc binding site 6 out of 8 in 1rjw

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Zinc binding site 6 out of 8 in the Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:57.0
occ:1.00
 NE2 C:HIS61 2.0 33.6 1.0
O C:ETF501 2.1 62.4 1.0
SG C:CYS148 2.1 40.1 1.0
SG C:CYS38 2.5 38.7 1.0
CD2 C:HIS61 2.9 29.9 1.0
CE1 C:HIS61 3.0 29.6 1.0
C2 C:ETF501 3.3 64.6 1.0
CB C:CYS38 3.4 31.6 1.0
CB C:CYS148 3.5 29.9 1.0
ND1 C:HIS61 4.0 29.7 1.0
CG C:HIS61 4.0 29.4 1.0
OG1 C:THR40 4.0 32.4 1.0
CB C:THR40 4.2 32.5 1.0
C1 C:ETF501 4.5 65.7 1.0
F2 C:ETF501 4.6 67.3 1.0
CA C:CYS148 4.7 29.0 1.0
CA C:CYS38 4.9 32.7 1.0

Zinc binding site 7 out of 8 in 1rjw

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Zinc binding site 7 out of 8 in the Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:21.2
occ:1.00
 SG D:CYS95 2.2 24.5 1.0
SG D:CYS98 2.3 30.9 1.0
SG D:CYS106 2.3 24.6 1.0
SG D:CYS92 2.3 25.7 1.0
CB D:CYS106 3.2 22.5 1.0
CB D:CYS98 3.4 33.0 1.0
CB D:CYS95 3.4 27.8 1.0
CB D:CYS92 3.5 26.6 1.0
N D:CYS92 3.6 29.5 1.0
N D:GLY93 3.6 30.9 1.0
N D:CYS95 3.8 29.5 1.0
CA D:CYS92 3.9 28.6 1.0
O D:HOH1009 3.9 20.3 1.0
N D:HIS94 4.1 31.8 1.0
CA D:CYS106 4.1 25.9 1.0
C D:CYS92 4.2 31.0 1.0
CA D:CYS95 4.2 27.9 1.0
N D:CYS98 4.3 31.9 1.0
CA D:CYS98 4.4 33.8 1.0
CB D:ALA91 4.5 25.3 1.0
CA D:GLY93 4.5 31.1 1.0
C D:ALA91 4.6 28.8 1.0
ND1 D:HIS108 4.8 35.9 1.0
C D:GLY93 4.8 32.6 1.0
C D:HIS94 4.9 31.4 1.0
C D:CYS95 4.9 28.1 1.0
CA D:ALA91 5.0 26.7 1.0
O D:CYS95 5.0 27.3 1.0

Zinc binding site 8 out of 8 in 1rjw

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Zinc binding site 8 out of 8 in the Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Nad(+)-Dependent Alcohol Dehydrogenase From Bacillus Stearothermophilus Strain Lld-R within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:38.2
occ:1.00
 O D:ETF501 2.0 55.2 1.0
NE2 D:HIS61 2.0 22.9 1.0
SG D:CYS148 2.2 34.2 1.0
SG D:CYS38 2.3 33.6 1.0
CD2 D:HIS61 3.0 21.7 1.0
CE1 D:HIS61 3.0 23.7 1.0
C2 D:ETF501 3.2 57.0 1.0
CB D:CYS38 3.3 31.7 1.0
CB D:CYS148 3.4 29.9 1.0
OG1 D:THR40 3.9 32.1 1.0
ND1 D:HIS61 4.1 21.5 1.0
CB D:THR40 4.1 32.4 1.0
CG D:HIS61 4.1 24.0 1.0
C1 D:ETF501 4.4 58.0 1.0
F2 D:ETF501 4.4 57.4 1.0
CA D:CYS38 4.8 31.6 1.0
CA D:CYS148 4.8 28.1 1.0
CG2 D:THR40 5.0 33.5 1.0

Reference:

C.Ceccarelli, Z.X.Liang, M.Strickler, G.Prehna, B.M.Goldstein, J.P.Klinman, B.J.Bahnson. Crystal Structure and Amide H/D Exchange of Binary Complexes of Alcohol Dehydrogenase From Bacillus Stearothermophilus: Insight Into Thermostability and Cofactor Binding Biochemistry V. 43 5266 2004.
ISSN: ISSN 0006-2960
PubMed: 15122892
DOI: 10.1021/BI049736P
Page generated: Wed Oct 16 18:35:54 2024

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