Zinc in PDB 8h2b: Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans

Protein crystallography data

The structure of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans, PDB code: 8h2b was solved by S.Brott, U.T.Bornscheuer, K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.58 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.569, 92.67, 154.118, 90, 90, 90
R / Rfree (%) 16.1 / 20.5

Other elements in 8h2b:

The structure of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans (pdb code 8h2b). 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 Alcohol Dehydrogenase From Zobellia Galactanivorans, PDB code: 8h2b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8h2b

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Zinc binding site 1 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans


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 Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:38.4
occ:1.00
 NE2 A:HIS58 2.3 36.5 1.0
SG A:CYS170 2.3 33.2 1.0
SG A:CYS41 2.3 39.1 1.0
O A:HOH605 2.5 23.6 1.0
CD2 A:HIS58 3.2 29.8 1.0
CB A:CYS41 3.2 38.7 1.0
CE1 A:HIS58 3.2 36.9 1.0
CB A:CYS170 3.4 30.4 1.0
C5N A:NAD401 3.6 28.1 1.0
OG1 A:THR43 3.8 39.1 1.0
CB A:THR43 4.1 36.3 1.0
C6N A:NAD401 4.2 26.7 1.0
C4N A:NAD401 4.3 28.6 1.0
ND1 A:HIS58 4.4 33.3 1.0
CG A:HIS58 4.4 31.7 1.0
NE1 A:TRP84 4.7 22.6 1.0
CA A:CYS41 4.7 39.1 1.0
CA A:CYS170 4.8 26.7 1.0
OE2 A:GLU59 4.9 41.9 1.0
N A:THR43 5.0 34.8 1.0

Zinc binding site 2 out of 8 in 8h2b

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Zinc binding site 2 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans


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 Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:24.7
occ:1.00
 SG A:CYS94 2.3 26.6 1.0
SG A:CYS102 2.3 21.2 1.0
SG A:CYS91 2.3 19.2 1.0
SG A:CYS88 2.4 23.0 1.0
CB A:CYS102 3.2 24.0 1.0
CB A:CYS91 3.3 24.2 1.0
CB A:CYS94 3.4 25.1 1.0
CB A:CYS88 3.4 26.7 1.0
N A:CYS88 3.6 25.6 1.0
CA A:CYS102 3.7 22.2 1.0
N A:CYS91 3.7 23.4 1.0
N A:MET89 3.8 25.6 1.0
CA A:CYS88 3.9 29.4 1.0
N A:GLU103 4.0 22.5 1.0
CA A:CYS91 4.1 24.0 1.0
N A:CYS94 4.2 19.5 1.0
C A:CYS102 4.2 20.1 1.0
C A:CYS88 4.2 26.8 1.0
CA A:CYS94 4.3 24.2 1.0
N A:HIS90 4.4 27.1 1.0
N A:ASN104 4.6 19.3 1.0
C A:CYS91 4.7 21.3 1.0
C A:PRO87 4.7 27.8 1.0
ND2 A:ASN104 4.8 21.1 1.0
CA A:MET89 4.8 24.9 1.0
O A:CYS91 4.8 24.3 1.0
C A:HIS90 4.9 28.1 1.0
N A:CYS102 5.0 17.7 1.0

Zinc binding site 3 out of 8 in 8h2b

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Zinc binding site 3 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans


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 Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:43.3
occ:1.00
 NE2 B:HIS58 2.3 36.4 1.0
SG B:CYS170 2.3 37.6 1.0
SG B:CYS41 2.4 36.2 1.0
O B:HOH579 2.5 25.2 1.0
CD2 B:HIS58 3.1 31.8 1.0
CB B:CYS41 3.2 37.6 1.0
CE1 B:HIS58 3.3 36.6 1.0
CB B:CYS170 3.4 30.8 1.0
C5N B:NAD401 3.5 29.6 1.0
OG1 B:THR43 4.0 41.1 1.0
CB B:THR43 4.1 39.0 1.0
C6N B:NAD401 4.2 28.3 1.0
C4N B:NAD401 4.2 26.8 1.0
CG B:HIS58 4.3 33.5 1.0
ND1 B:HIS58 4.4 36.0 1.0
NE1 B:TRP84 4.7 27.2 1.0
CA B:CYS41 4.7 39.6 1.0
CA B:CYS170 4.8 32.1 1.0
CG2 B:THR43 4.9 37.8 1.0

Zinc binding site 4 out of 8 in 8h2b

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Zinc binding site 4 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans


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 Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:26.8
occ:1.00
 SG B:CYS102 2.3 22.4 1.0
SG B:CYS94 2.3 23.1 1.0
SG B:CYS91 2.3 23.5 1.0
SG B:CYS88 2.4 24.2 1.0
CB B:CYS102 3.3 22.2 1.0
CB B:CYS94 3.4 23.4 1.0
CB B:CYS88 3.4 22.9 1.0
CB B:CYS91 3.5 24.3 1.0
N B:CYS88 3.5 24.6 1.0
CA B:CYS102 3.7 21.5 1.0
N B:MET89 3.7 29.4 1.0
N B:CYS91 3.8 21.7 1.0
CA B:CYS88 3.9 28.9 1.0
N B:GLU103 4.1 23.2 1.0
C B:CYS88 4.1 30.0 1.0
CA B:CYS91 4.2 23.5 1.0
N B:CYS94 4.2 18.6 1.0
C B:CYS102 4.2 22.8 1.0
N B:HIS90 4.3 24.9 1.0
CA B:CYS94 4.4 23.3 1.0
N B:ASN104 4.6 23.1 1.0
C B:PRO87 4.7 24.5 1.0
CA B:MET89 4.7 26.3 1.0
C B:CYS91 4.8 19.5 1.0
O B:CYS91 4.8 27.4 1.0
C B:HIS90 4.9 28.5 1.0
ND2 B:ASN104 4.9 27.2 1.0
C B:MET89 4.9 24.9 1.0
CA B:PRO87 5.0 28.2 1.0
N B:CYS102 5.0 26.9 1.0

Zinc binding site 5 out of 8 in 8h2b

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Zinc binding site 5 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans


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 Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:30.4
occ:1.00
 NE2 C:HIS58 2.2 28.8 1.0
SG C:CYS41 2.3 31.0 1.0
SG C:CYS170 2.3 23.4 1.0
O C:HOH575 2.4 16.5 1.0
CD2 C:HIS58 3.1 24.9 1.0
CB C:CYS41 3.2 25.9 1.0
CE1 C:HIS58 3.3 26.0 1.0
CB C:CYS170 3.5 26.6 1.0
C5N C:NAD401 3.5 22.3 1.0
OG1 C:THR43 3.9 25.2 1.0
CB C:THR43 4.1 29.5 1.0
C4N C:NAD401 4.2 23.3 1.0
C6N C:NAD401 4.2 23.8 1.0
CG C:HIS58 4.3 23.8 1.0
ND1 C:HIS58 4.3 25.4 1.0
NE1 C:TRP84 4.7 22.8 1.0
CA C:CYS41 4.7 28.6 1.0
O C:HOH592 4.7 34.9 1.0
CA C:CYS170 4.8 27.9 1.0
CG2 C:THR43 4.9 27.8 1.0

Zinc binding site 6 out of 8 in 8h2b

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Zinc binding site 6 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans


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 Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:23.2
occ:1.00
 SG C:CYS94 2.3 20.9 1.0
SG C:CYS91 2.3 20.8 1.0
SG C:CYS88 2.3 22.1 1.0
SG C:CYS102 2.3 20.4 1.0
CB C:CYS91 3.3 19.2 1.0
CB C:CYS102 3.3 16.5 1.0
CB C:CYS94 3.4 20.5 1.0
CB C:CYS88 3.4 23.9 1.0
N C:CYS88 3.5 23.5 1.0
N C:CYS91 3.7 19.8 1.0
N C:MET89 3.8 21.9 1.0
CA C:CYS102 3.8 20.6 1.0
CA C:CYS88 3.9 23.3 1.0
CA C:CYS91 4.1 22.4 1.0
N C:GLU103 4.1 20.9 1.0
C C:CYS88 4.2 28.3 1.0
N C:CYS94 4.2 20.8 1.0
C C:CYS102 4.3 20.8 1.0
N C:HIS90 4.3 23.6 1.0
CA C:CYS94 4.4 19.0 1.0
ND2 C:ASN104 4.5 22.6 1.0
N C:ASN104 4.6 20.2 1.0
C C:PRO87 4.6 23.6 1.0
CA C:MET89 4.7 24.8 1.0
C C:CYS91 4.7 23.5 1.0
CB C:ASN104 4.8 21.4 1.0
C C:HIS90 4.9 24.7 1.0
CA C:PRO87 4.9 21.5 1.0
C C:MET89 4.9 23.9 1.0
O C:CYS91 4.9 19.2 1.0

Zinc binding site 7 out of 8 in 8h2b

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Zinc binding site 7 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans


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 Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:47.6
occ:1.00
 OE2 D:GLU59 2.2 38.9 1.0
NE2 D:HIS58 2.3 38.2 1.0
SG D:CYS41 2.3 36.8 1.0
SG D:CYS170 2.4 44.0 1.0
O D:HOH557 2.9 38.3 1.0
CE1 D:HIS58 3.0 34.7 1.0
CB D:CYS170 3.1 32.1 1.0
CD D:GLU59 3.1 36.6 1.0
CD2 D:HIS58 3.2 31.1 1.0
CB D:CYS41 3.4 36.6 1.0
CG D:GLU59 3.5 28.6 1.0
ND1 D:HIS58 4.0 35.2 1.0
CG D:HIS58 4.2 30.6 1.0
OE1 D:GLU59 4.3 30.2 1.0
CA D:CYS41 4.5 32.3 1.0
N D:CYS41 4.5 30.1 1.0
O D:HOH580 4.6 39.4 1.0
CA D:CYS170 4.6 33.4 1.0
NZ D:LYS366 4.7 36.3 1.0
N D:GLY171 4.8 30.0 1.0
CB D:GLU59 5.0 29.6 1.0
CB D:THR43 5.0 38.9 1.0

Zinc binding site 8 out of 8 in 8h2b

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Zinc binding site 8 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans


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 Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:26.7
occ:1.00
 SG D:CYS88 2.3 23.6 1.0
SG D:CYS94 2.3 21.4 1.0
SG D:CYS91 2.3 21.5 1.0
SG D:CYS102 2.4 24.6 1.0
CB D:CYS102 3.2 25.1 1.0
CB D:CYS94 3.4 20.6 1.0
CB D:CYS91 3.4 17.3 1.0
CB D:CYS88 3.5 24.8 1.0
N D:CYS88 3.5 25.8 1.0
CA D:CYS102 3.7 22.0 1.0
N D:CYS91 3.8 22.6 1.0
N D:MET89 3.8 26.6 1.0
CA D:CYS88 3.9 22.0 1.0
N D:GLU103 4.1 23.1 1.0
CA D:CYS91 4.1 22.6 1.0
C D:CYS102 4.2 24.6 1.0
C D:CYS88 4.2 32.5 1.0
N D:CYS94 4.2 18.7 1.0
N D:HIS90 4.3 23.2 1.0
CA D:CYS94 4.4 24.1 1.0
N D:ASN104 4.5 24.8 1.0
C D:PRO87 4.7 27.8 1.0
ND2 D:ASN104 4.7 26.7 1.0
CA D:MET89 4.8 24.9 1.0
C D:CYS91 4.8 23.8 1.0
C D:HIS90 4.9 28.2 1.0
CB D:ASN104 4.9 29.2 1.0
C D:MET89 4.9 28.5 1.0
CA D:PRO87 4.9 29.0 1.0
O D:CYS91 4.9 22.2 1.0
N D:CYS102 5.0 28.1 1.0

Reference:

S.Brott, U.T.Bornscheuer, K.H.Nam. Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans To Be Published.
Page generated: Thu Oct 31 06:55:05 2024

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