Zinc in PDB 5vl0: Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide

Enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide, PDB code: 5vl0 was solved by B.V.Plapp, E.N.Brown, S.Ramaswamy, S.Baskar Raj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 1.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.160, 180.290, 86.920, 90.00, 106.18, 90.00
R / Rfree (%) 15.8 / 19.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide (pdb code 5vl0). 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 with Nadh and N- Benzyformamide, PDB code: 5vl0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5vl0

Go back to Zinc Binding Sites List in 5vl0
Zinc binding site 1 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide


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 with Nadh and N- Benzyformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:15.7
occ:1.00
 NE2 A:HIS67 2.0 14.6 1.0
O16 A:BNF404 2.1 16.6 1.0
SG A:CYS174 2.2 15.3 1.0
SG A:CYS46 2.3 15.3 1.0
C14 A:BNF404 2.9 19.1 1.0
CE1 A:HIS67 3.0 13.6 1.0
CD2 A:HIS67 3.0 14.4 1.0
CB A:CYS46 3.2 16.1 1.0
CB A:CYS174 3.3 13.9 1.0
C5N A:NAI403 3.5 13.0 1.0
OG A:SER48 4.0 14.9 1.0
C6N A:NAI403 4.1 12.6 1.0
C4N A:NAI403 4.1 13.5 1.0
ND1 A:HIS67 4.1 12.9 1.0
N13 A:BNF404 4.2 24.8 1.0
CG A:HIS67 4.2 13.1 1.0
CB A:SER48 4.2 13.8 1.0
OE2 A:GLU68 4.4 20.8 1.0
NH2 A:ARG369 4.6 18.1 1.0
CA A:CYS174 4.6 13.3 1.0
CA A:CYS46 4.7 15.2 1.0
N A:GLY175 4.9 14.0 1.0
N A:SER48 4.9 14.3 1.0
CE2 A:PHE93 4.9 16.7 1.0
C A:CYS174 4.9 13.7 1.0

Zinc binding site 2 out of 8 in 5vl0

Go back to Zinc Binding Sites List in 5vl0
Zinc binding site 2 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide


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 with Nadh and N- Benzyformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:15.4
occ:1.00
 SG A:CYS111 2.3 14.9 1.0
SG A:CYS103 2.3 15.7 1.0
SG A:CYS97 2.3 17.1 1.0
SG A:CYS100 2.4 15.6 1.0
CB A:CYS111 3.3 13.7 1.0
CB A:CYS103 3.4 17.8 1.0
CB A:CYS100 3.4 18.3 1.0
CB A:CYS97 3.4 16.1 1.0
N A:CYS97 3.5 13.9 1.0
CA A:CYS111 3.7 14.8 1.0
CA A:CYS97 3.9 15.7 1.0
N A:CYS100 3.9 19.1 1.0
N A:LEU112 3.9 14.5 1.0
N A:GLY98 4.0 17.4 1.0
CA A:CYS100 4.2 18.4 1.0
N A:CYS103 4.2 16.5 1.0
C A:CYS111 4.3 14.7 1.0
C A:CYS97 4.4 18.4 1.0
CA A:CYS103 4.4 16.4 1.0
N A:LYS99 4.5 17.7 1.0
C A:GLN96 4.6 14.2 1.0
N A:LYS113 4.8 15.3 1.0
CG A:LYS113 4.8 21.1 1.0
C A:CYS100 4.9 18.1 1.0
CA A:GLN96 4.9 14.5 1.0
CA A:GLY98 5.0 17.3 1.0
O A:CYS100 5.0 17.3 1.0

Zinc binding site 3 out of 8 in 5vl0

Go back to Zinc Binding Sites List in 5vl0
Zinc binding site 3 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide


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 with Nadh and N- Benzyformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:16.2
occ:1.00
 NE2 B:HIS67 2.0 14.7 1.0
O16 B:BNF404 2.1 16.5 1.0
SG B:CYS174 2.2 15.9 1.0
SG B:CYS46 2.3 15.3 1.0
C14 B:BNF404 3.0 19.7 1.0
CE1 B:HIS67 3.0 13.6 1.0
CD2 B:HIS67 3.1 15.3 1.0
CB B:CYS46 3.2 15.1 1.0
CB B:CYS174 3.3 15.2 1.0
C5N B:NAI403 3.5 13.6 1.0
OG B:SER48 4.0 16.1 1.0
C4N B:NAI403 4.1 13.7 1.0
C6N B:NAI403 4.1 12.8 1.0
CB B:SER48 4.2 15.2 1.0
ND1 B:HIS67 4.2 15.9 1.0
CG B:HIS67 4.2 14.8 1.0
N13 B:BNF404 4.2 27.9 1.0
NH2 B:ARG369 4.5 18.7 1.0
OE2 B:GLU68 4.6 20.5 1.0
CA B:CYS174 4.7 14.3 1.0
CA B:CYS46 4.7 15.8 1.0
CE2 B:PHE93 4.9 17.1 1.0
N B:SER48 4.9 13.9 1.0
C B:CYS174 5.0 13.6 1.0
N B:GLY175 5.0 13.7 1.0

