Atomistry » Zinc » PDB 3blo-3c37 » 3bto
Atomistry »
  Zinc »
    PDB 3blo-3c37 »
      3bto »

Zinc in PDB 3bto: Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide

Enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide, PDB code: 3bto was solved by S.Ramaswamy, B.V.Plapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.930, 180.200, 86.800, 90.00, 106.00, 90.00
R / Rfree (%) 18.5 / 22.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide (pdb code 3bto). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide, PDB code: 3bto:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3bto

Go back to Zinc Binding Sites List in 3bto
Zinc binding site 1 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:10.7
occ:1.00
 SG A:CYS46 2.1 10.0 1.0
NE2 A:HIS67 2.1 3.8 1.0
O6 A:SSB378 2.2 6.0 1.0
SG A:CYS174 2.3 9.0 1.0
CD2 A:HIS67 3.0 5.3 1.0
S1 A:SSB378 3.1 11.8 1.0
CE1 A:HIS67 3.2 7.8 1.0
CB A:CYS46 3.2 8.4 1.0
CB A:CYS174 3.3 6.4 1.0
C5N A:NAD377 3.4 7.0 1.0
C6N A:NAD377 4.0 5.3 1.0
OG A:SER48 4.0 8.8 1.0
C4N A:NAD377 4.0 4.7 1.0
C5 A:SSB378 4.1 12.1 1.0
CB A:SER48 4.2 6.1 1.0
CG A:HIS67 4.2 6.2 1.0
ND1 A:HIS67 4.2 5.6 1.0
NH2 A:ARG369 4.5 11.2 1.0
OE2 A:GLU68 4.6 12.7 1.0
CA A:CYS46 4.6 7.8 1.0
C2 A:SSB378 4.6 13.2 1.0
CA A:CYS174 4.7 6.8 1.0
N A:SER48 4.9 7.3 1.0
N A:GLY175 4.9 7.2 1.0
CE2 A:PHE93 4.9 9.2 1.0

Zinc binding site 2 out of 8 in 3bto

Go back to Zinc Binding Sites List in 3bto
Zinc binding site 2 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:9.6
occ:1.00
 SG A:CYS103 2.3 10.4 1.0
SG A:CYS100 2.3 8.7 1.0
SG A:CYS111 2.3 8.7 1.0
SG A:CYS97 2.3 10.9 1.0
CB A:CYS103 3.3 12.1 1.0
CB A:CYS111 3.3 7.3 1.0
CB A:CYS100 3.4 12.1 1.0
CB A:CYS97 3.5 10.2 1.0
N A:CYS97 3.6 9.4 1.0
CA A:CYS111 3.7 9.0 1.0
N A:CYS100 3.9 13.3 1.0
N A:LEU112 3.9 8.5 1.0
CA A:CYS97 3.9 9.1 1.0
N A:GLY98 3.9 12.1 1.0
CA A:CYS100 4.2 13.2 1.0
N A:CYS103 4.2 11.4 1.0
C A:CYS111 4.2 8.0 1.0
C A:CYS97 4.3 12.8 1.0
CA A:CYS103 4.3 11.3 1.0
N A:LYS99 4.5 15.3 1.0
C A:GLN96 4.7 10.4 1.0
N A:LYS113 4.7 10.1 1.0
O A:HOH595 4.8 23.7 1.0
CG A:LYS113 4.8 13.3 1.0
O A:CYS100 4.9 12.8 1.0
C A:CYS100 4.9 13.7 1.0
CA A:GLY98 4.9 13.2 1.0
CA A:GLN96 5.0 8.3 1.0

Zinc binding site 3 out of 8 in 3bto

Go back to Zinc Binding Sites List in 3bto
Zinc binding site 3 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:10.0
occ:1.00
 SG B:CYS46 2.1 11.2 1.0
NE2 B:HIS67 2.1 4.0 1.0
O6 B:SSB378 2.2 6.3 1.0
SG B:CYS174 2.3 8.4 1.0
CD2 B:HIS67 3.0 3.6 1.0
S1 B:SSB378 3.1 9.4 1.0
CE1 B:HIS67 3.1 7.8 1.0
CB B:CYS46 3.2 8.6 1.0
CB B:CYS174 3.4 7.4 1.0
C5N B:NAD377 3.4 6.1 1.0
OG B:SER48 4.0 6.8 1.0
C4N B:NAD377 4.0 5.7 1.0
C6N B:NAD377 4.0 6.2 1.0
CB B:SER48 4.1 5.1 1.0
C5 B:SSB378 4.2 11.6 1.0
ND1 B:HIS67 4.2 4.6 1.0
CG B:HIS67 4.2 5.2 1.0
NH2 B:ARG369 4.5 8.1 1.0
OE2 B:GLU68 4.6 10.6 1.0
C2 B:SSB378 4.6 10.4 1.0
CA B:CYS46 4.7 8.1 1.0
CA B:CYS174 4.7 7.7 1.0
N B:SER48 4.9 6.2 1.0
N B:GLY175 4.9 6.0 1.0
CE2 B:PHE93 4.9 7.6 1.0
C B:CYS174 5.0 7.0 1.0

Zinc binding site 4 out of 8 in 3bto

Go back to Zinc Binding Sites List in 3bto
Zinc binding site 4 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:11.3
occ:1.00
 SG B:CYS111 2.3 10.2 1.0
SG B:CYS103 2.3 11.2 1.0
SG B:CYS100 2.3 10.9 1.0
SG B:CYS97 2.4 13.5 1.0
CB B:CYS111 3.3 9.3 1.0
CB B:CYS103 3.4 10.8 1.0
CB B:CYS100 3.4 14.2 1.0
CB B:CYS97 3.5 12.4 1.0
N B:CYS97 3.6 10.5 1.0
CA B:CYS111 3.7 10.0 1.0
N B:CYS100 3.9 17.4 1.0
CA B:CYS97 3.9 11.2 1.0
N B:LEU112 4.0 9.7 1.0
N B:GLY98 4.0 14.0 1.0
N B:CYS103 4.2 11.6 1.0
CA B:CYS100 4.2 15.3 1.0
C B:CYS111 4.3 8.9 1.0
C B:CYS97 4.3 15.3 1.0
CA B:CYS103 4.3 11.4 1.0
N B:LYS99 4.5 16.3 1.0
C B:GLN96 4.6 11.5 1.0
O B:HOH607 4.8 32.4 1.0
N B:LYS113 4.8 9.7 1.0
C B:CYS100 4.9 15.8 1.0
CG B:LYS113 4.9 16.4 1.0
O B:CYS100 4.9 14.6 1.0
CA B:GLN96 4.9 9.5 1.0
CA B:GLY98 5.0 14.2 1.0

Zinc binding site 5 out of 8 in 3bto

Go back to Zinc Binding Sites List in 3bto
Zinc binding site 5 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn375

b:12.3
occ:1.00
 NE2 C:HIS67 2.1 9.4 1.0
SG C:CYS46 2.2 10.4 1.0
O6 C:SSB378 2.2 12.4 1.0
SG C:CYS174 2.3 12.7 1.0
CD2 C:HIS67 3.0 7.6 1.0
S1 C:SSB378 3.1 14.1 1.0
CE1 C:HIS67 3.1 9.2 1.0
CB C:CYS46 3.2 10.1 1.0
CB C:CYS174 3.4 10.1 1.0
C5N C:NAD377 3.4 10.4 1.0
OG C:SER48 4.0 10.1 1.0
C4N C:NAD377 4.1 7.9 1.0
C6N C:NAD377 4.1 8.6 1.0
C5 C:SSB378 4.1 14.4 1.0
CG C:HIS67 4.2 10.3 1.0
ND1 C:HIS67 4.3 7.5 1.0
CB C:SER48 4.3 9.7 1.0
NH2 C:ARG369 4.5 12.2 1.0
C2 C:SSB378 4.6 15.3 1.0
OE2 C:GLU68 4.7 13.1 1.0
CA C:CYS46 4.7 10.0 1.0
CA C:CYS174 4.7 9.5 1.0
N C:SER48 4.9 6.7 1.0
CE2 C:PHE93 4.9 10.4 1.0
N C:GLY175 5.0 8.8 1.0

