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Zinc in PDB 5vn1: Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide

Enzymatic activity of Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide

All present enzymatic activity of Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide, PDB code: 5vn1 was solved by B.V.Plapp, S.Ramaswamy, D.J.Ferraro, S.Baskar Raj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.212, 180.808, 86.841, 90.00, 106.12, 90.00
R / Rfree (%) 15.2 / 18.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide (pdb code 5vn1). 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 Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide, PDB code: 5vn1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5vn1

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Zinc binding site 1 out of 8 in the Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide


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 Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:21.3
occ:1.00
 NE2 A:HIS67 2.0 20.3 1.0
O A:NWH404 2.2 23.0 1.0
SG A:CYS174 2.3 20.6 1.0
SG A:CYS46 2.3 20.9 1.0
C A:NWH404 2.9 25.8 1.0
CE1 A:HIS67 3.0 18.9 1.0
CD2 A:HIS67 3.1 19.5 1.0
CB A:CYS46 3.2 19.9 1.0
CB A:CYS174 3.4 19.2 1.0
C5N A:NAI403 3.5 19.4 1.0
OG A:SER48 4.0 20.4 1.0
ND1 A:HIS67 4.1 19.1 1.0
C4N A:NAI403 4.1 18.8 1.0
C6N A:NAI403 4.1 19.4 1.0
CB A:SER48 4.2 20.5 1.0
CG A:HIS67 4.2 19.0 1.0
N A:NWH404 4.2 27.2 1.0
OE2 A:GLU68 4.6 25.1 1.0
NH2 A:ARG369 4.6 23.4 1.0
CA A:CYS46 4.7 20.3 1.0
CA A:CYS174 4.7 18.5 1.0
CE2 A:PHE93 4.9 22.1 1.0
N A:SER48 4.9 19.3 1.0
N A:GLY175 5.0 18.8 1.0

Zinc binding site 2 out of 8 in 5vn1

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Zinc binding site 2 out of 8 in the Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide


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 Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:20.1
occ:1.00
 SG A:CYS111 2.3 19.8 1.0
SG A:CYS97 2.3 21.9 1.0
SG A:CYS103 2.4 20.1 1.0
SG A:CYS100 2.4 20.5 1.0
CB A:CYS111 3.3 19.2 1.0
CB A:CYS103 3.4 20.5 1.0
CB A:CYS97 3.4 21.5 1.0
CB A:CYS100 3.4 22.5 1.0
N A:CYS97 3.5 18.8 1.0
CA A:CYS111 3.7 18.4 1.0
N A:CYS100 3.9 23.5 1.0
CA A:CYS97 3.9 20.3 1.0
N A:LEU112 4.0 19.1 1.0
N A:GLY98 4.0 21.4 1.0
CA A:CYS100 4.2 22.9 1.0
N A:CYS103 4.2 19.1 1.0
C A:CYS111 4.3 18.3 1.0
C A:CYS97 4.3 21.1 1.0
CA A:CYS103 4.4 20.2 1.0
N A:LYS99 4.5 23.1 1.0
C A:GLN96 4.6 19.0 1.0
N A:LYS113 4.8 19.4 1.0
CG A:LYS113 4.8 25.2 1.0
C A:CYS100 4.9 21.9 1.0
CA A:GLN96 4.9 18.5 1.0
O A:CYS100 4.9 22.0 1.0
CA A:GLY98 5.0 21.9 1.0

Zinc binding site 3 out of 8 in 5vn1

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Zinc binding site 3 out of 8 in the Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide


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 Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:21.9
occ:1.00
 NE2 B:HIS67 2.0 22.1 1.0
O B:NWH404 2.1 23.1 1.0
SG B:CYS174 2.2 21.3 1.0
SG B:CYS46 2.3 21.1 1.0
C B:NWH404 2.9 24.7 1.0
CE1 B:HIS67 3.0 20.2 1.0
CD2 B:HIS67 3.0 21.5 1.0
CB B:CYS46 3.2 20.7 1.0
CB B:CYS174 3.3 21.9 1.0
C5N B:NAI403 3.5 18.6 1.0
OG B:SER48 4.0 21.2 1.0
CB B:SER48 4.1 22.4 1.0
C4N B:NAI403 4.1 20.2 1.0
C6N B:NAI403 4.1 19.8 1.0
ND1 B:HIS67 4.1 21.1 1.0
CG B:HIS67 4.2 19.7 1.0
N B:NWH404 4.2 26.6 1.0
NH2 B:ARG369 4.5 23.3 1.0
OE2 B:GLU68 4.6 26.1 1.0
CA B:CYS174 4.7 18.7 1.0
CA B:CYS46 4.7 20.2 1.0
N B:GLY175 4.9 20.7 1.0
N B:SER48 4.9 19.1 1.0
CE2 B:PHE93 5.0 22.7 1.0
C B:CYS174 5.0 19.4 1.0

