Zinc in PDB 1d1s: Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase

All present enzymatic activity of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase:
1.1.1.1;

The structure of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase, PDB code: 1d1s was solved by P.T.Xie, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.400, 90.900, 121.100, 90.00, 99.60, 90.00
R / Rfree (%)	21.7 / 26.8

The structure of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase also contains other interesting chemical elements:

Arsenic

(As)

5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Zinc atom in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase (pdb code 1d1s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 19 binding sites of Zinc where determined in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase, PDB code: 1d1s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn375 b:42.2 occ:1.00 SG A:CYS103 2.1 37.8 1.0 SG A:CYS111 2.2 44.9 1.0 SG A:CYS100 2.4 44.5 1.0 SG A:CYS97 2.4 45.4 1.0 CB A:CYS111 3.1 43.2 1.0 CB A:CYS103 3.3 39.6 1.0 N A:CYS97 3.5 38.7 1.0 CB A:CYS97 3.5 41.5 1.0 CB A:CYS100 3.5 43.0 1.0 CA A:CYS111 3.6 42.0 1.0 N A:ILE112 3.7 43.3 1.0 N A:ARG98 3.9 42.1 1.0 CA A:CYS97 3.9 40.1 1.0 C A:CYS111 4.1 41.4 1.0 CG2 A:ILE112 4.3 43.0 1.0 N A:GLU99 4.3 41.9 1.0 C A:CYS97 4.3 40.2 1.0 N A:CYS100 4.3 44.1 1.0 C A:GLN96 4.3 37.8 1.0 CA A:CYS103 4.4 38.7 1.0 CA A:CYS100 4.5 43.6 1.0 N A:CYS103 4.5 38.5 1.0 C A:GLU99 4.5 45.3 1.0 CA A:GLN96 4.6 34.9 1.0 O A:GLU99 4.8 46.7 1.0 CA A:ARG98 4.8 41.7 1.0 N A:CYS111 4.8 41.0 1.0 CA A:ILE112 4.8 44.5 1.0 CB A:ILE112 4.9 43.6 1.0 N A:ARG113 5.0 44.9 1.0

Zinc binding site 2 out of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn376 b:33.8 occ:1.00 SG A:CYS174 2.0 28.2 1.0 NE2 A:HIS67 2.2 31.4 1.0 SG A:CYS46 2.4 29.3 1.0 O A:ACT501 2.6 45.3 1.0 CD2 A:HIS67 3.1 31.3 1.0 CE1 A:HIS67 3.2 28.2 1.0 CB A:CYS174 3.4 29.2 1.0 CB A:CYS46 3.4 33.1 1.0 C A:ACT501 3.5 45.0 1.0 CH3 A:ACT501 3.6 43.0 1.0 C5N A:NAD1377 3.8 20.6 1.0 CG A:HIS67 4.3 32.0 1.0 C6N A:NAD1377 4.3 21.5 1.0 C4N A:NAD1377 4.3 25.1 1.0 OG1 A:THR48 4.3 31.9 1.0 ND1 A:HIS67 4.3 29.8 1.0 CB A:THR48 4.3 31.4 1.0 OXT A:ACT501 4.6 46.6 1.0 CA A:CYS174 4.6 27.7 1.0 N A:GLY175 4.7 28.9 1.0 NH1 A:ARG369 4.8 31.4 1.0 CE1 A:PHE93 4.9 41.6 1.0 CA A:CYS46 4.9 33.6 1.0

Zinc binding site 3 out of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:40.3 occ:1.00 N7A A:NAD1377 2.0 22.2 1.0 OXT A:ACT504 2.1 20.4 1.0 NE2 A:HIS271 2.1 41.6 1.0 O A:HOH749 2.2 40.6 1.0 CD2 A:HIS271 3.0 38.6 1.0 C8A A:NAD1377 3.0 21.2 1.0 C5A A:NAD1377 3.1 24.4 1.0 C A:ACT504 3.2 20.5 1.0 CE1 A:HIS271 3.3 41.6 1.0 N6A A:NAD1377 3.4 30.0 1.0 C6A A:NAD1377 3.7 26.3 1.0 O A:ACT504 3.7 23.8 1.0 CG A:HIS271 4.2 37.5 1.0 N9A A:NAD1377 4.2 21.6 1.0 C4A A:NAD1377 4.2 22.1 1.0 ND1 A:HIS271 4.3 38.2 1.0 CG2 A:ILE269 4.5 18.0 1.0 CH3 A:ACT504 4.5 21.8 1.0 CD1 A:LEU224 4.9 20.7 1.0

