Zinc in PDB 6iqd: Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus

All present enzymatic activity of Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus:
1.1.1.1;

The structure of Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus, PDB code: 6iqd was solved by S.Xue, Y.Feng, X.Guo, Z.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.80 / 2.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.442, 149.186, 269.277, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 29.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus (pdb code 6iqd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus, PDB code: 6iqd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus


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 Alcohol Dehydrogenase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:32.8 occ:1.00 SG A:CYS92 2.3 31.6 1.0 SG A:CYS98 2.3 48.0 1.0 SG A:CYS106 2.3 34.6 1.0 SG A:CYS95 2.4 34.4 1.0 CB A:CYS106 3.1 37.1 1.0 CB A:CYS95 3.2 35.4 1.0 CB A:CYS98 3.4 34.8 1.0 CB A:CYS92 3.5 33.4 1.0 N A:CYS92 3.7 40.2 1.0 N A:CYS95 3.7 33.0 1.0 CA A:CYS106 3.8 38.6 1.0 N A:GLY93 3.9 38.0 1.0 CA A:CYS92 4.0 34.4 1.0 CA A:CYS95 4.0 37.8 1.0 N A:CYS98 4.1 37.5 1.0 CA A:CYS98 4.3 34.5 1.0 C A:CYS92 4.3 35.9 1.0 N A:GLU94 4.4 39.6 1.0 CD A:PRO107 4.5 32.4 1.0 ND1 A:HIS108 4.6 46.0 1.0 C A:CYS106 4.7 39.7 1.0 CB A:ALA91 4.7 33.6 1.0 C A:CYS95 4.7 34.6 1.0 CA A:GLY93 4.8 34.4 1.0 C A:ALA91 4.8 41.2 1.0 N A:PRO107 4.9 38.9 1.0 C A:GLU94 4.9 37.9 1.0 N A:CYS106 5.0 40.4 1.0 O A:CYS95 5.0 30.9 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus


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 Alcohol Dehydrogenase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:50.5 occ:1.00 NE2 A:HIS61 2.1 29.8 1.0 OE1 A:GLU62 2.1 48.3 1.0 SG A:CYS38 2.3 44.9 1.0 SG A:CYS148 2.4 40.5 1.0 CD A:GLU62 2.9 40.4 1.0 CB A:CYS148 3.0 25.7 1.0 CD2 A:HIS61 3.0 34.6 1.0 NH2 A:ARG331 3.0 41.6 1.0 CE1 A:HIS61 3.1 39.6 1.0 CB A:CYS38 3.2 36.1 1.0 CG A:GLU62 3.6 39.2 1.0 OE2 A:GLU62 3.7 53.2 1.0 CZ A:ARG331 4.1 41.1 1.0 CG A:HIS61 4.1 38.5 1.0 ND1 A:HIS61 4.1 42.6 1.0 CA A:CYS38 4.4 39.0 1.0 N A:CYS38 4.4 38.4 1.0 NH1 A:ARG331 4.4 36.4 1.0 CA A:CYS148 4.4 27.4 1.0 OG1 A:THR40 4.9 36.4 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus


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 Alcohol Dehydrogenase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:32.0 occ:1.00 SG B:CYS106 2.3 44.4 1.0 SG B:CYS92 2.4 29.1 1.0 SG B:CYS98 2.4 31.4 1.0 SG B:CYS95 2.5 39.8 1.0 CB B:CYS106 3.0 35.3 1.0 CB B:CYS95 3.2 32.1 1.0 CB B:CYS92 3.4 29.3 1.0 CB B:CYS98 3.5 31.9 1.0 N B:CYS92 3.6 30.1 1.0 N B:CYS95 3.8 32.9 1.0 CA B:CYS106 3.8 37.0 1.0 N B:GLY93 3.9 32.0 1.0 CA B:CYS92 4.0 34.0 1.0 CA B:CYS95 4.1 31.2 1.0 N B:CYS98 4.2 42.4 1.0 C B:CYS92 4.3 34.8 1.0 CA B:CYS98 4.5 35.8 1.0 CD B:PRO107 4.5 33.4 1.0 N B:GLU94 4.5 36.5 1.0 C B:CYS106 4.6 36.3 1.0 ND1 B:HIS108 4.7 45.9 1.0 CB B:ALA91 4.8 34.2 1.0 C B:ALA91 4.8 35.3 1.0 C B:CYS95 4.8 33.6 1.0 CA B:GLY93 4.9 28.2 1.0 N B:PRO107 4.9 38.5 1.0 C B:GLU94 4.9 34.9 1.0 N B:CYS106 5.0 35.7 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus


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 Alcohol Dehydrogenase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:57.9 occ:1.00 NE2 B:HIS61 2.1 39.7 1.0 OE1 B:GLU62 2.2 41.4 1.0 SG B:CYS38 2.3 40.6 1.0 SG B:CYS148 2.5 49.6 1.0 CD2 B:HIS61 2.9 35.2 1.0 CB B:CYS148 3.0 37.8 1.0 CE1 B:HIS61 3.1 39.1 1.0 CB B:CYS38 3.2 49.7 1.0 CD B:GLU62 3.2 42.9 1.0 CG B:GLU62 3.6 41.9 1.0 CG B:HIS61 4.1 37.9 1.0 NH1 B:ARG331 4.1 44.1 1.0 ND1 B:HIS61 4.2 36.6 1.0 OE2 B:GLU62 4.3 53.2 1.0 CA B:CYS38 4.4 50.5 1.0 CA B:CYS148 4.5 34.9 1.0 N B:CYS38 4.5 44.8 1.0 OG1 B:THR40 4.8 50.1 1.0 CB B:THR40 4.9 35.8 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus


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 Alcohol Dehydrogenase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn400 b:53.4 occ:1.00 SG C:CYS106 2.3 55.4 1.0 SG C:CYS95 2.3 56.6 1.0 SG C:CYS92 2.4 56.6 1.0 SG C:CYS98 2.6 64.9 1.0 CB C:CYS106 3.1 61.2 1.0 CB C:CYS95 3.3 53.9 1.0 CB C:CYS98 3.4 53.1 1.0 CB C:CYS92 3.5 51.8 1.0 N C:CYS92 3.6 53.0 1.0 N C:GLY93 3.8 52.3 1.0 N C:CYS95 3.9 62.0 1.0 CA C:CYS106 3.9 61.7 1.0 CA C:CYS92 4.0 57.4 1.0 CA C:CYS95 4.1 57.6 1.0 N C:CYS98 4.2 59.3 1.0 C C:CYS92 4.3 58.6 1.0 CA C:CYS98 4.4 56.3 1.0 N C:GLU94 4.5 62.7 1.0 CB C:ALA91 4.5 52.4 1.0 CD C:PRO107 4.6 51.0 1.0 ND1 C:HIS108 4.7 63.2 1.0 C C:ALA91 4.7 61.1 1.0 C C:CYS106 4.7 58.7 1.0 CA C:GLY93 4.8 52.2 1.0 C C:CYS95 4.9 59.4 1.0 N C:PRO107 5.0 55.9 1.0 CA C:ALA91 5.0 56.9 1.0 N C:CYS106 5.0 58.4 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus


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 Alcohol Dehydrogenase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:70.2 occ:1.00 OE2 C:GLU62 2.1 64.5 1.0 CE1 C:HIS61 2.2 66.5 1.0 SG C:CYS38 2.3 50.4 1.0 SG C:CYS148 2.5 67.3 1.0 CB C:CYS148 2.7 42.0 1.0 CD C:GLU62 3.1 55.0 1.0 NE2 C:HIS61 3.1 64.8 1.0 ND1 C:HIS61 3.2 69.5 1.0 CB C:CYS38 3.2 61.3 1.0 CG C:GLU62 3.5 52.2 1.0 OG1 C:THR40 4.0 72.2 1.0 OE1 C:GLU62 4.1 47.1 1.0 CD2 C:HIS61 4.3 58.6 1.0 CA C:CYS148 4.3 42.7 1.0 CG C:HIS61 4.3 59.8 1.0 N C:CYS38 4.4 69.5 1.0 CA C:CYS38 4.4 67.1 1.0 N C:ALA149 5.0 47.1 1.0 C C:CYS148 5.0 44.6 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus


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 Alcohol Dehydrogenase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn400 b:45.0 occ:1.00 SG D:CYS106 2.3 40.2 1.0 SG D:CYS95 2.4 38.8 1.0 SG D:CYS98 2.5 43.8 1.0 SG D:CYS92 2.6 45.3 1.0 CB D:CYS106 3.2 49.9 1.0 CB D:CYS98 3.3 34.8 1.0 CB D:CYS95 3.4 42.8 1.0 CB D:CYS92 3.6 42.8 1.0 N D:CYS95 3.7 45.9 1.0 N D:CYS92 3.8 46.4 1.0 N D:GLY93 3.8 45.3 1.0 CA D:CYS106 3.9 47.1 1.0 N D:CYS98 4.1 45.1 1.0 CA D:CYS92 4.1 45.4 1.0 CA D:CYS95 4.1 45.6 1.0 CA D:CYS98 4.3 41.6 1.0 N D:GLU94 4.3 50.0 1.0 C D:CYS92 4.4 47.4 1.0 CB D:ALA91 4.7 46.0 1.0 CD D:PRO107 4.7 43.4 1.0 CA D:GLY93 4.7 45.9 1.0 ND1 D:HIS108 4.8 52.3 1.0 C D:CYS95 4.8 44.1 1.0 C D:CYS106 4.8 49.8 1.0 C D:ALA91 4.8 48.1 1.0 C D:GLU94 4.9 49.9 1.0 C D:GLY93 5.0 48.1 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus


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 Alcohol Dehydrogenase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:55.3 occ:1.00 NE2 D:HIS61 2.1 64.1 1.0 SG D:CYS38 2.3 59.3 1.0 OE1 D:GLU62 2.4 62.0 1.0 SG D:CYS148 2.5 68.9 1.0 CB D:CYS148 3.0 41.3 1.0 CE1 D:HIS61 3.1 62.1 1.0 CD2 D:HIS61 3.1 58.3 1.0 CB D:CYS38 3.1 61.9 1.0 NH2 D:ARG331 3.2 64.5 1.0 CD D:GLU62 3.3 57.9 1.0 CG D:GLU62 3.8 55.5 1.0 ND1 D:HIS61 4.1 54.4 1.0 CZ D:ARG331 4.1 58.8 1.0 CG D:HIS61 4.2 54.8 1.0 OE2 D:GLU62 4.3 53.7 1.0 CA D:CYS38 4.3 63.4 1.0 NH1 D:ARG331 4.4 60.0 1.0 N D:CYS38 4.4 58.5 1.0 CA D:CYS148 4.5 48.7 1.0 CB D:THR40 4.8 51.7 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn400 b:58.0 occ:1.00 SG E:CYS106 2.4 57.5 1.0 SG E:CYS98 2.4 57.3 1.0 SG E:CYS92 2.4 51.4 1.0 SG E:CYS95 2.4 52.0 1.0 CB E:CYS95 3.0 52.2 1.0 CB E:CYS106 3.1 45.5 1.0 CB E:CYS98 3.4 52.3 1.0 CB E:CYS92 3.4 48.5 1.0 N E:CYS92 3.8 51.2 1.0 CA E:CYS106 3.8 53.8 1.0 N E:CYS95 3.8 43.0 1.0 N E:GLY93 3.9 55.1 1.0 CA E:CYS95 4.0 49.6 1.0 CA E:CYS92 4.1 51.4 1.0 N E:CYS98 4.2 51.3 1.0 CA E:CYS98 4.3 50.3 1.0 CD E:PRO107 4.4 57.9 1.0 C E:CYS92 4.5 54.8 1.0 N E:GLU94 4.6 63.9 1.0 ND1 E:HIS108 4.6 78.9 1.0 C E:CYS106 4.6 60.1 1.0 CB E:ALA91 4.7 54.1 1.0 C E:CYS95 4.8 53.1 1.0 C E:ALA91 4.8 50.7 1.0 N E:PRO107 4.9 62.4 1.0 N E:CYS106 4.9 54.0 1.0 CA E:GLY93 4.9 54.5 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Alcohol Dehydrogenase From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:62.2 occ:1.00 OE2 E:GLU62 2.1 73.2 1.0 NE2 E:HIS61 2.2 53.0 1.0 SG E:CYS38 2.3 55.0 1.0 SG E:CYS148 2.4 80.9 1.0 CB E:CYS148 2.8 47.6 1.0 CD2 E:HIS61 3.1 52.6 1.0 CD E:GLU62 3.2 68.9 1.0 CE1 E:HIS61 3.2 59.6 1.0 NH2 E:ARG331 3.3 50.2 1.0 CB E:CYS38 3.3 54.7 1.0 CG E:GLU62 3.7 54.0 1.0 NH1 E:ARG331 3.9 49.9 1.0 CZ E:ARG331 4.0 56.2 1.0 CG E:HIS61 4.2 49.2 1.0 OE1 E:GLU62 4.2 98.7 1.0 ND1 E:HIS61 4.3 59.4 1.0 CA E:CYS148 4.3 39.9 1.0 CA E:CYS38 4.6 62.5 1.0 N E:CYS38 4.6 54.5 1.0 CB E:THR40 4.9 59.4 1.0 OG1 E:THR40 5.0 57.4 1.0 C E:CYS148 5.0 37.1 1.0

X.Guo, Y.Feng, X.Wang, Y.Liu, W.Liu, Q.Li, J.Wang, S.Xue, Z.K.Zhao. Characterization of the Substrate Scope of An Alcohol Dehydrogenase Commonly Used As Methanol Dehydrogenase. Bioorg.Med.Chem.Lett. V. 29 1446 2019.
ISSN: ESSN 1464-3405
PubMed: 31006524
DOI: 10.1016/J.BMCL.2019.04.025