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Zinc in PDB 1deh: Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000

Enzymatic activity of Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000

All present enzymatic activity of Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000:
1.1.1.1;

Protein crystallography data

The structure of Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000, PDB code: 1deh was solved by T.D.Hurley, G.J.Davis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.040, 44.540, 93.320, 92.56, 103.26, 68.84
R / Rfree (%) 18 / 26.1

Other elements in 1deh:

The structure of Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000 also contains other interesting chemical elements:

Iodine (I) 2 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000 (pdb code 1deh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000, PDB code: 1deh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1deh

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Zinc binding site 1 out of 4 in the Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:24.9
occ:1.00
SG A:CYS111 2.3 23.4 1.0
SG A:CYS100 2.3 23.2 1.0
SG A:CYS103 2.4 20.9 1.0
SG A:CYS97 2.4 25.4 1.0
CB A:CYS100 3.3 23.8 1.0
CB A:CYS111 3.4 22.1 1.0
CB A:CYS97 3.4 19.9 1.0
CB A:CYS103 3.4 23.5 1.0
N A:CYS97 3.6 22.8 1.0
N A:CYS100 3.8 27.8 1.0
N A:GLY98 3.8 28.0 1.0
CA A:CYS111 3.9 22.8 1.0
CA A:CYS97 3.9 24.9 1.0
N A:LEU112 4.0 20.2 1.0
CA A:CYS100 4.1 24.7 1.0
N A:CYS103 4.2 23.0 1.0
C A:CYS97 4.2 27.8 1.0
N A:LYS99 4.3 28.8 1.0
CA A:CYS103 4.4 26.5 1.0
C A:CYS111 4.4 19.9 1.0
C A:GLN96 4.6 22.8 1.0
CA A:GLY98 4.7 26.3 1.0
C A:CYS100 4.8 23.6 1.0
O A:CYS100 4.9 21.0 1.0
C A:LYS99 4.9 32.6 1.0
CG A:LYS113 4.9 19.8 1.0
CA A:GLN96 4.9 22.4 1.0
N A:LYS113 5.0 19.6 1.0

Zinc binding site 2 out of 4 in 1deh

Go back to Zinc Binding Sites List in 1deh
Zinc binding site 2 out of 4 in the Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:26.6
occ:1.00
N1 A:PYZ378 2.1 28.5 1.0
NE2 A:HIS67 2.3 18.2 1.0
SG A:CYS174 2.3 19.0 1.0
SG A:CYS46 2.3 17.1 1.0
C5 A:PYZ378 3.0 28.0 1.0
C5N A:NAD377 3.1 2.0 1.0
N2 A:PYZ378 3.2 27.1 1.0
CD2 A:HIS67 3.2 17.8 1.0
CE1 A:HIS67 3.3 21.8 1.0
CB A:CYS46 3.3 14.9 1.0
CB A:CYS174 3.6 22.5 1.0
C4N A:NAD377 3.8 8.5 1.0
OG1 A:THR48 3.8 18.4 1.0
C6N A:NAD377 4.0 6.5 1.0
C4 A:PYZ378 4.2 25.9 1.0
CB A:THR48 4.2 13.9 1.0
C3 A:PYZ378 4.3 25.8 1.0
CG A:HIS67 4.3 22.8 1.0
ND1 A:HIS67 4.4 27.3 1.0
CE2 A:PHE93 4.7 25.4 1.0
OE1 A:GLU68 4.8 19.9 1.0
CA A:CYS46 4.8 16.7 1.0
NH2 A:ARG369 4.8 15.6 1.0
CA A:CYS174 4.9 19.2 1.0
N A:GLY175 4.9 18.8 1.0
CD2 A:PHE93 5.0 21.1 1.0
C3N A:NAD377 5.0 8.7 1.0

Zinc binding site 3 out of 4 in 1deh

Go back to Zinc Binding Sites List in 1deh
Zinc binding site 3 out of 4 in the Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:25.2
occ:1.00
SG B:CYS103 2.1 15.3 1.0
SG B:CYS111 2.2 30.0 1.0
SG B:CYS100 2.4 28.8 1.0
SG B:CYS97 2.4 28.9 1.0
CB B:CYS111 3.2 28.3 1.0
CB B:CYS103 3.3 24.3 1.0
CB B:CYS97 3.4 24.9 1.0
CB B:CYS100 3.5 26.8 1.0
N B:CYS97 3.5 29.6 1.0
CA B:CYS111 3.7 25.0 1.0
N B:GLY98 3.9 32.5 1.0
CA B:CYS97 3.9 31.1 1.0
N B:CYS100 3.9 28.2 1.0
N B:LEU112 4.0 27.9 1.0
N B:CYS103 4.2 26.6 1.0
C B:CYS97 4.2 34.2 1.0
CA B:CYS100 4.3 27.4 1.0
CA B:CYS103 4.3 25.8 1.0
C B:CYS111 4.3 25.9 1.0
N B:LYS99 4.4 30.6 1.0
C B:GLN96 4.5 28.4 1.0
NZ B:LYS99 4.6 40.8 1.0
CA B:GLN96 4.7 25.7 1.0
CA B:GLY98 4.8 31.3 1.0
O B:CYS100 4.8 28.9 1.0
O B:HOH644 4.8 25.0 1.0
C B:CYS100 4.9 26.5 1.0
N B:LYS113 4.9 32.0 1.0

Zinc binding site 4 out of 4 in 1deh

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Zinc binding site 4 out of 4 in the Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystallization of Human BETA1 Alcohol Dehydrogenase (15 Mg/Ml) in 50 Mm Sodium Phosphate (pH 7.5), 2.0 Mm Nad+ and 1 Mm 4-Iodopyrazole at 25 Oc, 13% (W/V) Peg 8000 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:34.3
occ:1.00
SG B:CYS174 2.0 27.3 1.0
N1 B:PYZ378 2.2 34.8 1.0
NE2 B:HIS67 2.3 29.2 1.0
SG B:CYS46 2.4 28.8 1.0
N2 B:PYZ378 3.0 34.0 1.0
C5N B:NAD377 3.1 22.2 1.0
CD2 B:HIS67 3.2 27.0 1.0
C5 B:PYZ378 3.3 33.8 1.0
CE1 B:HIS67 3.3 26.0 1.0
CB B:CYS174 3.3 34.3 1.0
CB B:CYS46 3.4 33.9 1.0
OG1 B:THR48 3.8 20.2 1.0
C4N B:NAD377 3.9 27.4 1.0
C6N B:NAD377 3.9 26.2 1.0
C3 B:PYZ378 4.2 34.4 1.0
C4 B:PYZ378 4.2 34.6 1.0
CB B:THR48 4.4 22.1 1.0
CG B:HIS67 4.4 28.4 1.0
CE2 B:PHE93 4.4 29.4 1.0
ND1 B:HIS67 4.4 28.3 1.0
CA B:CYS174 4.6 35.1 1.0
CZ B:PHE93 4.8 25.1 1.0
CD2 B:PHE93 4.8 27.7 1.0
N B:GLY175 4.9 34.2 1.0
CA B:CYS46 4.9 32.2 1.0
OE1 B:GLU68 4.9 37.3 1.0
NH2 B:ARG369 5.0 31.7 1.0
C B:CYS174 5.0 34.3 1.0

Reference:

G.J.Davis, W.F.Bosron, C.L.Stone, K.Owusu-Dekyi, T.D.Hurley. X-Ray Structure of Human BETA3BETA3 Alcohol Dehydrogenase. the Contribution of Ionic Interactions to Coenzyme Binding. J.Biol.Chem. V. 271 17057 1996.
ISSN: ISSN 0021-9258
PubMed: 8663387
DOI: 10.1074/JBC.271.29.17057
Page generated: Mon Jan 25 16:08:40 2021

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