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Zinc in PDB 3cos: Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn

Enzymatic activity of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn

All present enzymatic activity of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn:
1.1.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn, PDB code: 3cos was solved by K.L.Kavanagh, N.Shafqat, W.Yue, F.Von Delft, S.Bishop, A.Roos, J.Murray, A.M.Edwards, C.H.Arrowsmith, C.Bountra, U.Oppermann, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.299, 160.919, 88.739, 90.00, 111.64, 90.00
R / Rfree (%) 16.9 / 20.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn (pdb code 3cos). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn, PDB code: 3cos:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3cos

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Zinc binding site 1 out of 8 in the Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:20.0
occ:1.00
 NE2 A:HIS69 2.1 22.1 1.0
OXT A:ACY401 2.2 26.6 1.0
SG A:CYS180 2.3 20.7 1.0
SG A:CYS47 2.3 20.9 1.0
CD2 A:HIS69 3.1 25.6 1.0
CE1 A:HIS69 3.1 25.7 1.0
CB A:CYS47 3.3 22.2 1.0
C A:ACY401 3.3 30.4 1.0
CB A:CYS180 3.4 23.1 1.0
C5N A:NAD400 3.4 16.0 1.0
O A:ACY401 3.6 35.6 1.0
C6N A:NAD400 3.9 20.0 1.0
CB A:THR49 4.0 24.2 1.0
OG1 A:THR49 4.0 21.7 1.0
ND1 A:HIS69 4.2 22.7 1.0
C4N A:NAD400 4.2 23.3 1.0
CG A:HIS69 4.2 21.1 1.0
CH3 A:ACY401 4.6 30.0 1.0
CA A:CYS47 4.7 22.1 1.0
OE2 A:GLU70 4.7 26.3 1.0
CA A:CYS180 4.7 21.6 1.0
CE2 A:TYR95 4.8 22.5 1.0
OH A:TYR95 4.8 22.2 1.0
CG2 A:THR49 4.8 20.3 1.0
N1N A:NAD400 4.9 13.2 1.0
CZ A:TYR95 5.0 23.1 1.0

Zinc binding site 2 out of 8 in 3cos

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Zinc binding site 2 out of 8 in the Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:26.2
occ:1.00
 SG A:CYS105 2.3 24.4 1.0
SG A:CYS99 2.3 24.3 1.0
SG A:CYS113 2.5 25.4 1.0
SG A:CYS102 2.5 21.5 1.0
CB A:CYS99 3.3 26.3 1.0
CB A:CYS105 3.3 24.3 1.0
CB A:CYS113 3.4 23.9 1.0
N A:CYS99 3.5 24.3 1.0
CB A:CYS102 3.5 23.1 1.0
CA A:CYS113 3.7 24.0 1.0
CA A:CYS99 3.8 24.8 1.0
N A:ARG100 3.9 26.5 1.0
N A:GLY114 4.0 26.5 1.0
N A:CYS102 4.0 25.3 1.0
C A:CYS99 4.2 24.8 1.0
N A:CYS105 4.2 24.5 1.0
CA A:CYS102 4.3 23.6 1.0
C A:CYS113 4.3 24.7 1.0
CA A:CYS105 4.3 23.9 1.0
N A:LYS101 4.5 26.6 1.0
C A:LEU98 4.6 23.7 1.0
CA A:ARG100 4.9 26.3 1.0
C A:CYS102 4.9 23.8 1.0
CA A:LEU98 4.9 24.7 1.0

Zinc binding site 3 out of 8 in 3cos

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Zinc binding site 3 out of 8 in the Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:21.8
occ:1.00
 NE2 B:HIS69 2.1 20.2 1.0
OXT B:ACY401 2.2 25.6 1.0
SG B:CYS47 2.3 21.3 1.0
SG B:CYS180 2.4 21.7 1.0
CD2 B:HIS69 3.1 26.2 1.0
CE1 B:HIS69 3.1 25.2 1.0
CB B:CYS47 3.2 22.8 1.0
C B:ACY401 3.3 33.7 1.0
CB B:CYS180 3.4 20.9 1.0
C5N B:NAD400 3.5 19.4 1.0
O B:ACY401 3.8 36.4 1.0
OG1 B:THR49 3.9 22.7 1.0
CB B:THR49 3.9 23.2 1.0
C6N B:NAD400 3.9 17.1 1.0
C4N B:NAD400 4.2 27.6 1.0
ND1 B:HIS69 4.2 24.6 1.0
CG B:HIS69 4.2 23.6 1.0
CH3 B:ACY401 4.6 32.1 1.0
CG2 B:THR49 4.6 24.8 1.0
CA B:CYS47 4.7 22.1 1.0
OE2 B:GLU70 4.7 29.0 1.0
CA B:CYS180 4.8 21.7 1.0
CE2 B:TYR95 4.8 23.0 1.0
OH B:TYR95 4.8 20.4 1.0
N1N B:NAD400 4.9 22.4 1.0
N B:THR49 5.0 23.1 1.0

Zinc binding site 4 out of 8 in 3cos

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Zinc binding site 4 out of 8 in the Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:26.5
occ:1.00
 SG B:CYS105 2.2 25.6 1.0
SG B:CYS102 2.3 23.2 1.0
SG B:CYS113 2.4 22.9 1.0
SG B:CYS99 2.5 25.0 1.0
CB B:CYS113 3.3 24.1 1.0
CB B:CYS105 3.4 24.0 1.0
CB B:CYS99 3.4 26.5 1.0
CB B:CYS102 3.6 20.9 1.0
CA B:CYS113 3.6 23.9 1.0
N B:CYS99 3.7 24.4 1.0
N B:GLY114 3.7 26.3 1.0
N B:ARG100 3.9 25.2 1.0
N B:CYS102 4.0 24.4 1.0
CA B:CYS99 4.0 25.0 1.0
C B:CYS113 4.1 24.6 1.0
N B:CYS105 4.2 24.5 1.0
CA B:CYS102 4.3 24.6 1.0
C B:CYS99 4.3 24.7 1.0
CA B:CYS105 4.4 23.9 1.0
N B:LYS101 4.5 26.1 1.0
CA B:GLY114 4.8 26.7 1.0
C B:LEU98 4.8 23.7 1.0
N B:LYS115 4.8 26.6 1.0
CA B:ARG100 4.9 25.5 1.0
N B:CYS113 4.9 24.6 1.0
C B:CYS102 4.9 24.6 1.0
O B:LEU112 5.0 24.6 1.0
O B:CYS102 5.0 22.8 1.0

Zinc binding site 5 out of 8 in 3cos

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Zinc binding site 5 out of 8 in the Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:19.6
occ:1.00
 NE2 C:HIS69 2.0 21.6 1.0
OXT C:ACY401 2.3 24.2 1.0
SG C:CYS180 2.3 24.5 1.0
SG C:CYS47 2.4 20.9 1.0
CE1 C:HIS69 3.0 27.1 1.0
CD2 C:HIS69 3.0 26.1 1.0
CB C:CYS47 3.3 23.9 1.0
CB C:CYS180 3.3 19.8 1.0
C C:ACY401 3.4 31.2 1.0
C5N C:NAD400 3.4 17.2 1.0
O C:ACY401 3.9 37.5 1.0
C6N C:NAD400 3.9 13.5 1.0
OG1 C:THR49 4.0 20.9 1.0
CB C:THR49 4.1 22.8 1.0
ND1 C:HIS69 4.1 26.0 1.0
C4N C:NAD400 4.2 22.8 1.0
CG C:HIS69 4.2 23.1 1.0
CH3 C:ACY401 4.7 33.7 1.0
CA C:CYS180 4.7 21.7 1.0
CA C:CYS47 4.8 22.1 1.0
CE2 C:TYR95 4.8 21.9 1.0
OE2 C:GLU70 4.8 28.5 1.0
OH C:TYR95 4.8 23.7 1.0
CG2 C:THR49 4.9 21.1 1.0
N1N C:NAD400 5.0 14.2 1.0

Zinc binding site 6 out of 8 in 3cos

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Zinc binding site 6 out of 8 in the Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:23.1
occ:1.00
 SG C:CYS102 2.2 20.2 1.0
SG C:CYS105 2.3 23.1 1.0
SG C:CYS113 2.4 22.6 1.0
SG C:CYS99 2.4 23.4 1.0
CB C:CYS113 3.3 23.3 1.0
CB C:CYS99 3.4 26.6 1.0
CB C:CYS105 3.4 22.2 1.0
CB C:CYS102 3.4 23.4 1.0
CA C:CYS113 3.6 23.7 1.0
N C:CYS99 3.6 24.1 1.0
N C:GLY114 3.7 26.4 1.0
N C:CYS102 4.0 25.4 1.0
CA C:CYS99 4.0 25.0 1.0
N C:ARG100 4.0 25.1 1.0
C C:CYS113 4.1 24.5 1.0
N C:CYS105 4.3 24.4 1.0
CA C:CYS102 4.3 24.1 1.0
C C:CYS99 4.3 24.7 1.0
CA C:CYS105 4.4 24.0 1.0
N C:LYS101 4.6 26.7 1.0
CA C:GLY114 4.8 26.9 1.0
C C:LEU98 4.8 23.7 1.0
N C:LYS115 4.8 26.7 1.0
N C:CYS113 4.9 24.4 1.0
O C:LEU112 4.9 24.1 1.0
CA C:ARG100 4.9 26.1 1.0
C C:CYS102 5.0 24.1 1.0

Zinc binding site 7 out of 8 in 3cos

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Zinc binding site 7 out of 8 in the Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:19.5
occ:1.00
 NE2 D:HIS69 2.1 22.6 1.0
OXT D:ACY401 2.2 24.8 1.0
SG D:CYS180 2.3 22.7 1.0
SG D:CYS47 2.3 21.6 1.0
CD2 D:HIS69 3.0 24.1 1.0
CE1 D:HIS69 3.1 28.1 1.0
C D:ACY401 3.2 33.8 1.0
CB D:CYS47 3.3 22.3 1.0
CB D:CYS180 3.3 22.9 1.0
C5N D:NAD400 3.5 13.1 1.0
O D:ACY401 3.7 38.2 1.0
OG1 D:THR49 3.9 19.4 1.0
C6N D:NAD400 4.0 19.3 1.0
CB D:THR49 4.0 24.1 1.0
CG D:HIS69 4.2 21.8 1.0
ND1 D:HIS69 4.2 24.2 1.0
C4N D:NAD400 4.2 16.1 1.0
CH3 D:ACY401 4.5 34.3 1.0
CA D:CYS47 4.7 22.2 1.0
CA D:CYS180 4.7 21.7 1.0
OE2 D:GLU70 4.8 27.8 1.0
OH D:TYR95 4.8 21.4 1.0
CE2 D:TYR95 4.8 23.2 1.0
CG2 D:THR49 4.9 22.9 1.0

Zinc binding site 8 out of 8 in 3cos

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Zinc binding site 8 out of 8 in the Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:26.1
occ:1.00
 SG D:CYS102 2.3 21.3 1.0
SG D:CYS113 2.3 23.3 1.0
SG D:CYS105 2.4 26.0 1.0
SG D:CYS99 2.4 24.2 1.0
CB D:CYS105 3.3 25.7 1.0
CB D:CYS113 3.4 23.2 1.0
CB D:CYS99 3.4 26.1 1.0
CB D:CYS102 3.4 24.1 1.0
N D:CYS99 3.6 24.3 1.0
CA D:CYS113 3.7 24.0 1.0
N D:CYS102 3.9 25.4 1.0
CA D:CYS99 3.9 24.9 1.0
N D:GLY114 3.9 26.2 1.0
N D:ARG100 4.0 24.6 1.0
O D:HOH804 4.1 35.3 1.0
N D:CYS105 4.2 24.6 1.0
CA D:CYS102 4.2 24.3 1.0
C D:CYS99 4.2 24.6 1.0
CA D:CYS105 4.3 24.0 1.0
C D:CYS113 4.3 24.6 1.0
N D:LYS101 4.5 26.9 1.0
C D:LEU98 4.7 23.8 1.0
C D:CYS102 4.9 24.8 1.0
CA D:ARG100 4.9 25.3 1.0
CA D:GLY114 5.0 26.9 1.0
CA D:LEU98 5.0 24.6 1.0

Reference:

K.L.Kavanagh, N.Shafqat, W.Yue, F.Von Delft, S.Bishop, A.Roos, J.Murray, A.M.Edwards, C.H.Arrowsmith, C.Bountra, U.Oppermann. Crystal Structure of Human Class II Alcohol Dehydrogenase (ADH4) in Complex with Nad and Zn. To Be Published.
Page generated: Thu Oct 24 11:53:52 2024

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