Zinc binding site 6 out of 8 in 3bto

Go back to Zinc Binding Sites List in 3bto
Zinc binding site 6 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn376

b:10.2
occ:1.00
 SG C:CYS103 2.1 12.0 1.0
SG C:CYS100 2.3 10.7 1.0
SG C:CYS111 2.3 8.3 1.0
SG C:CYS97 2.4 10.7 1.0
CB C:CYS103 3.3 11.8 1.0
CB C:CYS100 3.3 11.2 1.0
CB C:CYS111 3.4 9.5 1.0
CB C:CYS97 3.6 8.7 1.0
N C:CYS97 3.6 8.3 1.0
CA C:CYS111 3.7 8.2 1.0
N C:CYS100 3.9 13.0 1.0
CA C:CYS97 3.9 7.0 1.0
N C:LEU112 4.0 8.0 1.0
N C:GLY98 4.0 12.9 1.0
CA C:CYS100 4.2 11.4 1.0
N C:CYS103 4.2 9.1 1.0
C C:CYS111 4.2 7.5 1.0
CA C:CYS103 4.3 9.8 1.0
C C:CYS97 4.3 12.1 1.0
N C:LYS99 4.5 13.4 1.0
C C:GLN96 4.6 7.2 1.0
N C:LYS113 4.9 10.3 1.0
O C:CYS100 4.9 10.2 1.0
CA C:GLN96 4.9 7.9 1.0
CG C:LYS113 4.9 14.7 1.0
C C:CYS100 4.9 10.7 1.0
CA C:GLY98 5.0 12.8 1.0

Zinc binding site 7 out of 8 in 3bto

Go back to Zinc Binding Sites List in 3bto
Zinc binding site 7 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn375

b:12.2
occ:1.00
 NE2 D:HIS67 2.1 10.4 1.0
O6 D:SSB378 2.2 14.4 1.0
SG D:CYS174 2.2 10.5 1.0
SG D:CYS46 2.3 10.8 1.0
CD2 D:HIS67 3.0 8.8 1.0
CE1 D:HIS67 3.1 11.4 1.0
S1 D:SSB378 3.1 14.6 1.0
CB D:CYS46 3.3 10.7 1.0
CB D:CYS174 3.4 9.2 1.0
C5N D:NAD377 3.4 6.6 1.0
C6N D:NAD377 4.1 5.5 1.0
C4N D:NAD377 4.1 7.5 1.0
OG D:SER48 4.1 10.3 1.0
C5 D:SSB378 4.1 16.5 1.0
CG D:HIS67 4.2 10.4 1.0
CB D:SER48 4.2 9.5 1.0
ND1 D:HIS67 4.2 9.5 1.0
NH2 D:ARG369 4.5 10.6 1.0
OE2 D:GLU68 4.6 11.7 1.0
C2 D:SSB378 4.6 14.4 1.0
CA D:CYS46 4.7 10.9 1.0
CA D:CYS174 4.7 8.1 1.0
N D:SER48 4.9 5.2 1.0
N D:GLY175 5.0 7.1 1.0
CE2 D:PHE93 5.0 9.6 1.0

Zinc binding site 8 out of 8 in 3bto

Go back to Zinc Binding Sites List in 3bto
Zinc binding site 8 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn376

b:11.8
occ:1.00
 SG D:CYS103 2.3 13.4 1.0
SG D:CYS111 2.3 10.4 1.0
SG D:CYS100 2.3 14.0 1.0
SG D:CYS97 2.4 11.4 1.0
CB D:CYS100 3.4 13.4 1.0
CB D:CYS111 3.4 9.5 1.0
CB D:CYS103 3.4 11.9 1.0
CB D:CYS97 3.5 7.7 1.0
N D:CYS97 3.5 8.3 1.0
CA D:CYS111 3.7 10.0 1.0
N D:CYS100 3.8 14.8 1.0
CA D:CYS97 3.9 9.1 1.0
N D:GLY98 4.0 14.1 1.0
N D:LEU112 4.0 10.4 1.0
N D:CYS103 4.2 11.6 1.0
CA D:CYS100 4.2 14.4 1.0
C D:CYS97 4.3 14.2 1.0
C D:CYS111 4.3 11.2 1.0
CA D:CYS103 4.4 10.9 1.0
N D:LYS99 4.5 16.8 1.0
C D:GLN96 4.6 8.7 1.0
O D:HOH603 4.8 27.2 1.0
N D:LYS113 4.9 11.4 1.0
CA D:GLN96 4.9 8.3 1.0
C D:CYS100 4.9 12.5 1.0
CA D:GLY98 4.9 15.3 1.0
O D:CYS100 4.9 12.8 1.0
CG D:LYS113 4.9 17.6 1.0

Reference:

H.Cho, S.Ramaswamy, B.V.Plapp. Flexibility of Liver Alcohol Dehydrogenase in Stereoselective Binding of 3-Butylthiolane 1-Oxides. Biochemistry V. 36 382 1997.
ISSN: ISSN 0006-2960
PubMed: 9003191
DOI: 10.1021/BI9624604
Page generated: Thu Oct 24 11:37:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy