Zinc in PDB 7kjy: Symmetry in Yeast Alcohol Dehydrogenase 1 - Open Form with Nadh

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

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

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 7kjy

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Zinc binding site 1 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 - Open 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 - Open Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:162.7
occ:1.00
NE2 A:HIS66 2.0 131.6 1.0
SG A:CYS153 2.2 113.6 1.0
SG A:CYS43 2.2 141.6 1.0
OE2 A:GLU67 2.3 130.1 1.0
CD A:GLU67 2.7 130.1 1.0
CB A:CYS153 2.8 113.6 1.0
CE1 A:HIS66 2.8 131.6 1.0
CD2 A:HIS66 3.0 131.6 1.0
CG A:GLU67 3.0 130.1 1.0
OE1 A:GLU67 3.5 130.1 1.0
CB A:CYS43 3.6 141.6 1.0
ND1 A:HIS66 3.9 131.6 1.0
CG A:HIS66 4.0 131.6 1.0
CA A:CYS153 4.1 113.6 1.0
C A:CYS153 4.3 113.6 1.0
C5N A:NAD403 4.4 124.8 1.0
N A:ALA154 4.5 103.8 1.0
CB A:GLU67 4.5 130.1 1.0
OG1 A:THR45 4.8 141.7 1.0
O A:CYS153 4.8 113.6 1.0
CA A:CYS43 4.8 141.6 1.0
C4N A:NAD403 4.8 124.8 1.0
N A:CYS153 4.9 113.6 1.0
N A:CYS43 4.9 141.6 1.0

Zinc binding site 2 out of 8 in 7kjy

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Zinc binding site 2 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 - Open 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 - Open Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:181.6
occ:1.00
SG A:CYS103 2.3 130.5 1.0
SG A:CYS100 2.3 133.7 1.0
SG A:CYS97 2.3 138.0 1.0
SG A:CYS111 2.3 131.4 1.0
CB A:CYS100 3.3 133.7 1.0
N A:CYS100 3.4 133.7 1.0
CB A:CYS97 3.4 138.0 1.0
CB A:CYS111 3.4 131.4 1.0
CB A:CYS103 3.4 130.5 1.0
N A:MET98 3.5 130.9 1.0
N A:CYS97 3.5 138.0 1.0
CA A:CYS97 3.7 138.0 1.0
C A:CYS97 3.7 138.0 1.0
N A:ALA99 3.8 129.6 1.0
CA A:CYS100 3.9 133.7 1.0
CA A:CYS111 4.2 131.4 1.0
OG A:SER96 4.4 131.8 1.0
CA A:MET98 4.4 130.9 1.0
C A:ALA99 4.4 129.6 1.0
CA A:CYS103 4.5 130.5 1.0
N A:CYS103 4.6 130.5 1.0
C A:MET98 4.6 130.9 1.0
C A:SER96 4.6 131.8 1.0
O A:CYS97 4.6 138.0 1.0
CA A:ALA99 4.7 129.6 1.0
C A:CYS100 4.7 133.7 1.0
CB A:SER96 4.9 131.8 1.0
CD A:PRO112 4.9 130.6 1.0
ND1 A:HIS113 5.0 131.8 1.0
C A:CYS111 5.0 131.4 1.0

Zinc binding site 3 out of 8 in 7kjy

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Zinc binding site 3 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 - Open 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 - Open Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:161.7
occ:1.00
NE2 B:HIS66 2.0 131.0 1.0
SG B:CYS153 2.2 114.3 1.0
SG B:CYS43 2.2 140.2 1.0
OE2 B:GLU67 2.3 129.1 1.0
CD B:GLU67 2.7 129.1 1.0
CB B:CYS153 2.8 114.3 1.0
CE1 B:HIS66 2.8 131.0 1.0
CD2 B:HIS66 3.0 131.0 1.0
CG B:GLU67 3.0 129.1 1.0
OE1 B:GLU67 3.5 129.1 1.0
CB B:CYS43 3.6 140.2 1.0
ND1 B:HIS66 3.9 131.0 1.0
CG B:HIS66 4.0 131.0 1.0
CA B:CYS153 4.1 114.3 1.0
C B:CYS153 4.3 114.3 1.0
C5N B:NAD403 4.4 124.6 1.0
N B:ALA154 4.5 104.0 1.0
CB B:GLU67 4.5 129.1 1.0
OG1 B:THR45 4.8 141.1 1.0
O B:CYS153 4.8 114.3 1.0
CA B:CYS43 4.8 140.2 1.0
C4N B:NAD403 4.8 124.6 1.0
N B:CYS153 4.9 114.3 1.0
N B:CYS43 4.9 140.2 1.0

Zinc binding site 4 out of 8 in 7kjy

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Zinc binding site 4 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 - Open 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 - Open Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:180.6
occ:1.00
SG B:CYS103 2.3 129.2 1.0
SG B:CYS97 2.3 138.5 1.0
SG B:CYS100 2.3 133.1 1.0
SG B:CYS111 2.3 130.3 1.0
CB B:CYS100 3.3 133.1 1.0
CB B:CYS97 3.3 138.5 1.0
CB B:CYS111 3.4 130.3 1.0
CB B:CYS103 3.4 129.2 1.0
N B:CYS100 3.4 133.1 1.0
N B:MET98 3.5 131.3 1.0
N B:CYS97 3.5 138.5 1.0
CA B:CYS97 3.6 138.5 1.0
C B:CYS97 3.8 138.5 1.0
N B:ALA99 3.9 130.6 1.0
CA B:CYS100 3.9 133.1 1.0
CA B:CYS111 4.1 130.3 1.0
OG B:SER96 4.4 132.4 1.0
CA B:MET98 4.4 131.3 1.0
C B:ALA99 4.5 130.6 1.0
CA B:CYS103 4.5 129.2 1.0
N B:CYS103 4.5 129.2 1.0
O B:CYS97 4.6 138.5 1.0
C B:MET98 4.7 131.3 1.0
C B:SER96 4.7 132.4 1.0
C B:CYS100 4.7 133.1 1.0
CA B:ALA99 4.7 130.6 1.0
CD B:PRO112 4.8 129.4 1.0
C B:CYS111 4.9 130.3 1.0
CB B:SER96 4.9 132.4 1.0
ND1 B:HIS113 5.0 129.1 1.0

Zinc binding site 5 out of 8 in 7kjy

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Zinc binding site 5 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 - Open 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 - Open Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:164.4
occ:1.00
NE2 C:HIS66 2.0 131.5 1.0
SG C:CYS153 2.2 114.2 1.0
SG C:CYS43 2.2 141.9 1.0
OE2 C:GLU67 2.3 130.6 1.0
CD C:GLU67 2.7 130.6 1.0
CB C:CYS153 2.8 114.2 1.0
CE1 C:HIS66 2.8 131.5 1.0
CD2 C:HIS66 3.0 131.5 1.0
CG C:GLU67 3.0 130.6 1.0
OE1 C:GLU67 3.5 130.6 1.0
CB C:CYS43 3.6 141.9 1.0
ND1 C:HIS66 3.9 131.5 1.0
CG C:HIS66 4.0 131.5 1.0
CA C:CYS153 4.1 114.2 1.0
C C:CYS153 4.3 114.2 1.0
C5N C:NAD403 4.4 127.5 1.0
N C:ALA154 4.5 104.2 1.0
CB C:GLU67 4.5 130.6 1.0
OG1 C:THR45 4.8 142.4 1.0
O C:CYS153 4.8 114.2 1.0
CA C:CYS43 4.8 141.9 1.0
C4N C:NAD403 4.8 127.5 1.0
N C:CYS153 4.9 114.2 1.0
N C:CYS43 4.9 141.9 1.0

