Atomistry » Zinc » PDB 5vmz-5vuq » 5vn1
Atomistry »
  Zinc »
    PDB 5vmz-5vuq »
      5vn1 »

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

Go back to Zinc Binding Sites List in 5vn1
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

Go back to Zinc Binding Sites List in 5vn1
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

Go back to Zinc Binding Sites List in 5vn1
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

Go back to Zinc Binding Sites List in 5vn1
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

Go back to Zinc Binding Sites List in 5vn1
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

Go back to Zinc Binding Sites List in 5vn1
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

Go back to Zinc Binding Sites List in 5vn1
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

Go back to Zinc Binding Sites List in 5vn1
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy