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Zinc in PDB 7kc2: Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh

Enzymatic activity of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh

All present enzymatic activity of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh:
1.1.1.1;

Zinc Binding Sites:

The binding sites of Zinc atom in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh (pdb code 7kc2). 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 -Closed Form with Nadh, PDB code: 7kc2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7kc2

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Zinc binding site 1 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh


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 -Closed Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:72.2
occ:1.00
 SG A:CYS111 2.3 41.2 1.0
SG A:CYS100 2.3 36.6 1.0
SG A:CYS103 2.3 37.1 1.0
SG A:CYS97 2.3 44.1 1.0
CB A:CYS111 3.3 41.2 1.0
CB A:CYS100 3.5 36.6 1.0
CB A:CYS103 3.7 37.1 1.0
CB A:CYS97 3.8 44.1 1.0
N A:CYS100 3.9 36.6 1.0
N A:CYS97 3.9 44.1 1.0
N A:MET98 4.1 40.8 1.0
N A:CYS103 4.2 37.1 1.0
CA A:CYS100 4.2 36.6 1.0
CA A:CYS97 4.3 44.1 1.0
CA A:CYS111 4.4 41.2 1.0
N A:ALA99 4.5 37.4 1.0
CB A:SER96 4.5 43.3 1.0
C A:CYS97 4.6 44.1 1.0
CA A:CYS103 4.6 37.1 1.0
CD A:PRO112 4.7 43.5 1.0
C A:CYS100 4.9 36.6 1.0
CA A:MET98 4.9 40.8 1.0
C A:SER96 5.0 43.3 1.0

Zinc binding site 2 out of 8 in 7kc2

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Zinc binding site 2 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh


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 -Closed Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:72.8
occ:1.00
 SG A:CYS153 2.3 35.1 1.0
C5N A:NAD403 2.3 40.7 1.0
SG A:CYS43 2.3 47.0 1.0
NE2 A:HIS66 2.3 42.6 1.0
O A:HOH501 3.1 36.8 1.0
C6N A:NAD403 3.2 40.7 1.0
CE1 A:HIS66 3.2 42.6 1.0
C4N A:NAD403 3.2 40.7 1.0
OG1 A:THR45 3.3 47.3 1.0
CD2 A:HIS66 3.3 42.6 1.0
CB A:CYS43 3.4 47.0 1.0
CB A:THR45 3.7 47.3 1.0
CB A:CYS153 4.0 35.1 1.0
OE2 A:GLU67 4.2 41.9 1.0
ND1 A:HIS66 4.3 42.6 1.0
N1N A:NAD403 4.4 40.7 1.0
CG A:HIS66 4.4 42.6 1.0
O A:CYS153 4.5 35.1 1.0
C3N A:NAD403 4.5 40.7 1.0
CG2 A:THR45 4.5 47.3 1.0
N A:THR45 4.6 47.3 1.0
C A:CYS153 4.7 35.1 1.0
NH2 A:ARG340 4.8 45.0 1.0
CA A:CYS43 4.8 47.0 1.0
CA A:THR45 4.8 47.3 1.0
C2N A:NAD403 5.0 40.7 1.0
CA A:CYS153 5.0 35.1 1.0

Zinc binding site 3 out of 8 in 7kc2

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Zinc binding site 3 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh


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 -Closed Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:74.5
occ:1.00
 SG B:CYS111 2.3 41.0 1.0
SG B:CYS100 2.3 36.9 1.0
SG B:CYS97 2.3 44.6 1.0
SG B:CYS103 2.3 37.5 1.0
CB B:CYS111 3.3 41.0 1.0
CB B:CYS100 3.5 36.9 1.0
CB B:CYS103 3.7 37.5 1.0
CB B:CYS97 3.8 44.6 1.0
N B:CYS100 3.9 36.9 1.0
N B:CYS97 3.9 44.6 1.0
N B:MET98 4.1 41.3 1.0
N B:CYS103 4.2 37.5 1.0
CA B:CYS100 4.2 36.9 1.0
CA B:CYS97 4.3 44.6 1.0
CA B:CYS111 4.4 41.0 1.0
N B:ALA99 4.5 38.9 1.0
CB B:SER96 4.5 43.1 1.0
C B:CYS97 4.6 44.6 1.0
CA B:CYS103 4.6 37.5 1.0
CD B:PRO112 4.7 42.5 1.0
C B:CYS100 4.9 36.9 1.0
CA B:MET98 4.9 41.3 1.0
C B:SER96 5.0 43.1 1.0

Zinc binding site 4 out of 8 in 7kc2

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Zinc binding site 4 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh


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 -Closed Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:73.0
occ:1.00
 SG B:CYS153 2.3 34.7 1.0
C5N B:NAD403 2.3 41.4 1.0
SG B:CYS43 2.3 47.2 1.0
NE2 B:HIS66 2.3 42.1 1.0
O B:HOH501 3.1 36.9 1.0
C6N B:NAD403 3.2 41.4 1.0
CE1 B:HIS66 3.2 42.1 1.0
C4N B:NAD403 3.2 41.4 1.0
OG1 B:THR45 3.3 47.5 1.0
CD2 B:HIS66 3.3 42.1 1.0
CB B:CYS43 3.4 47.2 1.0
CB B:THR45 3.7 47.5 1.0
CB B:CYS153 4.0 34.7 1.0
OE2 B:GLU67 4.2 42.1 1.0
ND1 B:HIS66 4.3 42.1 1.0
N1N B:NAD403 4.4 41.4 1.0
CG B:HIS66 4.4 42.1 1.0
O B:CYS153 4.5 34.7 1.0
C3N B:NAD403 4.5 41.4 1.0
CG2 B:THR45 4.5 47.5 1.0
N B:THR45 4.6 47.5 1.0
C B:CYS153 4.7 34.7 1.0
NH2 B:ARG340 4.8 44.6 1.0
CA B:CYS43 4.8 47.2 1.0
CA B:THR45 4.8 47.5 1.0
C2N B:NAD403 5.0 41.4 1.0
CA B:CYS153 5.0 34.7 1.0

Zinc binding site 5 out of 8 in 7kc2

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Zinc binding site 5 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh


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 -Closed Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:74.1
occ:1.00
 SG C:CYS111 2.3 42.0 1.0
SG C:CYS100 2.3 36.7 1.0
SG C:CYS103 2.3 37.4 1.0
SG C:CYS97 2.3 44.4 1.0
CB C:CYS111 3.3 42.0 1.0
CB C:CYS100 3.5 36.7 1.0
CB C:CYS103 3.7 37.4 1.0
CB C:CYS97 3.8 44.4 1.0
N C:CYS100 3.9 36.7 1.0
N C:CYS97 3.9 44.4 1.0
N C:MET98 4.1 41.5 1.0
N C:CYS103 4.2 37.4 1.0
CA C:CYS100 4.2 36.7 1.0
CA C:CYS97 4.3 44.4 1.0
CA C:CYS111 4.4 42.0 1.0
N C:ALA99 4.5 38.5 1.0
CB C:SER96 4.5 42.7 1.0
C C:CYS97 4.6 44.4 1.0
CA C:CYS103 4.6 37.4 1.0
CD C:PRO112 4.7 44.1 1.0
C C:CYS100 4.9 36.7 1.0
CA C:MET98 4.9 41.5 1.0
C C:SER96 5.0 42.7 1.0

Zinc binding site 6 out of 8 in 7kc2

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Zinc binding site 6 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh


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 -Closed Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:72.5
occ:1.00
 SG C:CYS153 2.3 34.6 1.0
C5N C:NAD403 2.3 43.1 1.0
SG C:CYS43 2.3 47.1 1.0
NE2 C:HIS66 2.3 42.2 1.0
O C:HOH501 3.0 37.0 1.0
C6N C:NAD403 3.2 43.1 1.0
CE1 C:HIS66 3.2 42.2 1.0
C4N C:NAD403 3.2 43.1 1.0
OG1 C:THR45 3.3 47.7 1.0
CD2 C:HIS66 3.3 42.2 1.0
CB C:CYS43 3.4 47.1 1.0
CB C:THR45 3.7 47.7 1.0
CB C:CYS153 4.0 34.6 1.0
OE2 C:GLU67 4.2 42.0 1.0
ND1 C:HIS66 4.3 42.2 1.0
N1N C:NAD403 4.4 43.1 1.0
CG C:HIS66 4.4 42.2 1.0
O C:CYS153 4.5 34.6 1.0
C3N C:NAD403 4.5 43.1 1.0
CG2 C:THR45 4.5 47.7 1.0
N C:THR45 4.6 47.7 1.0
C C:CYS153 4.7 34.6 1.0
NH2 C:ARG340 4.8 44.4 1.0
CA C:CYS43 4.8 47.1 1.0
CA C:THR45 4.8 47.7 1.0
C2N C:NAD403 5.0 43.1 1.0
CA C:CYS153 5.0 34.6 1.0

Zinc binding site 7 out of 8 in 7kc2

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Zinc binding site 7 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh


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 -Closed Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:73.0
occ:1.00
 SG D:CYS111 2.3 41.3 1.0
SG D:CYS100 2.3 36.8 1.0
SG D:CYS97 2.3 44.2 1.0
SG D:CYS103 2.3 37.5 1.0
CB D:CYS111 3.3 41.3 1.0
CB D:CYS100 3.5 36.8 1.0
CB D:CYS103 3.7 37.5 1.0
CB D:CYS97 3.8 44.2 1.0
N D:CYS100 3.9 36.8 1.0
N D:CYS97 3.9 44.2 1.0
N D:MET98 4.1 40.6 1.0
N D:CYS103 4.2 37.5 1.0
CA D:CYS100 4.2 36.8 1.0
CA D:CYS97 4.3 44.2 1.0
CA D:CYS111 4.4 41.3 1.0
N D:ALA99 4.5 37.8 1.0
CB D:SER96 4.5 43.1 1.0
C D:CYS97 4.6 44.2 1.0
CA D:CYS103 4.6 37.5 1.0
CD D:PRO112 4.7 43.3 1.0
C D:CYS100 4.9 36.8 1.0
CA D:MET98 4.9 40.6 1.0
C D:SER96 5.0 43.1 1.0

Zinc binding site 8 out of 8 in 7kc2

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Zinc binding site 8 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nadh


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 -Closed Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:71.2
occ:1.00
 SG D:CYS153 2.3 34.7 1.0
C5N D:NAD403 2.3 41.3 1.0
SG D:CYS43 2.3 47.1 1.0
NE2 D:HIS66 2.3 42.0 1.0
O D:HOH501 3.1 36.4 1.0
C6N D:NAD403 3.2 41.3 1.0
CE1 D:HIS66 3.2 42.0 1.0
C4N D:NAD403 3.2 41.3 1.0
OG1 D:THR45 3.3 48.0 1.0
CD2 D:HIS66 3.3 42.0 1.0
CB D:CYS43 3.4 47.1 1.0
CB D:THR45 3.7 48.0 1.0
CB D:CYS153 4.0 34.7 1.0
OE2 D:GLU67 4.2 41.5 1.0
ND1 D:HIS66 4.3 42.0 1.0
N1N D:NAD403 4.4 41.3 1.0
CG D:HIS66 4.4 42.0 1.0
O D:CYS153 4.5 34.7 1.0
C3N D:NAD403 4.5 41.3 1.0
CG2 D:THR45 4.5 48.0 1.0
N D:THR45 4.6 48.0 1.0
C D:CYS153 4.7 34.7 1.0
NH2 D:ARG340 4.8 45.1 1.0
CA D:CYS43 4.8 47.1 1.0
CA D:THR45 4.8 48.0 1.0
C2N D:NAD403 5.0 41.3 1.0
CA D:CYS153 5.0 34.7 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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