Zinc binding site 4 out of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:40.0 occ:0.50 NE2 A:HIS138 2.0 48.5 1.0 OXT A:ACT502 2.1 47.7 0.5 O A:ACT513 2.3 52.2 0.5 OXT A:ACT513 2.4 53.1 0.5 O A:ACT502 2.5 46.8 0.5 C A:ACT513 2.6 53.7 0.5 C A:ACT502 2.6 47.9 0.5 CE1 A:HIS138 2.6 49.4 1.0 CD2 A:HIS138 3.2 48.7 1.0 ND1 A:HIS138 3.8 49.8 1.0 CG A:HIS138 4.1 47.8 1.0 CH3 A:ACT502 4.1 47.8 0.5 CH3 A:ACT513 4.1 55.0 0.5 CD A:LYS60 4.5 59.7 1.0

Zinc binding site 5 out of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:48.2 occ:1.00 OXT B:ACT507 1.7 30.9 1.0 N7A B:NAD2377 2.0 24.6 1.0 O B:HOH735 2.0 35.9 1.0 NE2 B:HIS271 2.1 39.4 1.0 C B:ACT507 2.9 28.4 1.0 C8A B:NAD2377 3.0 26.2 1.0 CD2 B:HIS271 3.0 36.5 1.0 N6A B:NAD2377 3.1 30.9 1.0 CE1 B:HIS271 3.1 39.0 1.0 C5A B:NAD2377 3.1 25.6 1.0 C6A B:NAD2377 3.6 27.9 1.0 O B:ACT507 3.6 31.5 1.0 CH3 B:ACT507 4.0 20.7 1.0 CG B:HIS271 4.2 38.3 1.0 ND1 B:HIS271 4.2 38.3 1.0 N9A B:NAD2377 4.2 25.2 1.0 C4A B:NAD2377 4.3 26.7 1.0 CG2 B:ILE269 4.4 26.0 1.0 N1A B:NAD2377 5.0 26.6 1.0 CD1 B:LEU224 5.0 40.3 1.0

Zinc binding site 6 out of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:37.8 occ:1.00 OE2 A:GLU360 1.8 24.8 1.0 OE2 A:GLU357 1.9 13.2 1.0 O A:HOH793 2.1 22.4 1.0 OE1 A:GLU357 2.4 20.5 1.0 CD A:GLU357 2.4 21.4 1.0 CD A:GLU360 3.0 36.1 1.0 OE1 A:GLU360 3.8 39.7 1.0 CG A:GLU357 3.9 24.2 1.0 O A:HOH727 3.9 46.9 1.0 CG A:GLU360 4.0 35.2 1.0 CD2 A:LEU361 4.0 19.6 1.0 CB A:GLU360 4.4 36.0 1.0 CG A:LEU361 4.6 26.4 1.0 CB A:GLU357 4.9 31.8 1.0

Zinc binding site 7 out of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn375 b:24.3 occ:1.00 SG B:CYS111 2.2 23.8 1.0 SG B:CYS97 2.2 25.7 1.0 SG B:CYS103 2.3 20.7 1.0 SG B:CYS100 2.4 25.0 1.0 CB B:CYS111 3.1 25.9 1.0 CB B:CYS103 3.3 22.7 1.0 CB B:CYS97 3.4 23.2 1.0 CB B:CYS100 3.5 16.8 1.0 N B:CYS97 3.5 16.1 1.0 CA B:CYS111 3.6 24.5 1.0 N B:CYS100 3.9 19.6 1.0 N B:ARG98 3.9 19.9 1.0 CA B:CYS97 4.0 17.2 1.0 N B:ILE112 4.1 22.5 1.0 CA B:CYS100 4.2 19.0 1.0 C B:CYS111 4.3 23.7 1.0 C B:CYS97 4.3 17.5 1.0 C B:GLN96 4.5 15.1 1.0 CA B:CYS103 4.5 24.2 1.0 CG1 B:ILE112 4.5 23.5 1.0 N B:GLU99 4.5 20.8 1.0 N B:CYS103 4.5 21.1 1.0 CA B:GLN96 4.6 13.6 1.0 CA B:ARG98 4.8 21.6 1.0 N B:CYS111 4.9 22.0 1.0 C B:CYS100 4.9 22.1 1.0 O B:CYS100 5.0 23.6 1.0