Zinc binding site 4 out of 8 in 5vl0

Go back to Zinc Binding Sites List in 5vl0
Zinc binding site 4 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide


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 with Nadh and N- Benzyformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:17.2
occ:1.00
 SG B:CYS100 2.3 17.9 1.0
SG B:CYS111 2.3 16.5 1.0
SG B:CYS97 2.4 18.9 1.0
SG B:CYS103 2.4 17.2 1.0
CB B:CYS111 3.3 15.5 1.0
CB B:CYS100 3.4 18.2 1.0
CB B:CYS97 3.4 17.1 1.0
CB B:CYS103 3.4 17.4 1.0
N B:CYS97 3.6 15.5 1.0
CA B:CYS111 3.8 16.9 1.0
N B:CYS100 3.9 22.8 1.0
CA B:CYS97 3.9 17.2 1.0
N B:LEU112 3.9 16.3 1.0
N B:GLY98 4.0 18.7 1.0
CA B:CYS100 4.2 19.5 1.0
N B:CYS103 4.2 17.5 1.0
C B:CYS111 4.3 16.0 1.0
C B:CYS97 4.3 19.2 1.0
CA B:CYS103 4.4 17.0 1.0
N B:LYS99 4.5 19.0 1.0
O B:HOH766 4.6 34.5 1.0
C B:GLN96 4.6 16.0 1.0
C B:CYS100 4.8 17.7 1.0
N B:LYS113 4.9 16.9 1.0
CA B:GLN96 4.9 15.1 1.0
O B:CYS100 4.9 19.6 1.0
CG B:LYS113 5.0 22.3 1.0
CA B:GLY98 5.0 18.8 1.0

Zinc binding site 5 out of 8 in 5vl0

Go back to Zinc Binding Sites List in 5vl0
Zinc binding site 5 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide


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 with Nadh and N- Benzyformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:15.5
occ:1.00
 NE2 C:HIS67 2.0 13.9 1.0
O16 C:BNF404 2.1 17.5 1.0
SG C:CYS174 2.3 15.2 1.0
SG C:CYS46 2.3 14.7 1.0
C14 C:BNF404 2.9 19.6 1.0
CE1 C:HIS67 3.0 14.1 1.0
CD2 C:HIS67 3.0 13.9 1.0
CB C:CYS174 3.3 13.5 1.0
CB C:CYS46 3.3 15.7 1.0
C5N C:NAI403 3.5 12.1 1.0
OG C:SER48 4.1 14.5 1.0
C6N C:NAI403 4.1 11.4 1.0
C4N C:NAI403 4.1 12.3 1.0
ND1 C:HIS67 4.1 14.1 1.0
CB C:SER48 4.2 13.6 1.0
N13 C:BNF404 4.2 26.4 1.0
CG C:HIS67 4.2 13.2 1.0
OE2 C:GLU68 4.5 20.0 1.0
NH2 C:ARG369 4.6 17.0 1.0
CA C:CYS174 4.6 12.4 1.0
CA C:CYS46 4.7 15.7 1.0
N C:GLY175 4.9 13.3 1.0
C C:CYS174 4.9 12.3 1.0
N C:SER48 4.9 12.3 1.0
CE2 C:PHE93 4.9 18.0 1.0

Zinc binding site 6 out of 8 in 5vl0

Go back to Zinc Binding Sites List in 5vl0
Zinc binding site 6 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide


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 with Nadh and N- Benzyformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:17.1
occ:1.00
 SG C:CYS111 2.3 16.8 1.0
SG C:CYS97 2.3 19.7 1.0
SG C:CYS100 2.4 17.6 1.0
SG C:CYS103 2.4 17.2 1.0
CB C:CYS111 3.3 14.9 1.0
CB C:CYS103 3.3 18.5 1.0
CB C:CYS100 3.4 20.5 1.0
CB C:CYS97 3.4 18.8 1.0
N C:CYS97 3.6 14.8 1.0
CA C:CYS111 3.8 16.2 1.0
N C:CYS100 3.8 21.3 1.0
CA C:CYS97 3.9 19.1 1.0
N C:LEU112 4.0 16.4 1.0
N C:GLY98 4.0 20.1 1.0
CA C:CYS100 4.2 19.3 1.0
N C:CYS103 4.2 18.0 1.0
C C:CYS111 4.3 16.0 1.0
C C:CYS97 4.3 19.9 1.0
CA C:CYS103 4.3 17.9 1.0
N C:LYS99 4.5 19.9 1.0
C C:GLN96 4.6 16.2 1.0
O C:HOH807 4.8 36.0 1.0
N C:LYS113 4.9 16.0 1.0
C C:CYS100 4.9 19.4 1.0
O C:CYS100 4.9 18.7 1.0
CG C:LYS113 4.9 21.7 1.0
CA C:GLN96 4.9 16.4 1.0
CA C:GLY98 5.0 19.7 1.0

Zinc binding site 7 out of 8 in 5vl0

Go back to Zinc Binding Sites List in 5vl0
Zinc binding site 7 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide


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 with Nadh and N- Benzyformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:16.3
occ:1.00
 NE2 D:HIS67 2.0 14.8 1.0
O16 D:BNF404 2.1 16.7 1.0
SG D:CYS174 2.2 15.9 1.0
SG D:CYS46 2.3 15.1 1.0
C14 D:BNF404 2.9 22.5 1.0
CE1 D:HIS67 3.0 13.9 1.0
CD2 D:HIS67 3.1 15.3 1.0
CB D:CYS46 3.3 16.9 1.0
CB D:CYS174 3.3 15.0 1.0
C5N D:NAI403 3.5 13.9 1.0
OG D:SER48 4.0 15.5 1.0
C4N D:NAI403 4.1 14.0 1.0
C6N D:NAI403 4.1 12.3 1.0
ND1 D:HIS67 4.1 13.7 1.0
CB D:SER48 4.2 14.4 1.0
CG D:HIS67 4.2 14.5 1.0
N13 D:BNF404 4.2 28.4 1.0
NH2 D:ARG369 4.4 18.7 1.0
OE2 D:GLU68 4.6 19.9 1.0
CA D:CYS174 4.7 14.3 1.0
CA D:CYS46 4.8 16.2 1.0
CE2 D:PHE93 4.9 17.4 1.0
N D:GLY175 4.9 14.1 1.0
N D:SER48 4.9 13.9 1.0

Zinc binding site 8 out of 8 in 5vl0

Go back to Zinc Binding Sites List in 5vl0
Zinc binding site 8 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and N- Benzyformamide


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 with Nadh and N- Benzyformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:16.1
occ:1.00
 SG D:CYS103 2.3 16.5 1.0
SG D:CYS100 2.3 16.2 1.0
SG D:CYS111 2.3 15.6 1.0
SG D:CYS97 2.4 17.4 1.0
CB D:CYS111 3.3 15.0 1.0
CB D:CYS103 3.4 16.8 1.0
CB D:CYS100 3.4 17.9 1.0
CB D:CYS97 3.4 17.6 1.0
N D:CYS97 3.6 15.0 1.0
CA D:CYS111 3.7 14.7 1.0
N D:CYS100 3.9 18.6 1.0
CA D:CYS97 3.9 15.5 1.0
N D:LEU112 4.0 14.7 1.0
N D:GLY98 4.0 17.1 1.0
CA D:CYS100 4.2 18.9 1.0
N D:CYS103 4.2 16.0 1.0
C D:CYS111 4.3 14.3 1.0
C D:CYS97 4.3 17.6 1.0
CA D:CYS103 4.4 16.9 1.0
N D:LYS99 4.5 17.4 1.0
C D:GLN96 4.7 15.0 1.0
C D:CYS100 4.8 17.8 1.0
N D:LYS113 4.9 15.7 1.0
O D:HOH761 4.9 33.2 1.0
CA D:GLN96 4.9 14.2 1.0
CG D:LYS113 4.9 21.4 1.0
O D:CYS100 4.9 17.3 1.0
CA D:GLY98 5.0 17.1 1.0

Reference:

B.V.Plapp, B.R.Savarimuthu, D.J.Ferraro, J.K.Rubach, E.N.Brown, S.Ramaswamy. Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Biochemistry V. 56 3632 2017.
ISSN: ISSN 1520-4995
PubMed: 28640600
DOI: 10.1021/ACS.BIOCHEM.7B00446
Page generated: Wed Dec 16 11:10:58 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy