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Zinc in PDB 4jbi: 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum

Enzymatic activity of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum

All present enzymatic activity of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum:
1.1.1.1;

Protein crystallography data

The structure of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum, PDB code: 4jbi was solved by S.Lovell, K.P.Battaile, A.Vitale, N.Throne, X.Hu, M.Shen, S.D'auria, D.S.Auld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.59 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 138.133, 169.262, 149.151, 90.00, 116.25, 90.00
R / Rfree (%) 16.1 / 21.3

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum (pdb code 4jbi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum, PDB code: 4jbi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 4jbi

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Zinc binding site 1 out of 16 in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:30.9
occ:1.00
SG A:CYS94 2.2 32.1 1.0
SG A:CYS105 2.3 28.5 1.0
SG A:CYS91 2.3 31.6 1.0
SG A:CYS97 2.4 30.3 1.0
CB A:CYS94 3.3 38.2 1.0
CB A:CYS105 3.3 32.5 1.0
CB A:CYS97 3.4 29.3 1.0
N A:CYS91 3.5 32.5 1.0
CB A:CYS91 3.5 27.8 1.0
CA A:CYS105 3.7 32.9 1.0
N A:CYS94 3.7 37.4 1.0
N A:GLY92 3.8 32.1 1.0
CA A:CYS91 3.9 27.8 1.0
CA A:CYS94 4.0 31.2 1.0
N A:GLU106 4.1 38.2 1.0
N A:CYS97 4.2 23.0 1.0
C A:CYS105 4.3 35.3 1.0
C A:CYS91 4.3 31.2 1.0
N A:HIS93 4.3 37.0 1.0
N A:VAL107 4.4 32.4 1.0
CA A:CYS97 4.4 32.9 1.0
CB A:VAL107 4.5 30.7 1.0
C A:TYR90 4.6 31.1 1.0
C A:CYS94 4.7 34.6 1.0
CG2 A:VAL107 4.8 33.4 1.0
CA A:GLY92 4.8 32.2 1.0
CA A:TYR90 4.8 31.0 1.0
O A:CYS94 4.8 34.5 1.0
C A:HIS93 4.9 37.1 1.0
N A:CYS105 4.9 30.2 1.0
C A:GLY92 5.0 40.9 1.0
CB A:TYR90 5.0 32.6 1.0

Zinc binding site 2 out of 16 in 4jbi

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Zinc binding site 2 out of 16 in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:30.5
occ:1.00
SG B:CYS91 2.3 30.7 1.0
SG B:CYS94 2.3 31.3 1.0
SG B:CYS105 2.3 27.3 1.0
SG B:CYS97 2.3 30.1 1.0
CB B:CYS105 3.4 33.5 1.0
CB B:CYS94 3.4 26.4 1.0
CB B:CYS97 3.4 31.0 1.0
N B:CYS91 3.6 27.9 1.0
CB B:CYS91 3.6 27.4 1.0
CA B:CYS105 3.6 33.3 1.0
N B:CYS94 3.7 30.1 1.0
N B:GLY92 3.9 33.0 1.0
N B:GLU106 4.0 26.0 1.0
CA B:CYS91 4.0 36.0 1.0
CA B:CYS94 4.1 29.9 1.0
N B:CYS97 4.2 28.6 1.0
C B:CYS105 4.2 35.0 1.0
C B:CYS91 4.3 33.5 1.0
N B:HIS93 4.3 36.8 1.0
CA B:CYS97 4.4 33.7 1.0
N B:VAL107 4.4 42.6 1.0
C B:TYR90 4.7 39.7 1.0
C B:CYS94 4.7 32.9 1.0
CB B:VAL107 4.7 41.6 1.0
CG2 B:VAL107 4.8 27.8 1.0
CA B:GLY92 4.8 37.9 1.0
O B:CYS94 4.9 33.2 1.0
N B:CYS105 4.9 24.5 1.0
C B:HIS93 4.9 31.1 1.0
CA B:TYR90 4.9 28.6 1.0
C B:GLY92 5.0 34.6 1.0

Zinc binding site 3 out of 16 in 4jbi

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Zinc binding site 3 out of 16 in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:32.7
occ:1.00
SG C:CYS105 2.2 32.3 1.0
SG C:CYS94 2.3 29.9 1.0
SG C:CYS97 2.3 34.2 1.0
SG C:CYS91 2.4 37.2 1.0
CB C:CYS105 3.2 31.9 1.0
CB C:CYS97 3.3 34.9 1.0
CB C:CYS94 3.4 35.1 1.0
CB C:CYS91 3.4 34.1 1.0
N C:CYS91 3.5 37.5 1.0
CA C:CYS105 3.7 30.2 1.0
N C:GLY92 3.7 37.2 1.0
N C:CYS94 3.8 40.8 1.0
CA C:CYS91 3.8 38.2 1.0
N C:GLU106 4.1 33.5 1.0
CA C:CYS94 4.1 32.6 1.0
C C:CYS91 4.2 33.0 1.0
N C:CYS97 4.2 29.5 1.0
C C:CYS105 4.3 32.0 1.0
N C:HIS93 4.3 40.6 1.0
CA C:CYS97 4.4 34.7 1.0
N C:VAL107 4.6 35.8 1.0
C C:TYR90 4.6 37.9 1.0
CG2 C:VAL107 4.6 34.7 1.0
CA C:GLY92 4.7 35.3 1.0
CB C:VAL107 4.7 41.5 1.0
C C:CYS94 4.8 34.6 1.0
O C:CYS94 4.8 32.4 1.0
C C:HIS93 4.9 43.3 1.0
CA C:TYR90 4.9 32.0 1.0
N C:CYS105 5.0 31.4 1.0

Zinc binding site 4 out of 16 in 4jbi

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Zinc binding site 4 out of 16 in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:31.3
occ:1.00
SG D:CYS94 2.2 33.8 1.0
SG D:CYS97 2.3 39.5 1.0
SG D:CYS91 2.3 35.0 1.0
SG D:CYS105 2.3 32.3 1.0
CB D:CYS105 3.2 36.4 1.0
CB D:CYS94 3.3 36.5 1.0
CB D:CYS97 3.3 36.1 1.0
CB D:CYS91 3.5 28.9 1.0
N D:CYS91 3.5 35.6 1.0
CA D:CYS105 3.6 36.5 1.0
N D:CYS94 3.7 36.0 1.0
N D:GLY92 3.8 34.5 1.0
CA D:CYS91 3.9 36.7 1.0
N D:GLU106 4.0 34.0 1.0
CA D:CYS94 4.1 28.8 1.0
C D:CYS105 4.2 34.5 1.0
C D:CYS91 4.3 34.5 1.0
N D:CYS97 4.3 35.3 1.0
N D:HIS93 4.4 36.4 1.0
N D:VAL107 4.4 36.0 1.0
CA D:CYS97 4.4 40.5 1.0
CB D:VAL107 4.6 33.6 1.0
C D:TYR90 4.7 37.1 1.0
CG2 D:VAL107 4.7 37.1 1.0
C D:CYS94 4.7 36.6 1.0
CA D:GLY92 4.8 31.6 1.0
O D:CYS94 4.8 30.8 1.0
CA D:TYR90 4.9 39.0 1.0
C D:HIS93 4.9 32.1 1.0
N D:CYS105 5.0 31.5 1.0
CB D:TYR90 5.0 32.4 1.0

Zinc binding site 5 out of 16 in 4jbi

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Zinc binding site 5 out of 16 in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:29.3
occ:1.00
SG E:CYS91 2.3 31.5 1.0
SG E:CYS105 2.3 29.0 1.0
SG E:CYS94 2.3 29.6 1.0
SG E:CYS97 2.4 31.1 1.0
CB E:CYS105 3.2 26.1 1.0
CB E:CYS97 3.4 30.2 1.0
CB E:CYS94 3.4 37.6 1.0
N E:CYS91 3.6 30.9 1.0
CB E:CYS91 3.6 26.8 1.0
CA E:CYS105 3.6 34.0 1.0
N E:GLY92 3.7 37.6 1.0
N E:CYS94 3.9 33.5 1.0
CA E:CYS91 4.0 27.6 1.0
N E:GLU106 4.1 36.3 1.0
CA E:CYS94 4.2 27.9 1.0
C E:CYS105 4.2 36.2 1.0
N E:CYS97 4.2 29.6 1.0
C E:CYS91 4.3 32.0 1.0
N E:HIS93 4.4 34.8 1.0
CA E:CYS97 4.4 35.6 1.0
N E:VAL107 4.4 34.6 1.0
CB E:VAL107 4.6 31.4 1.0
CG2 E:VAL107 4.6 26.2 1.0
CA E:GLY92 4.7 31.7 1.0
C E:TYR90 4.7 38.1 1.0
C E:CYS94 4.8 34.1 1.0
O E:CYS94 4.8 38.3 1.0
N E:CYS105 4.9 28.1 1.0
C E:GLY92 4.9 35.5 1.0
CA E:TYR90 4.9 35.8 1.0

Zinc binding site 6 out of 16 in 4jbi

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Zinc binding site 6 out of 16 in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:34.8
occ:1.00
SG F:CYS97 2.2 33.1 1.0
SG F:CYS105 2.3 32.3 1.0
SG F:CYS94 2.4 34.1 1.0
SG F:CYS91 2.4 36.3 1.0
CB F:CYS105 3.2 32.1 1.0
CB F:CYS94 3.3 38.0 1.0
CB F:CYS97 3.4 37.0 1.0
CB F:CYS91 3.4 33.9 1.0
N F:CYS91 3.4 32.1 1.0
CA F:CYS105 3.7 35.3 1.0
N F:CYS94 3.7 37.2 1.0
CA F:CYS91 3.8 27.8 1.0
N F:GLY92 3.9 41.4 1.0
N F:GLU106 4.0 40.5 1.0
CA F:CYS94 4.1 32.2 1.0
N F:CYS97 4.2 33.6 1.0
C F:CYS105 4.3 34.8 1.0
C F:CYS91 4.3 31.9 1.0
CA F:CYS97 4.4 30.2 1.0
N F:HIS93 4.4 37.9 1.0
N F:VAL107 4.4 40.6 1.0
CB F:VAL107 4.6 43.5 1.0
C F:TYR90 4.6 43.2 1.0
CG2 F:VAL107 4.6 35.8 1.0
C F:CYS94 4.8 37.5 1.0
CA F:TYR90 4.8 37.1 1.0
CA F:GLY92 4.9 33.1 1.0
C F:HIS93 4.9 41.1 1.0
O F:CYS94 4.9 35.5 1.0
CB F:TYR90 4.9 30.8 1.0
N F:CYS105 4.9 29.0 1.0

Zinc binding site 7 out of 16 in 4jbi

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Zinc binding site 7 out of 16 in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn402

b:36.6
occ:1.00
SG G:CYS91 2.3 40.3 1.0
SG G:CYS97 2.3 36.6 1.0
SG G:CYS94 2.3 36.1 1.0
SG G:CYS105 2.3 28.7 1.0
CB G:CYS105 3.2 26.7 1.0
CB G:CYS91 3.4 35.2 1.0
CB G:CYS97 3.4 36.5 1.0
CB G:CYS94 3.5 28.1 1.0
CA G:CYS105 3.5 37.7 1.0
N G:CYS91 3.6 36.1 1.0
N G:CYS94 3.9 40.2 1.0
CA G:CYS91 3.9 33.7 1.0
N G:GLY92 4.0 35.4 1.0
N G:GLU106 4.1 33.7 1.0
C G:CYS105 4.2 34.7 1.0
N G:CYS97 4.2 28.4 1.0
CA G:CYS94 4.3 28.8 1.0
C G:CYS91 4.3 38.5 1.0
CA G:CYS97 4.4 36.5 1.0
N G:HIS93 4.5 38.6 1.0
N G:VAL107 4.5 35.9 1.0
C G:TYR90 4.7 38.5 1.0
CB G:VAL107 4.7 37.8 1.0
N G:CYS105 4.8 30.3 1.0
C G:CYS94 4.8 32.5 1.0
CG2 G:VAL107 4.8 36.1 1.0
O G:CYS94 4.9 33.0 1.0
CA G:TYR90 5.0 35.5 1.0
CA G:GLY92 5.0 30.9 1.0

Zinc binding site 8 out of 16 in 4jbi

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Zinc binding site 8 out of 16 in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn402

b:34.9
occ:1.00
SG H:CYS105 2.3 34.5 1.0
SG H:CYS97 2.3 32.6 1.0
SG H:CYS91 2.3 36.8 1.0
SG H:CYS94 2.3 28.0 1.0
CB H:CYS105 3.2 30.9 1.0
CB H:CYS94 3.4 32.0 1.0
CB H:CYS97 3.4 33.3 1.0
N H:CYS91 3.6 37.0 1.0
CB H:CYS91 3.6 31.8 1.0
CA H:CYS105 3.6 38.6 1.0
N H:CYS94 3.8 36.7 1.0
N H:GLY92 3.8 34.6 1.0
CA H:CYS91 4.0 33.5 1.0
N H:GLU106 4.1 36.0 1.0
CA H:CYS94 4.1 28.2 1.0
N H:CYS97 4.2 33.7 1.0
C H:CYS105 4.3 38.0 1.0
C H:CYS91 4.3 35.7 1.0
CA H:CYS97 4.4 41.2 1.0
N H:HIS93 4.4 45.0 1.0
N H:VAL107 4.5 41.7 1.0
CB H:VAL107 4.6 44.5 1.0
CG2 H:VAL107 4.7 43.9 1.0
C H:TYR90 4.7 38.3 1.0
C H:CYS94 4.8 34.2 1.0
CA H:GLY92 4.8 40.7 1.0
O H:CYS94 4.8 36.5 1.0
CA H:TYR90 4.9 35.7 1.0
N H:CYS105 4.9 34.1 1.0
C H:HIS93 4.9 38.0 1.0

Zinc binding site 9 out of 16 in 4jbi

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Zinc binding site 9 out of 16 in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn402

b:32.3
occ:1.00
SG I:CYS105 2.2 33.4 1.0
SG I:CYS94 2.3 32.9 1.0
SG I:CYS97 2.3 33.0 1.0
SG I:CYS91 2.4 31.7 1.0
CB I:CYS105 3.1 30.2 1.0
CB I:CYS97 3.4 37.5 1.0
CB I:CYS94 3.4 38.3 1.0
N I:CYS91 3.5 37.9 1.0
CB I:CYS91 3.6 34.2 1.0
CA I:CYS105 3.6 39.7 1.0
N I:CYS94 3.8 44.0 1.0
N I:GLY92 3.8 41.6 1.0
CA I:CYS91 4.0 42.3 1.0
N I:GLU106 4.2 34.9 1.0
CA I:CYS94 4.2 38.7 1.0
N I:CYS97 4.2 36.2 1.0
C I:CYS105 4.2 40.0 1.0
C I:CYS91 4.3 36.8 1.0
N I:HIS93 4.4 39.4 1.0
CA I:CYS97 4.4 30.8 1.0
N I:VAL107 4.4 33.4 1.0
C I:TYR90 4.6 34.4 1.0
CB I:VAL107 4.6 44.7 1.0
CG2 I:VAL107 4.7 36.3 1.0
CA I:GLY92 4.8 38.2 1.0
C I:CYS94 4.8 39.9 1.0
CA I:TYR90 4.9 36.5 1.0
O I:CYS94 4.9 36.5 1.0
N I:CYS105 4.9 39.2 1.0
C I:HIS93 4.9 44.0 1.0
C I:GLY92 4.9 45.1 1.0
CB I:TYR90 5.0 37.7 1.0

Zinc binding site 10 out of 16 in 4jbi

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Zinc binding site 10 out of 16 in the 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of 2.35A Resolution Structure of Nadph Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn402

b:33.9
occ:1.00
SG J:CYS94 2.3 36.1 1.0
SG J:CYS105 2.3 35.8 1.0
SG J:CYS97 2.3 33.5 1.0
SG J:CYS91 2.4 34.6 1.0
CB J:CYS105 3.3 32.2 1.0
CB J:CYS94 3.3 38.3 1.0
CB J:CYS97 3.3 31.3 1.0
CA J:CYS105 3.6 36.3 1.0
N J:CYS91 3.6 35.7 1.0
CB J:CYS91 3.6 35.1 1.0
N J:CYS94 3.8 34.8 1.0
N J:GLY92 3.9 34.3 1.0
N J:GLU106 4.0 36.7 1.0
CA J:CYS91 4.0 34.3 1.0
CA J:CYS94 4.1 32.5 1.0
N J:CYS97 4.2 34.4 1.0
C J:CYS105 4.2 38.3 1.0
CA J:CYS97 4.3 34.5 1.0
C J:CYS91 4.4 37.0 1.0
N J:VAL107 4.4 39.9 1.0
N J:HIS93 4.6 36.8 1.0
CB J:VAL107 4.6 40.6 1.0
CG2 J:VAL107 4.6 36.8 1.0
C J:CYS94 4.7 33.3 1.0
O J:CYS94 4.7 33.9 1.0
C J:TYR90 4.7 34.5 1.0
N J:CYS105 4.8 28.7 1.0
CA J:GLY92 4.9 36.1 1.0
CA J:TYR90 4.9 40.2 1.0

Reference:

A.Vitale, N.Thorne, S.Lovell, K.P.Battaile, X.Hu, M.Shen, S.D'auria, D.S.Auld. Physicochemical Characterization of A Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum. Plos One V. 8 63828 2013.
ISSN: ESSN 1932-6203
PubMed: 23755111
DOI: 10.1371/JOURNAL.PONE.0063828
Page generated: Wed Dec 16 05:25:13 2020

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