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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Oct 28 13:04:03 2024

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