Zinc in PDB 7utc: Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso

Enzymatic activity of Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso

All present enzymatic activity of Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso:
1.1.1.80;

Protein crystallography data

The structure of Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso, PDB code: 7utc was solved by T.Dinh, R.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.26 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.709, 125.325, 137.366, 90, 90, 90
R / Rfree (%) 17.8 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso (pdb code 7utc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso, PDB code: 7utc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7utc

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Zinc binding site 1 out of 4 in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso


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 Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:62.2
occ:0.72
 OD2 A:ASP150 1.9 65.5 1.0
NE2 A:HIS59 2.1 68.2 1.0
O A:DMS405 2.2 74.9 0.8
SG A:CYS37 2.3 74.4 1.0
CG A:ASP150 2.9 56.4 1.0
CE1 A:HIS59 3.0 75.3 1.0
CB A:CYS37 3.1 66.4 1.0
CD2 A:HIS59 3.2 64.2 1.0
S A:DMS405 3.2 56.9 0.8
C5N A:NAP402 3.3 50.5 0.8
OD1 A:ASP150 3.4 56.8 1.0
OG A:SER39 3.5 72.4 1.0
OE2 A:GLU60 3.8 64.2 1.0
CB A:SER39 3.9 68.4 1.0
C4N A:NAP402 4.0 57.4 0.8
C6N A:NAP402 4.1 58.2 0.8
CE A:MET151 4.1 56.0 1.0
ND1 A:HIS59 4.2 70.5 1.0
CB A:ASP150 4.2 55.3 1.0
CG A:HIS59 4.3 71.7 1.0
C1 A:DMS405 4.3 62.8 0.8
CA A:CYS37 4.5 65.9 1.0
CD A:GLU60 4.6 61.7 1.0
C2 A:DMS405 4.7 54.9 0.8
N A:SER39 4.8 80.8 1.0
CG A:GLU60 4.9 56.9 1.0
CA A:SER39 5.0 82.9 1.0

Zinc binding site 2 out of 4 in 7utc

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Zinc binding site 2 out of 4 in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso


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 Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:43.6
occ:0.64
 OD2 B:ASP150 1.9 51.3 1.0
NE2 B:HIS59 2.1 56.6 1.0
O B:DMS404 2.2 44.7 0.8
SG B:CYS37 2.3 56.6 1.0
CG B:ASP150 2.9 45.9 1.0
CD2 B:HIS59 3.0 49.7 1.0
CE1 B:HIS59 3.1 59.9 1.0
CB B:CYS37 3.2 53.4 1.0
OD1 B:ASP150 3.3 45.9 1.0
S B:DMS404 3.3 58.9 0.8
OG B:SER39 3.4 56.4 1.0
C5N B:NAP402 3.5 46.1 0.8
CB B:SER39 3.8 55.2 1.0
OE2 B:GLU60 3.9 66.0 1.0
C4N B:NAP402 4.1 50.7 0.8
CG B:HIS59 4.1 50.2 1.0
ND1 B:HIS59 4.1 54.9 1.0
C1 B:DMS404 4.2 52.5 0.8
CB B:ASP150 4.2 41.4 1.0
C6N B:NAP402 4.2 48.0 0.8
CE B:MET151 4.4 43.4 1.0
CA B:CYS37 4.7 58.3 1.0
CD B:GLU60 4.8 53.6 1.0
N B:SER39 4.8 71.2 1.0
C2 B:DMS404 4.9 40.3 0.8
CG B:GLU60 4.9 54.2 1.0
CA B:SER39 4.9 67.1 1.0
O B:HOH557 4.9 51.6 1.0

Zinc binding site 3 out of 4 in 7utc

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Zinc binding site 3 out of 4 in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso


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 Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:28.2
occ:0.70
 OD2 C:ASP150 1.8 31.9 1.0
NE2 C:HIS59 2.1 32.1 1.0
O C:DMS403 2.2 36.3 0.9
SG C:CYS37 2.2 32.8 1.0
CD2 C:HIS59 3.0 27.4 1.0
CG C:ASP150 3.0 23.4 1.0
CB C:CYS37 3.1 32.9 1.0
CE1 C:HIS59 3.1 30.7 1.0
S C:DMS403 3.5 43.4 0.9
C5N C:NAP402 3.5 31.3 0.8
OD1 C:ASP150 3.6 34.2 1.0
OG C:SER39 3.6 37.6 1.0
CB C:SER39 3.9 32.5 1.0
C2 C:DMS403 3.9 32.3 0.9
OE2 C:GLU60 4.0 29.8 1.0
CG C:HIS59 4.1 31.6 1.0
C4N C:NAP402 4.1 31.4 0.8
CB C:ASP150 4.2 21.1 1.0
ND1 C:HIS59 4.2 31.4 1.0
CE C:MET151 4.2 26.9 1.0
C6N C:NAP402 4.2 32.1 0.8
CD C:GLU60 4.5 23.7 1.0
CA C:CYS37 4.5 35.4 1.0
CG C:GLU60 4.8 22.4 1.0
C1 C:DMS403 4.8 37.6 0.9
N C:SER39 4.9 23.5 1.0
O C:HOH533 5.0 27.5 1.0

Zinc binding site 4 out of 4 in 7utc

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Zinc binding site 4 out of 4 in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso


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 Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:31.3
occ:0.76
 OD2 D:ASP150 1.8 29.2 1.0
NE2 D:HIS59 2.0 33.3 1.0
O D:DMS806 2.1 36.6 0.9
SG D:CYS37 2.2 33.7 1.0
CG D:ASP150 3.0 30.5 1.0
CD2 D:HIS59 3.0 31.6 1.0
CE1 D:HIS59 3.1 34.0 1.0
CB D:CYS37 3.1 32.1 1.0
S D:DMS806 3.3 44.3 0.9
C5N D:NAP803 3.4 31.7 0.8
OD1 D:ASP150 3.5 37.0 1.0
OG D:SER39 3.8 35.5 1.0
C1 D:DMS806 3.9 27.6 0.9
CB D:SER39 3.9 31.4 1.0
OE1 D:GLU60 4.1 34.8 1.0
C4N D:NAP803 4.1 39.7 0.8
C6N D:NAP803 4.1 42.3 0.8
CG D:HIS59 4.1 30.8 1.0
ND1 D:HIS59 4.2 30.6 1.0
CB D:ASP150 4.2 28.0 1.0
CE D:MET151 4.3 26.3 1.0
CD D:GLU60 4.4 26.4 1.0
CA D:CYS37 4.6 33.5 1.0
C2 D:DMS806 4.8 35.8 0.9
N D:SER39 4.8 36.8 1.0
CG D:GLU60 4.8 29.9 1.0
OE2 D:GLU60 4.9 27.0 1.0

Reference:

T.Dinh, K.T.Rahn, R.S.Phillips. Crystallographic Snapshots of Ternary Complexes of Thermophilic Secondary Alcohol Dehydrogenase From Thermoanaerobacter Pseudoethanolicus Reveal the Dynamics of Ligand Exchange and the Proton Relay Network. Proteins V. 90 1570 2022.
ISSN: ESSN 1097-0134
PubMed: 35357038
DOI: 10.1002/PROT.26339
Page generated: Sat Apr 8 04:29:03 2023

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