Atomistry » Zinc » PDB 5kiv-5kzz » 5kjc
Atomistry »
  Zinc »
    PDB 5kiv-5kzz »
      5kjc »

Zinc in PDB 5kjc: V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol

Enzymatic activity of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol

All present enzymatic activity of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol, PDB code: 5kjc 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) 20.00 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.230, 51.250, 92.550, 92.02, 103.01, 109.88
R / Rfree (%) 12.9 / 16.8

Other elements in 5kjc:

The structure of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol also contains other interesting chemical elements:

Fluorine (F) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol (pdb code 5kjc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol, PDB code: 5kjc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5kjc

Go back to Zinc Binding Sites List in 5kjc
Zinc binding site 1 out of 4 in the V222I Horse Liver 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:16.9
occ:0.80
 O1 A:PFB378 1.9 15.8 0.8
NE2 A:HIS67 2.1 14.0 1.0
SG A:CYS174 2.3 15.4 1.0
SG A:CYS46 2.3 16.4 0.8
C7 A:PFB378 2.9 21.5 0.8
CD2 A:HIS67 3.1 13.8 1.0
CE1 A:HIS67 3.1 12.7 1.0
C5N A:NAJ377 3.3 12.8 1.0
CB A:CYS174 3.4 12.1 1.0
CB A:CYS46 3.4 14.8 0.8
CB A:CYS46 3.5 16.4 0.2
SG A:CYS46 3.7 18.2 0.2
C4N A:NAJ377 3.8 14.1 1.0
OG A:SER48 3.9 14.4 1.0
C6N A:NAJ377 3.9 11.7 1.0
F6 A:PFB378 4.1 20.5 0.8
CB A:SER48 4.1 12.7 1.0
ND1 A:HIS67 4.2 12.3 1.0
CG A:HIS67 4.2 11.1 1.0
C1 A:PFB378 4.2 18.8 0.8
C6 A:PFB378 4.6 20.9 0.8
NH2 A:ARG369 4.7 20.8 1.0
CA A:CYS174 4.8 10.6 1.0
CE2 A:PHE93 4.8 14.1 1.0
N A:SER48 4.9 12.4 1.0
N1N A:NAJ377 5.0 10.6 1.0
CA A:CYS46 5.0 15.4 1.0

Zinc binding site 2 out of 4 in 5kjc

Go back to Zinc Binding Sites List in 5kjc
Zinc binding site 2 out of 4 in the V222I Horse Liver 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:12.5
occ:1.00
 SG A:CYS97 2.3 14.2 1.0
SG A:CYS100 2.3 13.3 1.0
SG A:CYS111 2.3 12.0 1.0
SG A:CYS103 2.4 12.0 1.0
CB A:CYS111 3.3 11.5 1.0
CB A:CYS103 3.4 13.0 1.0
CB A:CYS100 3.4 13.9 1.0
CB A:CYS97 3.4 13.8 1.0
N A:CYS97 3.5 11.7 1.0
CA A:CYS111 3.7 10.9 1.0
N A:CYS100 3.9 15.4 1.0
CA A:CYS97 3.9 13.4 1.0
N A:GLY98 3.9 13.6 1.0
N A:LEU112 4.0 11.7 1.0
N A:CYS103 4.2 12.5 1.0
CA A:CYS100 4.2 15.8 1.0
C A:CYS111 4.3 11.2 1.0
C A:CYS97 4.3 13.8 1.0
CA A:CYS103 4.4 11.7 1.0
N A:LYS99 4.5 16.2 1.0
C A:GLN96 4.6 11.6 1.0
N A:LYS113 4.8 11.8 1.0
C A:CYS100 4.9 14.2 1.0
CG A:LYS113 4.9 18.0 1.0
O A:CYS100 4.9 14.4 1.0
CA A:GLN96 4.9 11.7 1.0
CA A:GLY98 4.9 14.8 1.0
O A:HOH552 5.0 32.9 1.0

Zinc binding site 3 out of 4 in 5kjc

Go back to Zinc Binding Sites List in 5kjc
Zinc binding site 3 out of 4 in the V222I Horse Liver 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:20.7
occ:0.90
 O1 B:PFB378 1.9 20.4 1.0
NE2 B:HIS67 2.1 16.0 1.0
SG B:CYS174 2.3 18.2 1.0
SG B:CYS46 2.3 21.6 1.0
C7 B:PFB378 2.9 25.8 1.0
CE1 B:HIS67 3.0 14.7 1.0
CD2 B:HIS67 3.1 16.3 1.0
C5N B:NAJ377 3.3 15.1 1.0
CB B:CYS46 3.4 18.2 1.0
CB B:CYS174 3.4 15.2 1.0
C4N B:NAJ377 3.8 17.3 1.0
OG B:SER48 3.9 16.1 1.0
C6N B:NAJ377 3.9 15.3 1.0
CB B:SER48 4.0 15.3 1.0
F6 B:PFB378 4.1 25.7 1.0
ND1 B:HIS67 4.2 14.6 1.0
CG B:HIS67 4.2 14.0 1.0
C1 B:PFB378 4.2 23.7 1.0
NH2 B:ARG369 4.6 23.4 1.0
C6 B:PFB378 4.6 25.1 1.0
CA B:CYS174 4.8 13.6 1.0
CE2 B:PHE93 4.9 15.9 1.0
N B:SER48 4.9 15.1 1.0
CA B:CYS46 4.9 17.6 1.0
N1N B:NAJ377 5.0 12.9 1.0

Zinc binding site 4 out of 4 in 5kjc

Go back to Zinc Binding Sites List in 5kjc
Zinc binding site 4 out of 4 in the V222I Horse Liver 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:15.8
occ:1.00
 SG B:CYS111 2.3 15.2 1.0
SG B:CYS97 2.3 18.7 1.0
SG B:CYS100 2.3 16.3 1.0
SG B:CYS103 2.4 14.6 1.0
CB B:CYS111 3.3 13.6 1.0
CB B:CYS97 3.4 16.3 1.0
CB B:CYS103 3.4 14.8 1.0
CB B:CYS100 3.4 17.7 1.0
N B:CYS97 3.5 14.9 1.0
CA B:CYS111 3.7 12.8 1.0
N B:CYS100 3.9 19.5 1.0
CA B:CYS97 3.9 17.7 1.0
N B:GLY98 3.9 17.6 1.0
N B:LEU112 4.0 14.3 1.0
CA B:CYS100 4.2 18.9 1.0
N B:CYS103 4.2 14.8 1.0
C B:CYS111 4.3 13.9 1.0
C B:CYS97 4.3 18.5 1.0
CA B:CYS103 4.4 13.8 1.0
N B:LYS99 4.5 18.9 1.0
C B:GLN96 4.6 14.1 1.0
N B:LYS113 4.8 15.0 1.0
C B:CYS100 4.8 18.2 1.0
CG B:LYS113 4.9 19.4 1.0
CA B:GLN96 4.9 13.8 1.0
O B:CYS100 5.0 17.1 1.0
CA B:GLY98 5.0 19.3 1.0
O B:HOH482 5.0 39.7 1.0

Reference:

K.K.Shanmuganatham, R.S.Wallace, A.Ting-I Lee, B.V.Plapp. Contribution of Buried Distal Amino Acid Residues in Horse Liver Alcohol Dehydrogenase to Structure and Catalysis. Protein Sci. V. 27 750 2018.
ISSN: ESSN 1469-896X
PubMed: 29271062
DOI: 10.1002/PRO.3370
Page generated: Sun Oct 27 20:27:08 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy