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Zinc in PDB 7kcq: Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme

Enzymatic activity of Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme

All present enzymatic activity of Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme:
1.1.1.1;

Zinc Binding Sites:

The binding sites of Zinc atom in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme (pdb code 7kcq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme, PDB code: 7kcq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7kcq

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Zinc binding site 1 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:53.0
occ:1.00
 OE2 A:GLU67 2.0 20.7 1.0
NE2 A:HIS66 2.0 22.5 1.0
SG A:CYS43 2.2 31.5 1.0
SG A:CYS153 2.3 13.9 1.0
CE1 A:HIS66 2.9 22.5 1.0
CD2 A:HIS66 3.0 22.5 1.0
CB A:CYS153 3.1 13.9 1.0
CD A:GLU67 3.1 20.7 1.0
CB A:CYS43 3.3 31.5 1.0
CG A:GLU67 3.7 20.7 1.0
ND1 A:HIS66 4.0 22.5 1.0
CG A:HIS66 4.1 22.5 1.0
OE1 A:GLU67 4.1 20.7 1.0
NH2 A:ARG340 4.3 31.4 1.0
OG1 A:THR45 4.4 31.0 1.0
CA A:CYS153 4.5 13.9 1.0
CB A:THR45 4.5 31.0 1.0
CA A:CYS43 4.6 31.5 1.0
C A:CYS153 4.9 13.9 1.0
N A:CYS43 5.0 31.5 1.0

Zinc binding site 2 out of 8 in 7kcq

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Zinc binding site 2 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:69.2
occ:1.00
 SG A:CYS97 2.3 27.7 1.0
SG A:CYS103 2.4 17.3 1.0
SG A:CYS111 2.4 24.1 1.0
SG A:CYS100 2.4 18.6 1.0
N A:CYS97 2.8 27.7 1.0
N A:MET98 2.9 25.3 1.0
CA A:CYS97 3.3 27.7 1.0
CB A:CYS97 3.4 27.7 1.0
C A:CYS97 3.4 27.7 1.0
CB A:CYS111 3.5 24.1 1.0
CB A:CYS103 3.5 17.3 1.0
CB A:CYS100 3.6 18.6 1.0
N A:CYS100 3.8 18.6 1.0
CB A:SER96 3.8 25.1 1.0
C A:SER96 3.8 25.1 1.0
CA A:MET98 4.0 25.3 1.0
N A:ALA99 4.0 21.8 1.0
CA A:CYS100 4.3 18.6 1.0
CA A:SER96 4.3 25.1 1.0
C A:MET98 4.5 25.3 1.0
O A:CYS97 4.5 27.7 1.0
OG A:SER96 4.6 25.1 1.0
CA A:CYS111 4.6 24.1 1.0
CA A:CYS103 4.7 17.3 1.0
N A:CYS103 4.7 17.3 1.0
O A:SER96 4.8 25.1 1.0
C A:ALA99 4.9 21.8 1.0

Zinc binding site 3 out of 8 in 7kcq

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Zinc binding site 3 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:51.9
occ:1.00
 OE2 B:GLU67 2.0 20.3 1.0
NE2 B:HIS66 2.0 22.2 1.0
SG B:CYS43 2.2 31.5 1.0
SG B:CYS153 2.3 13.8 1.0
CE1 B:HIS66 2.9 22.2 1.0
CD2 B:HIS66 3.0 22.2 1.0
CB B:CYS153 3.1 13.8 1.0
CD B:GLU67 3.1 20.3 1.0
CB B:CYS43 3.3 31.5 1.0
CG B:GLU67 3.7 20.3 1.0
ND1 B:HIS66 4.0 22.2 1.0
CG B:HIS66 4.1 22.2 1.0
OE1 B:GLU67 4.1 20.3 1.0
NH2 B:ARG340 4.3 31.9 1.0
OG1 B:THR45 4.4 30.8 1.0
CA B:CYS153 4.5 13.8 1.0
CB B:THR45 4.5 30.8 1.0
CA B:CYS43 4.6 31.5 1.0
C B:CYS153 4.9 13.8 1.0
N B:CYS43 5.0 31.5 1.0

Zinc binding site 4 out of 8 in 7kcq

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Zinc binding site 4 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:70.3
occ:1.00
 SG B:CYS97 2.3 26.9 1.0
SG B:CYS103 2.4 17.3 1.0
SG B:CYS111 2.4 23.8 1.0
SG B:CYS100 2.4 18.6 1.0
N B:CYS97 2.8 26.9 1.0
N B:MET98 2.9 24.7 1.0
CA B:CYS97 3.3 26.9 1.0
CB B:CYS97 3.4 26.9 1.0
C B:CYS97 3.4 26.9 1.0
CB B:CYS111 3.5 23.8 1.0
CB B:CYS103 3.5 17.3 1.0
CB B:CYS100 3.6 18.6 1.0
N B:CYS100 3.8 18.6 1.0
CB B:SER96 3.8 24.5 1.0
C B:SER96 3.8 24.5 1.0
CA B:MET98 4.0 24.7 1.0
N B:ALA99 4.0 21.4 1.0
CA B:CYS100 4.3 18.6 1.0
CA B:SER96 4.3 24.5 1.0
C B:MET98 4.5 24.7 1.0
O B:CYS97 4.5 26.9 1.0
OG B:SER96 4.6 24.5 1.0
CA B:CYS111 4.6 23.8 1.0
CA B:CYS103 4.7 17.3 1.0
N B:CYS103 4.7 17.3 1.0
O B:SER96 4.8 24.5 1.0
C B:ALA99 4.9 21.4 1.0

Zinc binding site 5 out of 8 in 7kcq

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Zinc binding site 5 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:51.6
occ:1.00
 OE2 C:GLU67 2.0 20.2 1.0
NE2 C:HIS66 2.0 22.3 1.0
SG C:CYS43 2.2 31.1 1.0
SG C:CYS153 2.3 13.8 1.0
CE1 C:HIS66 2.9 22.3 1.0
CD2 C:HIS66 3.0 22.3 1.0
CB C:CYS153 3.1 13.8 1.0
CD C:GLU67 3.1 20.2 1.0
CB C:CYS43 3.3 31.1 1.0
CG C:GLU67 3.7 20.2 1.0
ND1 C:HIS66 4.0 22.3 1.0
CG C:HIS66 4.1 22.3 1.0
OE1 C:GLU67 4.1 20.2 1.0
NH2 C:ARG340 4.3 30.4 1.0
OG1 C:THR45 4.4 30.9 1.0
CA C:CYS153 4.5 13.8 1.0
CB C:THR45 4.5 30.9 1.0
CA C:CYS43 4.6 31.1 1.0
C C:CYS153 4.9 13.8 1.0
N C:CYS43 5.0 31.1 1.0

Zinc binding site 6 out of 8 in 7kcq

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Zinc binding site 6 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:69.5
occ:1.00
 SG C:CYS97 2.3 27.8 1.0
SG C:CYS103 2.4 17.6 1.0
SG C:CYS111 2.4 24.2 1.0
SG C:CYS100 2.4 18.9 1.0
N C:CYS97 2.8 27.8 1.0
N C:MET98 2.9 25.1 1.0
CA C:CYS97 3.3 27.8 1.0
CB C:CYS97 3.4 27.8 1.0
C C:CYS97 3.4 27.8 1.0
CB C:CYS111 3.5 24.2 1.0
CB C:CYS103 3.5 17.6 1.0
CB C:CYS100 3.6 18.9 1.0
N C:CYS100 3.8 18.9 1.0
CB C:SER96 3.8 24.9 1.0
C C:SER96 3.8 24.9 1.0
CA C:MET98 3.9 25.1 1.0
N C:ALA99 4.0 22.0 1.0
CA C:CYS100 4.3 18.9 1.0
CA C:SER96 4.3 24.9 1.0
C C:MET98 4.5 25.1 1.0
O C:CYS97 4.5 27.8 1.0
OG C:SER96 4.6 24.9 1.0
CA C:CYS111 4.6 24.2 1.0
CA C:CYS103 4.7 17.6 1.0
N C:CYS103 4.7 17.6 1.0
O C:SER96 4.8 24.9 1.0
C C:ALA99 4.9 22.0 1.0

Zinc binding site 7 out of 8 in 7kcq

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Zinc binding site 7 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:51.0
occ:1.00
 OE2 D:GLU67 2.0 20.0 1.0
NE2 D:HIS66 2.0 21.8 1.0
SG D:CYS43 2.2 30.9 1.0
SG D:CYS153 2.3 13.5 1.0
CE1 D:HIS66 2.9 21.8 1.0
CD2 D:HIS66 3.0 21.8 1.0
CB D:CYS153 3.1 13.5 1.0
CD D:GLU67 3.1 20.0 1.0
CB D:CYS43 3.3 30.9 1.0
CG D:GLU67 3.7 20.0 1.0
ND1 D:HIS66 4.0 21.8 1.0
CG D:HIS66 4.1 21.8 1.0
OE1 D:GLU67 4.1 20.0 1.0
NH2 D:ARG340 4.3 31.0 1.0
OG1 D:THR45 4.4 30.9 1.0
CA D:CYS153 4.5 13.5 1.0
CB D:THR45 4.5 30.9 1.0
CA D:CYS43 4.6 30.9 1.0
C D:CYS153 4.9 13.5 1.0
N D:CYS43 5.0 30.9 1.0

Zinc binding site 8 out of 8 in 7kcq

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Zinc binding site 8 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:68.6
occ:1.00
 SG D:CYS97 2.3 27.1 1.0
SG D:CYS103 2.4 17.3 1.0
SG D:CYS111 2.4 24.1 1.0
SG D:CYS100 2.4 18.7 1.0
N D:CYS97 2.8 27.1 1.0
N D:MET98 2.9 24.9 1.0
CA D:CYS97 3.3 27.1 1.0
CB D:CYS97 3.4 27.1 1.0
C D:CYS97 3.4 27.1 1.0
CB D:CYS111 3.5 24.1 1.0
CB D:CYS103 3.5 17.3 1.0
CB D:CYS100 3.6 18.7 1.0
N D:CYS100 3.8 18.7 1.0
CB D:SER96 3.8 24.4 1.0
C D:SER96 3.8 24.4 1.0
CA D:MET98 3.9 24.9 1.0
N D:ALA99 4.0 21.6 1.0
CA D:CYS100 4.3 18.7 1.0
CA D:SER96 4.3 24.4 1.0
C D:MET98 4.5 24.9 1.0
O D:CYS97 4.5 27.1 1.0
OG D:SER96 4.6 24.4 1.0
CA D:CYS111 4.6 24.1 1.0
CA D:CYS103 4.7 17.3 1.0
N D:CYS103 4.7 17.3 1.0
O D:SER96 4.8 24.4 1.0
C D:ALA99 4.9 21.6 1.0

Reference:

S.R.Guntupalli, Z.Li, L.Chang, B.V.Plapp, R.Subramanian. Cryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase. Biochemistry V. 60 663 2021.
ISSN: ISSN 0006-2960
PubMed: 33620215
DOI: 10.1021/ACS.BIOCHEM.0C00921
Page generated: Tue Oct 29 22:06:00 2024

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