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Zinc in PDB 5kcp: Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

Enzymatic activity of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

All present enzymatic activity of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 5kcp was solved by B.V.Plapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.40 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.440, 51.590, 92.560, 91.87, 103.06, 110.33
R / Rfree (%) 11.8 / 13.8

Other elements in 5kcp:

The structure of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol also contains other interesting chemical elements:

Fluorine (F) 20 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol (pdb code 5kcp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 5kcp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5kcp

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Zinc binding site 1 out of 4 in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:12.9
occ:1.00
 O1 A:PFB378 1.9 12.8 1.0
NE2 A:HIS67 2.0 11.9 1.0
SG A:CYS174 2.3 12.0 1.0
SG A:CYS46 2.4 11.3 1.0
C7 A:PFB378 2.9 14.1 1.0
CE1 A:HIS67 3.0 11.3 1.0
CD2 A:HIS67 3.1 10.8 1.0
CB A:CYS46 3.3 12.3 1.0
CB A:CYS46 3.3 12.6 0.0
C5N A:NAJ377 3.4 10.5 1.0
CB A:CYS174 3.4 10.6 1.0
OG1 A:THR48 3.7 11.5 1.0
SG A:CYS46 3.7 12.8 0.0
C4N A:NAJ377 4.0 11.2 1.0
C6N A:NAJ377 4.0 9.8 1.0
CB A:THR48 4.1 12.4 1.0
F6 A:PFB378 4.1 18.4 1.0
ND1 A:HIS67 4.2 10.6 1.0
CG A:HIS67 4.2 10.6 1.0
C1 A:PFB378 4.2 14.4 1.0
NH2 A:ARG369 4.6 12.6 1.0
C6 A:PFB378 4.7 16.1 1.0
CA A:CYS174 4.8 10.3 1.0
CA A:CYS46 4.8 11.7 1.0
N A:THR48 4.8 9.7 1.0
CE2 A:PHE93 4.8 11.4 1.0
OE2 A:GLU68 4.9 13.6 1.0
N1N A:NAJ377 5.0 9.3 1.0

Zinc binding site 2 out of 4 in 5kcp

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Zinc binding site 2 out of 4 in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:12.2
occ:1.00
 SG A:CYS111 2.3 11.8 1.0
SG A:CYS100 2.3 12.4 1.0
SG A:CYS97 2.3 13.9 1.0
SG A:CYS103 2.3 12.0 1.0
CB A:CYS111 3.3 11.0 1.0
CB A:CYS103 3.4 12.6 1.0
CB A:CYS100 3.4 13.1 1.0
CB A:CYS97 3.4 13.7 1.0
N A:CYS97 3.6 12.2 1.0
CA A:CYS111 3.7 10.8 1.0
N A:CYS100 3.9 14.9 1.0
CA A:CYS97 3.9 13.2 1.0
N A:GLY98 4.0 14.0 1.0
N A:LEU112 4.0 11.4 1.0
CA A:CYS100 4.2 14.1 1.0
N A:CYS103 4.2 11.7 1.0
C A:CYS111 4.3 10.9 1.0
C A:CYS97 4.3 13.4 1.0
CA A:CYS103 4.4 11.7 1.0
N A:LYS99 4.5 15.3 1.0
C A:GLN96 4.6 11.8 1.0
C A:CYS100 4.8 13.8 1.0
N A:LYS113 4.9 12.1 1.0
O A:CYS100 4.9 13.7 1.0
CG A:LYS113 4.9 17.1 1.0
CA A:GLN96 4.9 11.2 1.0
O A:HOH552 4.9 29.1 1.0
CA A:GLY98 5.0 15.5 1.0

Zinc binding site 3 out of 4 in 5kcp

Go back to Zinc Binding Sites List in 5kcp
Zinc binding site 3 out of 4 in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:15.1
occ:1.00
 O1 B:PFB378 1.9 15.4 1.0
NE2 B:HIS67 2.1 14.5 1.0
SG B:CYS174 2.3 14.1 1.0
SG B:CYS46 2.3 14.0 1.0
C7 B:PFB378 2.9 15.7 1.0
CE1 B:HIS67 3.0 13.3 1.0
CD2 B:HIS67 3.1 13.8 1.0
CB B:CYS46 3.3 13.5 1.0
C5N B:NAJ377 3.4 12.6 1.0
CB B:CYS174 3.4 12.8 1.0
OG1 B:THR48 3.7 13.7 1.0
C4N B:NAJ377 3.9 14.2 1.0
C6N B:NAJ377 4.0 12.1 1.0
CB B:THR48 4.1 13.8 1.0
F6 B:PFB378 4.1 19.6 1.0
ND1 B:HIS67 4.2 13.1 1.0
CG B:HIS67 4.2 12.8 1.0
C1 B:PFB378 4.2 17.8 1.0
NH2 B:ARG369 4.6 14.6 1.0
C6 B:PFB378 4.7 17.1 1.0
CA B:CYS174 4.8 12.2 1.0
CA B:CYS46 4.8 14.1 1.0
N B:THR48 4.8 12.5 1.0
CE2 B:PHE93 4.9 13.2 1.0
OE2 B:GLU68 4.9 15.4 1.0
N1N B:NAJ377 5.0 11.7 1.0

Zinc binding site 4 out of 4 in 5kcp

Go back to Zinc Binding Sites List in 5kcp
Zinc binding site 4 out of 4 in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:14.2
occ:1.00
 SG B:CYS111 2.3 13.9 1.0
SG B:CYS97 2.3 16.9 1.0
SG B:CYS103 2.4 13.4 1.0
SG B:CYS100 2.4 14.7 1.0
CB B:CYS111 3.3 12.8 1.0
CB B:CYS103 3.4 13.8 1.0
CB B:CYS97 3.4 16.4 1.0
CB B:CYS100 3.4 16.4 1.0
N B:CYS97 3.5 14.3 1.0
CA B:CYS111 3.7 12.5 1.0
N B:CYS100 3.8 17.0 1.0
CA B:CYS97 3.9 16.3 1.0
N B:LEU112 4.0 13.7 1.0
N B:GLY98 4.0 16.0 1.0
CA B:CYS100 4.2 16.9 1.0
N B:CYS103 4.2 13.5 1.0
C B:CYS111 4.3 12.8 1.0
C B:CYS97 4.3 17.2 1.0
CA B:CYS103 4.4 13.3 1.0
N B:LYS99 4.5 17.7 1.0
C B:GLN96 4.6 13.5 1.0
N B:LYS113 4.8 14.1 1.0
C B:CYS100 4.8 15.6 1.0
O B:HOH482 4.9 29.5 1.0
CA B:GLN96 4.9 13.0 1.0
O B:CYS100 4.9 15.7 1.0
CG B:LYS113 5.0 19.7 1.0
CA B:GLY98 5.0 17.2 1.0
C B:LYS99 5.0 19.0 1.0

Reference:

K.Kim, B.V.Plapp. Inversion of Substrate Stereoselectivity of Horse Liver Alcohol Dehydrogenase By Substitutions of Ser-48 and Phe-93. Chem. Biol. Interact. V. 276 77 2017.
ISSN: ISSN 1872-7786
PubMed: 28025168
DOI: 10.1016/J.CBI.2016.12.016
Page generated: Sun Oct 27 20:17:29 2024

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