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Zinc in PDB 1axg: Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution

Enzymatic activity of Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution

All present enzymatic activity of Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution:
1.1.1.1;

Protein crystallography data

The structure of Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution, PDB code: 1axg was solved by T.D.Colby, J.K.Chin, B.J.Bahnson, B.M.Goldstein, J.P.Klinman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.348, 86.734, 90.635, 102.66, 99.24, 101.63
R / Rfree (%) 21.4 / 29.4

Other elements in 1axg:

The structure of Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution (pdb code 1axg). 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 the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution, PDB code: 1axg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1axg

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Zinc binding site 1 out of 8 in the Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom 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 VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:24.0
occ:1.00
 SG A:CYS174 2.2 15.4 1.0
NE2 A:HIS67 2.2 13.3 1.0
SG A:CYS46 2.4 26.9 1.0
O A:ETF404 2.6 16.9 1.0
CD2 A:HIS67 3.0 10.1 1.0
CB A:CYS174 3.3 12.4 1.0
CE1 A:HIS67 3.4 8.3 1.0
C5N A:NAD403 3.4 2.0 1.0
CB A:CYS46 3.5 15.1 1.0
C2 A:ETF404 3.7 11.8 1.0
C4N A:NAD403 3.9 7.7 1.0
OG A:SER48 3.9 8.6 1.0
C6N A:NAD403 4.1 2.0 1.0
CB A:SER48 4.2 8.7 1.0
CG A:HIS67 4.2 9.9 1.0
ND1 A:HIS67 4.4 10.9 1.0
OE1 A:GLU68 4.6 8.6 1.0
N A:GLY175 4.6 15.5 1.0
CE2 A:PHE93 4.7 9.7 1.0
CA A:CYS174 4.7 15.1 1.0
NH2 A:ARG369 4.7 13.0 1.0
F1 A:ETF404 4.7 9.7 1.0
C1 A:ETF404 4.8 10.0 1.0
C3N A:NAD403 4.9 2.0 1.0
CZ A:PHE93 4.9 5.0 1.0
CA A:CYS46 4.9 15.2 1.0

Zinc binding site 2 out of 8 in 1axg

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Zinc binding site 2 out of 8 in the Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom 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 VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:11.5
occ:1.00
 SG A:CYS111 1.8 20.9 1.0
SG A:CYS97 1.8 11.5 1.0
SG A:CYS103 2.1 5.7 1.0
SG A:CYS100 2.2 20.2 1.0
CB A:CYS111 3.2 15.1 1.0
CB A:CYS100 3.3 15.6 1.0
CB A:CYS97 3.3 11.2 1.0
N A:CYS97 3.5 9.1 1.0
CB A:CYS103 3.5 5.3 1.0
CA A:CYS111 3.8 8.3 1.0
CA A:CYS97 3.9 10.4 1.0
N A:CYS100 3.9 13.9 1.0
N A:GLY98 4.0 10.9 1.0
N A:LEU112 4.0 6.4 1.0
CA A:CYS100 4.1 12.7 1.0
CG A:LYS113 4.3 14.2 1.0
C A:CYS111 4.3 7.3 1.0
C A:CYS97 4.3 11.8 1.0
N A:CYS103 4.4 4.9 1.0
C A:GLN96 4.5 7.9 1.0
CA A:CYS103 4.5 10.2 1.0
O A:CYS100 4.6 17.1 1.0
N A:LYS99 4.6 8.6 1.0
C A:CYS100 4.6 13.6 1.0
N A:LYS113 4.6 5.8 1.0
CA A:GLN96 4.7 4.1 1.0
CB A:LYS113 5.0 9.5 1.0

Zinc binding site 3 out of 8 in 1axg

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Zinc binding site 3 out of 8 in the Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom 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 VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:17.0
occ:1.00
 SG B:CYS174 2.1 6.6 1.0
NE2 B:HIS67 2.3 2.0 1.0
SG B:CYS46 2.4 17.1 1.0
O B:ETF404 2.7 12.6 1.0
OG B:SER48 3.2 6.3 1.0
C5N B:NAD403 3.2 4.2 1.0
CE1 B:HIS67 3.3 6.2 1.0
CD2 B:HIS67 3.3 2.5 1.0
CB B:CYS46 3.5 2.0 1.0
CB B:CYS174 3.7 8.6 1.0
C4N B:NAD403 3.7 2.0 1.0
C6N B:NAD403 3.8 2.3 1.0
CB B:SER48 3.9 8.3 1.0
C2 B:ETF404 4.0 2.0 1.0
O B:HOH406 4.2 4.2 1.0
ND1 B:HIS67 4.4 10.0 1.0
CG B:HIS67 4.5 6.0 1.0
C3N B:NAD403 4.7 2.0 1.0
N1N B:NAD403 4.7 2.0 1.0
CE1 B:PHE93 4.8 5.1 1.0
CZ B:PHE93 4.8 2.0 1.0
CA B:CYS174 4.9 10.2 1.0
OE1 B:GLU68 4.9 2.0 1.0
CA B:CYS46 4.9 6.2 1.0
N B:SER48 4.9 8.3 1.0
F2 B:ETF404 4.9 24.7 1.0
N B:GLY175 5.0 12.6 1.0

