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Zinc in PDB 1h2b: Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution

Enzymatic activity of Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution

All present enzymatic activity of Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution:
1.1.1.1;

Protein crystallography data

The structure of Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution, PDB code: 1h2b was solved by J.E.Guy, M.N.Isupov, J.A.Littlechild, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.62
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.661, 103.186, 67.521, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution (pdb code 1h2b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution, PDB code: 1h2b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 1h2b

Go back to Zinc Binding Sites List in 1h2b
Zinc binding site 1 out of 5 in the Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution


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 the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1362

b:19.1
occ:1.00
 O1 A:OCA1360 1.9 19.7 1.0
NE2 A:HIS79 2.0 17.4 1.0
OD1 A:ASP168 2.1 17.7 1.0
SG A:CYS54 2.3 16.8 1.0
C1 A:OCA1360 2.9 22.6 1.0
CD2 A:HIS79 3.0 16.1 1.0
CE1 A:HIS79 3.0 16.9 1.0
CB A:CYS54 3.1 17.8 1.0
CG A:ASP168 3.1 22.2 1.0
O2 A:OCA1360 3.2 20.8 1.0
C5N A:NAJ1361 3.3 17.7 1.0
OD2 A:ASP168 3.5 19.5 1.0
CB A:THR56 3.7 18.3 1.0
OG1 A:THR56 3.7 15.2 1.0
C6N A:NAJ1361 3.9 18.7 1.0
ND1 A:HIS79 4.1 17.5 1.0
CG A:HIS79 4.2 19.7 1.0
C4N A:NAJ1361 4.2 16.8 1.0
C2 A:OCA1360 4.3 25.1 1.0
CB A:ASP168 4.3 15.6 1.0
CG2 A:THR56 4.4 18.7 1.0
NH2 A:ARG354 4.4 16.8 1.0
CA A:CYS54 4.6 17.7 1.0
N A:THR56 4.8 16.6 1.0
CA A:THR56 4.9 16.0 1.0

Zinc binding site 2 out of 5 in 1h2b

Go back to Zinc Binding Sites List in 1h2b
Zinc binding site 2 out of 5 in the Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution


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 the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1363

b:22.5
occ:1.00
 O A:HOH2311 1.9 31.0 1.0
OD1 A:ASP332 2.0 21.3 1.0
NE2 A:HIS334 2.1 28.1 1.0
CG A:ASP332 2.7 21.0 1.0
OD2 A:ASP332 2.8 29.7 1.0
CE1 A:HIS334 2.9 33.1 1.0
CD2 A:HIS334 3.1 20.0 1.0
NH1 A:ARG345 3.9 24.6 1.0
O A:HOH2274 3.9 35.1 1.0
ND1 A:HIS334 4.0 26.6 1.0
CG A:HIS334 4.1 25.8 1.0
CB A:ASP332 4.2 18.2 1.0
O A:HOH2276 4.3 43.7 1.0
O A:ILE333 4.3 22.6 1.0
NH2 A:ARG345 4.4 22.2 1.0
CZ A:ARG345 4.5 23.0 1.0
CA A:ASP332 4.7 19.5 1.0
C A:ASP332 4.7 18.8 1.0
N A:ILE333 4.8 21.6 1.0

Zinc binding site 3 out of 5 in 1h2b

Go back to Zinc Binding Sites List in 1h2b
Zinc binding site 3 out of 5 in the Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution


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 the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1364

b:30.7
occ:0.50
 OD1 A:ASP109 2.2 40.1 1.0
SG A:CYS123 2.3 27.3 0.5
SG A:CYS115 2.3 33.4 1.0
SG A:CYS112 2.4 46.6 1.0
CB A:CYS123 2.7 27.0 0.5
CB A:CYS123 2.7 28.7 0.5
SG A:CYS123 2.8 26.6 0.5
CG A:ASP109 3.1 45.3 1.0
CB A:CYS115 3.1 34.0 1.0
OD2 A:ASP109 3.3 50.8 1.0
CA A:CYS123 3.4 25.6 1.0
CB A:CYS112 3.6 38.6 1.0
N A:CYS112 3.8 38.8 1.0
N A:GLU124 3.8 28.1 1.0
N A:GLY110 3.8 37.7 1.0
C A:CYS123 4.0 26.7 1.0
N A:ASP109 4.1 33.4 1.0
N A:CYS115 4.2 27.9 1.0
CA A:CYS112 4.2 39.1 1.0
CA A:CYS115 4.2 30.9 1.0
N A:THR111 4.2 41.3 1.0
CB A:ASP109 4.4 39.4 1.0
O A:CYS112 4.5 35.5 1.0
CA A:GLY110 4.5 38.6 1.0
CA A:ASP109 4.6 37.9 1.0
CB A:THR108 4.6 26.2 1.0
N A:CYS123 4.6 19.9 1.0
C A:CYS112 4.6 35.4 1.0
C A:ASP109 4.7 39.5 1.0
C A:GLY110 4.7 41.0 1.0
N A:ASN125 4.8 36.3 1.0
C A:THR111 4.9 40.4 1.0