Zinc binding site 4 out of 8 in 5vn1

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Zinc binding site 4 out of 8 in the Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide


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 Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:21.9
occ:1.00
 SG B:CYS100 2.3 22.5 1.0
SG B:CYS111 2.3 21.5 1.0
SG B:CYS103 2.4 22.0 1.0
SG B:CYS97 2.4 23.8 1.0
CB B:CYS111 3.3 20.7 1.0
CB B:CYS100 3.4 24.2 1.0
CB B:CYS103 3.4 21.9 1.0
CB B:CYS97 3.4 22.7 1.0
N B:CYS97 3.6 21.3 1.0
CA B:CYS111 3.8 20.6 1.0
N B:CYS100 3.9 24.8 1.0
CA B:CYS97 3.9 22.1 1.0
N B:LEU112 4.0 21.2 1.0
N B:GLY98 4.0 22.4 1.0
CA B:CYS100 4.2 26.4 1.0
N B:CYS103 4.2 21.0 1.0
C B:CYS111 4.3 21.0 1.0
CA B:CYS103 4.3 21.9 1.0
C B:CYS97 4.4 22.2 1.0
N B:LYS99 4.5 23.3 1.0
C B:GLN96 4.7 20.7 1.0
O B:HOH762 4.8 40.5 1.0
C B:CYS100 4.9 23.9 1.0
N B:LYS113 4.9 22.2 1.0
O B:CYS100 4.9 23.7 1.0
CA B:GLN96 4.9 20.1 1.0
CG B:LYS113 5.0 27.4 1.0
CA B:GLY98 5.0 22.6 1.0

Zinc binding site 5 out of 8 in 5vn1

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Zinc binding site 5 out of 8 in the Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide


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 Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:20.8
occ:1.00
 NE2 C:HIS67 2.0 20.0 1.0
O C:NWH404 2.1 20.8 0.8
SG C:CYS174 2.2 20.0 1.0
SG C:CYS46 2.3 20.1 1.0
O C:NMH405 2.4 20.6 0.2
C C:NWH404 2.9 24.7 0.8
CE1 C:HIS67 3.0 18.5 1.0
CD2 C:HIS67 3.1 19.3 1.0
C C:NMH405 3.1 19.9 0.2
CB C:CYS46 3.2 20.1 1.0
CB C:CYS174 3.3 18.4 1.0
C5N C:NAI403 3.5 18.7 1.0
OG C:SER48 4.0 20.1 1.0
CB C:SER48 4.1 20.1 1.0
C4N C:NAI403 4.1 19.0 1.0
ND1 C:HIS67 4.1 18.9 1.0
C6N C:NAI403 4.1 19.6 1.0
CG C:HIS67 4.2 18.5 1.0
N C:NWH404 4.2 24.8 0.8
N C:NMH405 4.4 21.3 0.2
OE2 C:GLU68 4.6 23.6 1.0
NH2 C:ARG369 4.6 22.7 1.0
CA C:CYS174 4.7 17.1 1.0
CA C:CYS46 4.7 20.0 1.0
N C:GLY175 4.9 18.9 1.0
N C:SER48 5.0 19.5 1.0
CE2 C:PHE93 5.0 21.4 1.0
C C:CYS174 5.0 17.9 1.0

Zinc binding site 6 out of 8 in 5vn1

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Zinc binding site 6 out of 8 in the Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide


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 Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:21.3
occ:1.00
 SG C:CYS111 2.3 21.1 1.0
SG C:CYS97 2.3 23.5 1.0
SG C:CYS103 2.4 21.3 1.0
SG C:CYS100 2.4 21.8 1.0
CB C:CYS111 3.3 19.6 1.0
CB C:CYS97 3.4 22.8 1.0
CB C:CYS100 3.4 24.3 1.0
CB C:CYS103 3.4 21.4 1.0
N C:CYS97 3.6 21.5 1.0
CA C:CYS111 3.7 19.0 1.0
N C:CYS100 3.9 24.4 1.0
CA C:CYS97 3.9 21.7 1.0
N C:LEU112 4.0 20.5 1.0
N C:GLY98 4.0 23.0 1.0
CA C:CYS100 4.2 24.9 1.0
N C:CYS103 4.2 20.1 1.0
C C:CYS111 4.3 20.4 1.0
C C:CYS97 4.3 22.3 1.0
CA C:CYS103 4.4 20.8 1.0
N C:LYS99 4.5 23.0 1.0
C C:GLN96 4.7 20.5 1.0
N C:LYS113 4.8 20.8 1.0
O C:HOH791 4.9 40.1 1.0
C C:CYS100 4.9 23.0 1.0
CG C:LYS113 4.9 26.9 1.0
CA C:GLN96 5.0 19.4 1.0
O C:CYS100 5.0 23.1 1.0

Zinc binding site 7 out of 8 in 5vn1

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Zinc binding site 7 out of 8 in the Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide


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 Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:21.3
occ:1.00
 NE2 D:HIS67 2.0 21.8 1.0
O D:NWH404 2.1 21.5 1.0
SG D:CYS174 2.2 20.5 1.0
SG D:CYS46 2.3 21.1 1.0
C D:NWH404 2.9 24.5 1.0
CE1 D:HIS67 3.0 20.0 1.0
CD2 D:HIS67 3.0 19.9 1.0
CB D:CYS46 3.2 20.4 1.0
CB D:CYS174 3.3 20.8 1.0
C5N D:NAI403 3.5 18.3 1.0
OG D:SER48 4.0 20.2 1.0
C6N D:NAI403 4.1 17.9 1.0
ND1 D:HIS67 4.1 19.6 1.0
C4N D:NAI403 4.1 19.2 1.0
CB D:SER48 4.1 19.9 1.0
CG D:HIS67 4.2 19.6 1.0
N D:NWH404 4.2 26.4 1.0
NH2 D:ARG369 4.5 22.8 1.0
OE2 D:GLU68 4.6 25.5 1.0
CA D:CYS174 4.7 18.6 1.0
CA D:CYS46 4.7 20.1 1.0
CE2 D:PHE93 4.9 23.0 1.0
N D:SER48 4.9 18.7 1.0
N D:GLY175 5.0 20.4 1.0

Zinc binding site 8 out of 8 in 5vn1

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Zinc binding site 8 out of 8 in the Horse Liver Alcohol Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide


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 Dehydrogenae Complexed with Nadh (R,S)-N-1- Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:20.6
occ:1.00
 SG D:CYS100 2.3 20.8 1.0
SG D:CYS103 2.3 21.1 1.0
SG D:CYS111 2.4 20.3 1.0
SG D:CYS97 2.4 22.9 1.0
CB D:CYS111 3.3 18.8 1.0
CB D:CYS100 3.4 22.5 1.0
CB D:CYS103 3.4 21.4 1.0
CB D:CYS97 3.5 23.4 1.0
N D:CYS97 3.6 20.9 1.0
CA D:CYS111 3.7 18.6 1.0
N D:CYS100 3.9 24.8 1.0
CA D:CYS97 4.0 21.8 1.0
N D:LEU112 4.0 20.1 1.0
N D:GLY98 4.0 22.1 1.0
CA D:CYS100 4.2 24.0 1.0
N D:CYS103 4.2 19.2 1.0
C D:CYS111 4.3 19.0 1.0
CA D:CYS103 4.4 20.4 1.0
C D:CYS97 4.4 22.9 1.0
N D:LYS99 4.5 23.8 1.0
C D:GLN96 4.7 19.9 1.0
C D:CYS100 4.8 22.2 1.0
N D:LYS113 4.9 19.6 1.0
O D:HOH726 4.9 35.8 1.0
CA D:GLN96 4.9 20.3 1.0
O D:CYS100 4.9 22.2 1.0
CG D:LYS113 5.0 25.1 1.0
CA D:GLY98 5.0 23.5 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 13:12:56 2024

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