Zinc binding site 4 out of 8 in 1axg

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Zinc binding site 4 out of 8 in the Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom 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 VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:14.2
occ:1.00
 SG B:CYS103 1.9 3.8 1.0
SG B:CYS100 1.9 2.0 1.0
SG B:CYS111 1.9 10.4 1.0
SG B:CYS97 2.0 15.1 1.0
CB B:CYS111 3.2 8.9 1.0
CB B:CYS103 3.4 8.6 1.0
CB B:CYS100 3.4 4.8 1.0
CB B:CYS97 3.5 4.7 1.0
N B:CYS97 3.6 6.1 1.0
CA B:CYS111 3.7 10.7 1.0
N B:GLY98 3.9 12.1 1.0
N B:CYS100 3.9 13.6 1.0
CA B:CYS97 4.0 9.7 1.0
N B:LEU112 4.2 14.3 1.0
CA B:CYS100 4.2 8.9 1.0
N B:CYS103 4.3 8.3 1.0
C B:CYS111 4.3 10.2 1.0
CA B:CYS103 4.4 6.3 1.0
C B:CYS97 4.4 8.7 1.0
C B:GLN96 4.6 4.0 1.0
N B:LYS99 4.6 10.1 1.0
O B:CYS100 4.7 17.9 1.0
CA B:GLN96 4.8 6.6 1.0
CA B:GLY98 4.8 12.1 1.0
O B:HOH446 4.8 2.0 1.0
C B:CYS100 4.8 12.8 1.0
CG B:LYS113 4.8 25.1 1.0
N B:LYS113 4.9 23.8 1.0
N B:CYS111 5.0 8.8 1.0

Zinc binding site 5 out of 8 in 1axg

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Zinc binding site 5 out of 8 in the Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom 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 VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:11.0
occ:1.00
 SG C:CYS174 2.1 10.6 1.0
NE2 C:HIS67 2.3 16.9 1.0
SG C:CYS46 2.3 12.7 1.0
O C:ETF404 2.5 15.1 1.0
CE1 C:HIS67 3.2 13.1 1.0
CD2 C:HIS67 3.3 14.0 1.0
C5N C:NAD403 3.4 16.4 1.0
CB C:CYS46 3.4 2.0 1.0
CB C:CYS174 3.5 9.5 1.0
OG C:SER48 3.6 6.1 1.0
C6N C:NAD403 3.8 18.0 1.0
C2 C:ETF404 3.8 11.9 1.0
C4N C:NAD403 4.0 17.9 1.0
CB C:SER48 4.0 6.0 1.0
ND1 C:HIS67 4.4 10.9 1.0
CG C:HIS67 4.4 11.6 1.0
N C:GLY175 4.7 2.0 1.0
OE1 C:GLU68 4.7 12.2 1.0
N1N C:NAD403 4.8 10.6 1.0
CA C:CYS46 4.8 7.9 1.0
NH2 C:ARG369 4.8 4.6 1.0
CA C:CYS174 4.8 6.7 1.0
C1 C:ETF404 4.8 2.0 1.0
F1 C:ETF404 4.9 13.1 1.0
C3N C:NAD403 4.9 15.1 1.0
N C:SER48 4.9 6.1 1.0
CE2 C:PHE93 5.0 2.0 1.0

Zinc binding site 6 out of 8 in 1axg

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Zinc binding site 6 out of 8 in the Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution


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 the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:33.8
occ:1.00
 SG C:CYS100 1.8 18.1 1.0
SG C:CYS103 2.0 19.4 1.0
SG C:CYS111 2.2 16.6 1.0
SG C:CYS97 2.2 11.7 1.0
CB C:CYS100 3.3 16.9 1.0
CB C:CYS111 3.4 10.8 1.0
CB C:CYS103 3.4 13.6 1.0
N C:CYS97 3.4 8.6 1.0
CB C:CYS97 3.6 2.0 1.0
N C:GLY98 3.9 15.5 1.0
CA C:CYS111 3.9 15.4 1.0
CA C:CYS97 3.9 9.9 1.0
N C:CYS100 3.9 21.4 1.0
CA C:CYS100 4.0 18.3 1.0
N C:CYS103 4.2 11.2 1.0
N C:LEU112 4.2 16.1 1.0
C C:CYS97 4.2 14.0 1.0
C C:GLN96 4.3 6.6 1.0
O C:CYS100 4.3 18.1 1.0
CA C:CYS103 4.4 12.0 1.0
C C:CYS111 4.5 13.5 1.0
CA C:GLN96 4.5 6.8 1.0
C C:CYS100 4.6 17.4 1.0
O C:HOH465 4.7 5.3 1.0
N C:LYS99 4.7 18.3 1.0
CA C:GLY98 4.8 15.6 1.0
C C:GLY98 5.0 17.5 1.0

Zinc binding site 7 out of 8 in 1axg

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Zinc binding site 7 out of 8 in the Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution


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 the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:25.2
occ:1.00
 NE2 D:HIS67 2.1 18.4 1.0
SG D:CYS174 2.2 6.4 1.0
SG D:CYS46 2.4 9.1 1.0
O D:ETF404 2.5 9.4 1.0
CE1 D:HIS67 3.1 14.8 1.0
CD2 D:HIS67 3.2 15.6 1.0
CB D:CYS46 3.3 2.0 1.0
C5N D:NAD403 3.3 3.4 1.0
CB D:CYS174 3.6 9.9 1.0
OG D:SER48 3.6 3.5 1.0
C2 D:ETF404 3.6 5.2 1.0
C4N D:NAD403 3.8 8.3 1.0
C6N D:NAD403 3.9 5.3 1.0
CB D:SER48 3.9 3.9 1.0
ND1 D:HIS67 4.3 17.1 1.0
CG D:HIS67 4.3 14.5 1.0
N D:GLY175 4.7 10.8 1.0
N1N D:NAD403 4.7 7.8 1.0
C3N D:NAD403 4.7 13.3 1.0
CA D:CYS46 4.7 8.2 1.0
C1 D:ETF404 4.8 5.5 1.0
CA D:CYS174 4.8 11.1 1.0
N D:SER48 4.9 7.6 1.0
OE1 D:GLU68 4.9 4.3 1.0
CZ D:PHE93 5.0 11.9 1.0
C D:CYS174 5.0 13.1 1.0

Zinc binding site 8 out of 8 in 1axg

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Zinc binding site 8 out of 8 in the Crystal Structure of the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution


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 the VAL203->Ala Mutant of Liver Alcohol Dehydrogenase Complexed with Cofactor Nad and Inhibitor Trifluoroethanol Solved to 2.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:27.2
occ:1.00
 SG D:CYS103 1.8 16.9 1.0
SG D:CYS111 2.0 25.1 1.0
SG D:CYS97 2.1 20.9 1.0
SG D:CYS100 2.1 21.1 1.0
CB D:CYS103 3.3 15.4 1.0
CB D:CYS111 3.4 18.2 1.0
CB D:CYS100 3.4 20.3 1.0
N D:CYS97 3.5 10.7 1.0
CB D:CYS97 3.5 11.2 1.0
CA D:CYS111 3.8 15.6 1.0
N D:CYS100 3.9 22.9 1.0
N D:GLY98 4.0 22.9 1.0
CA D:CYS97 4.0 15.3 1.0
N D:LEU112 4.0 8.8 1.0
CA D:CYS100 4.2 19.7 1.0
N D:CYS103 4.2 14.9 1.0
CA D:CYS103 4.3 15.8 1.0
C D:CYS111 4.3 9.4 1.0
C D:CYS97 4.4 17.2 1.0
C D:GLN96 4.4 11.9 1.0
CA D:GLN96 4.6 10.3 1.0
O D:CYS100 4.7 16.7 1.0
N D:LYS99 4.7 24.1 1.0
CG D:LYS113 4.7 11.5 1.0
N D:LYS113 4.8 10.7 1.0
C D:CYS100 4.8 18.7 1.0
CA D:GLY98 4.9 20.8 1.0

Reference:

B.J.Bahnson, T.D.Colby, J.K.Chin, B.M.Goldstein, J.P.Klinman. A Link Between Protein Structure and Enzyme Catalyzed Hydrogen Tunneling. Proc.Natl.Acad.Sci.Usa V. 94 12797 1997.
ISSN: ISSN 0027-8424
PubMed: 9371755
DOI: 10.1073/PNAS.94.24.12797
Page generated: Sat Oct 12 22:17:56 2024

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