Zinc binding site 4 out of 5 in 1h2b

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Zinc binding site 4 out of 5 in the Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution


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 the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1362

b:17.6
occ:1.00
 O1 B:OCA1360 1.9 19.7 1.0
OD1 B:ASP168 2.1 15.4 1.0
NE2 B:HIS79 2.1 16.2 1.0
SG B:CYS54 2.3 16.1 1.0
C1 B:OCA1360 2.9 21.4 1.0
CD2 B:HIS79 3.0 16.7 1.0
CG B:ASP168 3.1 17.2 1.0
CE1 B:HIS79 3.1 19.0 1.0
CB B:CYS54 3.1 16.6 1.0
O2 B:OCA1360 3.2 19.2 1.0
C5N B:NAJ1361 3.4 16.3 1.0
OD2 B:ASP168 3.5 18.6 1.0
CB B:THR56 3.7 16.9 1.0
OG1 B:THR56 3.7 15.3 1.0
C6N B:NAJ1361 3.9 16.1 1.0
CG B:HIS79 4.2 14.4 1.0
ND1 B:HIS79 4.2 14.7 1.0
C4N B:NAJ1361 4.2 16.8 1.0
CB B:ASP168 4.3 14.3 1.0
C2 B:OCA1360 4.3 22.8 1.0
NH2 B:ARG354 4.4 17.3 1.0
CG2 B:THR56 4.5 18.0 1.0
CA B:CYS54 4.6 13.8 1.0
N B:THR56 4.8 15.9 1.0
CA B:THR56 4.9 14.3 1.0

Zinc binding site 5 out of 5 in 1h2b

Go back to Zinc Binding Sites List in 1h2b
Zinc binding site 5 out of 5 in the Crystal Structure of the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution


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 the Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix at 1.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1363

b:32.6
occ:0.50
 SG B:CYS115 2.3 31.5 1.0
SG B:CYS123 2.3 28.9 0.5
OD1 B:ASP109 2.4 44.0 1.0
SG B:CYS112 2.4 43.4 1.0
CB B:CYS123 2.9 27.6 0.5
CB B:CYS123 2.9 25.9 0.5
SG B:CYS123 3.0 27.3 0.5
CB B:CYS115 3.1 35.5 1.0
CG B:ASP109 3.2 45.6 1.0
CB B:CYS112 3.4 40.5 1.0
OD2 B:ASP109 3.5 48.4 1.0
CA B:CYS123 3.5 24.1 1.0
N B:CYS112 3.8 37.8 1.0
N B:GLU124 3.9 26.1 1.0
N B:GLY110 4.0 36.4 1.0
C B:CYS123 4.1 23.6 1.0
CA B:CYS112 4.1 38.0 1.0
N B:CYS115 4.1 30.1 1.0
N B:ASP109 4.2 31.9 1.0
CA B:CYS115 4.2 31.5 1.0
N B:THR111 4.3 42.1 1.0
CB B:ASP109 4.5 39.2 1.0
O B:CYS112 4.5 34.7 1.0
C B:CYS112 4.6 36.0 1.0
CB B:THR108 4.6 24.1 1.0
CA B:ASP109 4.6 37.3 1.0
CA B:GLY110 4.6 38.9 1.0
C B:ASP109 4.7 38.4 1.0
N B:CYS123 4.8 20.2 1.0
N B:ASN125 4.8 31.9 1.0
C B:GLY110 4.8 42.6 1.0
C B:THR111 4.9 40.9 1.0
CA B:GLU124 5.0 31.3 1.0

Reference:

J.E.Guy, M.N.Isupov, J.A.Littlechild. The Structure of An Alcohol Dehydrogenase From the Hyperthermophilic Archaeon Aeropyrum Pernix. J.Mol.Biol. V. 331 1041 2003.
ISSN: ISSN 0022-2836
PubMed: 12927540
DOI: 10.1016/S0022-2836(03)00857-X
Page generated: Sun Oct 13 01:54:56 2024

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