Zinc binding site 8 out of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn376 b:24.6 occ:1.00 SG B:CYS174 2.1 16.4 1.0 NE2 B:HIS67 2.2 10.4 1.0 SG B:CYS46 2.3 24.6 1.0 OXT B:ACT506 2.5 29.1 1.0 CE1 B:HIS67 3.0 7.4 1.0 CB B:CYS46 3.2 25.1 1.0 CD2 B:HIS67 3.3 12.2 1.0 C B:ACT506 3.3 27.5 1.0 CB B:CYS174 3.4 17.7 1.0 CH3 B:ACT506 3.5 17.7 1.0 C5N B:NAD2377 3.6 16.1 1.0 OG1 B:THR48 4.0 26.7 1.0 C6N B:NAD2377 4.1 15.2 1.0 ND1 B:HIS67 4.2 8.1 1.0 CB B:THR48 4.2 24.8 1.0 C4N B:NAD2377 4.3 16.9 1.0 CG B:HIS67 4.4 12.8 1.0 O B:ACT506 4.5 32.6 1.0 OE2 B:GLU68 4.6 31.0 1.0 NH2 B:ARG369 4.6 31.9 1.0 CA B:CYS46 4.7 21.4 1.0 N B:GLY175 4.7 22.9 1.0 CA B:CYS174 4.8 18.3 1.0

Zinc binding site 9 out of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:27.7 occ:1.00 O B:HOH725 1.8 10.4 1.0 NE2 B:HIS138 2.1 18.8 1.0 CE1 B:HIS138 2.9 17.0 1.0 CD2 B:HIS138 3.3 18.6 1.0 ND1 B:HIS138 4.1 18.3 1.0 CG B:HIS138 4.3 19.9 1.0 O B:HOH649 4.3 29.4 1.0 O B:PHE61 4.4 31.4 1.0 CD B:LYS60 4.7 38.1 1.0 CB B:LYS60 4.9 29.8 1.0

Zinc binding site 10 out of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:48.4 occ:1.00 OE1 D:GLU99 2.0 27.5 1.0 OD1 B:ASP341 2.4 41.8 1.0 O D:ACT509 2.5 16.5 1.0 OD2 B:ASP341 2.7 46.0 1.0 CD D:GLU99 2.8 29.3 1.0 OXT D:ACT509 2.8 13.7 1.0 CG B:ASP341 2.8 42.8 1.0 OE2 D:GLU99 2.9 31.3 1.0 O D:ACT508 2.9 23.4 1.0 OXT D:ACT508 2.9 22.4 1.0 C D:ACT509 3.0 14.1 1.0 C D:ACT508 3.2 21.3 1.0 CB B:ASP341 4.2 40.2 1.0 CG D:GLU99 4.2 25.4 1.0 O B:HOH842 4.3 29.3 1.0 CH3 D:ACT509 4.4 13.2 1.0 CB B:ASP343 4.6 28.3 1.0 CG B:GLN344 4.6 46.3 1.0 CH3 D:ACT508 4.7 18.3 1.0 CB D:GLU99 4.8 29.1 1.0

P.T.Xie, T.D.Hurley. Methionine-141 Directly Influences the Binding of 4-Methylpyrazole in Human Sigma Sigma Alcohol Dehydrogenase. Protein Sci. V. 8 2639 1999.
ISSN: ISSN 0961-8368
PubMed: 10631979