Zinc binding site 6 out of 8 in 7kjy

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Zinc binding site 6 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 - Open 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 - Open Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:183.0
occ:1.00
SG C:CYS103 2.3 130.5 1.0
SG C:CYS97 2.3 137.9 1.0
SG C:CYS100 2.3 133.5 1.0
SG C:CYS111 2.3 131.1 1.0
CB C:CYS100 3.3 133.5 1.0
CB C:CYS97 3.4 137.9 1.0
CB C:CYS111 3.4 131.1 1.0
N C:CYS100 3.4 133.5 1.0
CB C:CYS103 3.4 130.5 1.0
N C:MET98 3.5 131.0 1.0
N C:CYS97 3.5 137.9 1.0
CA C:CYS97 3.7 137.9 1.0
C C:CYS97 3.8 137.9 1.0
N C:ALA99 3.8 129.8 1.0
CA C:CYS100 3.9 133.5 1.0
CA C:CYS111 4.2 131.1 1.0
OG C:SER96 4.4 130.7 1.0
CA C:MET98 4.4 131.0 1.0
C C:ALA99 4.5 129.8 1.0
CA C:CYS103 4.5 130.5 1.0
N C:CYS103 4.5 130.5 1.0
O C:CYS97 4.6 137.9 1.0
C C:MET98 4.6 131.0 1.0
C C:SER96 4.7 130.7 1.0
CA C:ALA99 4.7 129.8 1.0
C C:CYS100 4.7 133.5 1.0
CD C:PRO112 4.9 129.2 1.0
CB C:SER96 4.9 130.7 1.0
ND1 C:HIS113 5.0 129.5 1.0
C C:CYS111 5.0 131.1 1.0

Zinc binding site 7 out of 8 in 7kjy

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Zinc binding site 7 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 - Open 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 - Open Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:164.1
occ:1.00
NE2 D:HIS66 2.0 131.8 1.0
SG D:CYS153 2.2 112.4 1.0
SG D:CYS43 2.2 141.0 1.0
OE2 D:GLU67 2.3 129.9 1.0
CD D:GLU67 2.7 129.9 1.0
CB D:CYS153 2.8 112.4 1.0
CE1 D:HIS66 2.8 131.8 1.0
CD2 D:HIS66 3.0 131.8 1.0
CG D:GLU67 3.0 129.9 1.0
OE1 D:GLU67 3.5 129.9 1.0
CB D:CYS43 3.6 141.0 1.0
ND1 D:HIS66 3.9 131.8 1.0
CG D:HIS66 4.0 131.8 1.0
CA D:CYS153 4.1 112.4 1.0
C D:CYS153 4.3 112.4 1.0
C5N D:NAD403 4.4 126.6 1.0
N D:ALA154 4.5 102.4 1.0
CB D:GLU67 4.5 129.9 1.0
OG1 D:THR45 4.8 142.9 1.0
O D:CYS153 4.8 112.4 1.0
CA D:CYS43 4.8 141.0 1.0
C4N D:NAD403 4.8 126.6 1.0
N D:CYS153 4.9 112.4 1.0
N D:CYS43 4.9 141.0 1.0

Zinc binding site 8 out of 8 in 7kjy

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Zinc binding site 8 out of 8 in the Symmetry in Yeast Alcohol Dehydrogenase 1 - Open 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 - Open Form with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:179.9
occ:1.00
SG D:CYS103 2.3 129.4 1.0
SG D:CYS97 2.3 136.8 1.0
SG D:CYS100 2.3 131.9 1.0
SG D:CYS111 2.3 129.5 1.0
CB D:CYS100 3.3 131.9 1.0
CB D:CYS97 3.3 136.8 1.0
CB D:CYS111 3.4 129.5 1.0
CB D:CYS103 3.4 129.4 1.0
N D:CYS100 3.4 131.9 1.0
N D:CYS97 3.5 136.8 1.0
N D:MET98 3.6 129.7 1.0
CA D:CYS97 3.7 136.8 1.0
C D:CYS97 3.8 136.8 1.0
N D:ALA99 3.9 128.6 1.0
CA D:CYS100 3.9 131.9 1.0
CA D:CYS111 4.1 129.5 1.0
CA D:MET98 4.5 129.7 1.0
CA D:CYS103 4.5 129.4 1.0
N D:CYS103 4.5 129.4 1.0
C D:ALA99 4.5 128.6 1.0
O D:CYS97 4.7 136.8 1.0
C D:MET98 4.7 129.7 1.0
C D:SER96 4.7 130.6 1.0
CA D:ALA99 4.8 128.6 1.0
CD D:PRO112 4.8 127.1 1.0
C D:CYS100 4.8 131.9 1.0
C D:CYS111 4.9 129.5 1.0
ND1 D:HIS113 5.0 126.9 1.0
CB D:SER96 5.0 130.6 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: Sat Apr 3 18:37:00 2021

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