Zinc in PDB 6xt2: Eqadh-Nadh-Heptafluorobutanol, P21

Enzymatic activity of Eqadh-Nadh-Heptafluorobutanol, P21

All present enzymatic activity of Eqadh-Nadh-Heptafluorobutanol, P21:
1.1.1.1;

Protein crystallography data

The structure of Eqadh-Nadh-Heptafluorobutanol, P21, PDB code: 6xt2 was solved by B.V.Plapp, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.150, 180.270, 86.900, 90.00, 105.83, 90.00
R / Rfree (%) 13.8 / 19.2

Other elements in 6xt2:

The structure of Eqadh-Nadh-Heptafluorobutanol, P21 also contains other interesting chemical elements:

Fluorine (F) 56 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Eqadh-Nadh-Heptafluorobutanol, P21 (pdb code 6xt2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Eqadh-Nadh-Heptafluorobutanol, P21, PDB code: 6xt2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6xt2

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Zinc binding site 1 out of 8 in the Eqadh-Nadh-Heptafluorobutanol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Eqadh-Nadh-Heptafluorobutanol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.9
occ:1.00
 NE2 A:HIS67 2.1 12.8 1.0
O1 A:B7F404 2.1 16.6 0.6
O1 A:B7F404 2.1 17.7 0.4
SG A:CYS46 2.3 16.5 1.0
SG A:CYS174 2.3 15.7 1.0
C1 A:B7F404 3.0 19.7 0.4
CE1 A:HIS67 3.0 14.3 1.0
C1 A:B7F404 3.1 23.7 0.6
CD2 A:HIS67 3.1 14.3 1.0
CB A:CYS46 3.3 14.0 1.0
CB A:CYS174 3.4 12.8 1.0
C5N A:NAI403 3.5 14.4 1.0
OG A:SER48 3.8 14.8 1.0
C6N A:NAI403 3.9 14.0 1.0
C4N A:NAI403 4.0 13.8 1.0
CB A:SER48 4.0 14.1 1.0
ND1 A:HIS67 4.2 13.7 1.0
CG A:HIS67 4.2 12.7 1.0
F4 A:B7F404 4.4 28.6 0.6
C2 A:B7F404 4.5 21.3 0.4
C2 A:B7F404 4.5 23.1 0.6
NH2 A:ARG369 4.5 19.7 1.0
CA A:CYS46 4.7 14.3 1.0
F2 A:B7F404 4.7 20.6 0.4
F1 A:B7F404 4.7 19.1 0.6
OE2 A:GLU68 4.7 18.6 1.0
CA A:CYS174 4.7 13.3 1.0
N A:SER48 4.8 14.7 1.0
CE2 A:PHE93 4.9 15.2 1.0
F1 A:B7F404 5.0 26.2 0.4

Zinc binding site 2 out of 8 in 6xt2

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Zinc binding site 2 out of 8 in the Eqadh-Nadh-Heptafluorobutanol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Eqadh-Nadh-Heptafluorobutanol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:17.4
occ:1.00
 SG A:CYS103 2.3 16.7 1.0
SG A:CYS111 2.3 16.3 1.0
SG A:CYS100 2.3 17.6 1.0
SG A:CYS97 2.3 18.8 1.0
CB A:CYS111 3.3 16.3 1.0
CB A:CYS103 3.3 17.8 1.0
CB A:CYS100 3.4 22.2 1.0
CB A:CYS97 3.5 17.1 1.0
N A:CYS97 3.6 14.3 1.0
CA A:CYS111 3.7 15.3 1.0
N A:CYS100 3.8 20.9 1.0
N A:GLY98 4.0 19.2 1.0
N A:LEU112 4.0 16.0 1.0
CA A:CYS97 4.0 14.8 1.0
CA A:CYS100 4.1 17.9 1.0
N A:CYS103 4.2 15.6 1.0
C A:CYS111 4.3 16.4 1.0
CA A:CYS103 4.4 16.8 1.0
C A:CYS97 4.4 17.2 1.0
N A:LYS99 4.4 21.6 1.0
C A:GLN96 4.7 16.6 1.0
C A:CYS100 4.8 19.9 1.0
N A:LYS113 4.8 17.1 1.0
CG A:LYS113 4.9 22.0 1.0
O A:CYS100 4.9 17.2 1.0
CA A:GLY98 5.0 18.5 1.0
CA A:GLN96 5.0 14.9 1.0
C A:LYS99 5.0 23.6 1.0

Zinc binding site 3 out of 8 in 6xt2

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Zinc binding site 3 out of 8 in the Eqadh-Nadh-Heptafluorobutanol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Eqadh-Nadh-Heptafluorobutanol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:18.9
occ:1.00
 NE2 B:HIS67 2.1 16.8 1.0
O1 B:B7F404 2.1 19.4 0.4
O1 B:B7F404 2.1 20.9 0.6
SG B:CYS174 2.3 16.9 1.0
SG B:CYS46 2.3 16.9 1.0
CE1 B:HIS67 3.0 17.0 1.0
C1 B:B7F404 3.1 22.5 0.6
CD2 B:HIS67 3.1 16.6 1.0
C1 B:B7F404 3.2 19.8 0.4
CB B:CYS46 3.3 17.2 1.0
CB B:CYS174 3.4 16.0 1.0
C5N B:NAI403 3.5 15.1 1.0
OG B:SER48 3.9 17.2 1.0
C6N B:NAI403 3.9 14.8 1.0
C4N B:NAI403 4.0 14.4 1.0
CB B:SER48 4.0 16.0 1.0
ND1 B:HIS67 4.2 17.8 1.0
CG B:HIS67 4.2 17.6 1.0
F2 B:B7F404 4.3 28.4 0.4
C2 B:B7F404 4.4 23.7 0.4
C2 B:B7F404 4.5 25.9 0.6
NH2 B:ARG369 4.5 17.5 1.0
F1 B:B7F404 4.6 25.4 0.6
CA B:CYS174 4.7 14.8 1.0
CA B:CYS46 4.7 19.5 1.0
OE2 B:GLU68 4.7 20.4 1.0
N B:SER48 4.9 15.8 1.0
F4 B:B7F404 4.9 35.7 0.6
CE2 B:PHE93 4.9 15.5 1.0
F1 B:B7F404 4.9 24.2 0.4

Zinc binding site 4 out of 8 in 6xt2

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Zinc binding site 4 out of 8 in the Eqadh-Nadh-Heptafluorobutanol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Eqadh-Nadh-Heptafluorobutanol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:20.2
occ:1.00
 SG B:CYS111 2.3 19.0 1.0
SG B:CYS103 2.3 20.6 1.0
SG B:CYS100 2.3 19.7 1.0
SG B:CYS97 2.3 20.8 1.0
CB B:CYS111 3.3 18.4 1.0
CB B:CYS97 3.4 17.8 1.0
CB B:CYS103 3.4 20.9 1.0
CB B:CYS100 3.5 17.1 1.0
N B:CYS97 3.6 18.2 1.0
CA B:CYS111 3.7 17.2 1.0
N B:CYS100 3.8 23.8 1.0
CA B:CYS97 3.9 19.1 1.0
N B:GLY98 4.0 20.0 1.0
N B:LEU112 4.0 17.2 1.0
CA B:CYS100 4.2 21.5 1.0
N B:CYS103 4.2 18.9 1.0
C B:CYS111 4.3 20.9 1.0
C B:CYS97 4.4 22.1 1.0
O B:HOH748 4.4 38.9 1.0
CA B:CYS103 4.4 19.7 1.0
N B:LYS99 4.5 23.8 1.0
C B:GLN96 4.6 16.7 1.0
C B:CYS100 4.9 20.7 1.0
CA B:GLN96 4.9 17.7 1.0
N B:LYS113 4.9 19.6 1.0
O B:CYS100 4.9 20.7 1.0
CA B:GLY98 5.0 22.2 1.0
C B:LYS99 5.0 26.6 1.0

Zinc binding site 5 out of 8 in 6xt2

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Zinc binding site 5 out of 8 in the Eqadh-Nadh-Heptafluorobutanol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Eqadh-Nadh-Heptafluorobutanol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:17.2
occ:1.00
 O1 C:B7F404 2.1 17.8 0.6
NE2 C:HIS67 2.1 14.1 1.0
O1 C:B7F404 2.1 18.7 0.4
SG C:CYS174 2.3 15.6 1.0
SG C:CYS46 2.3 17.2 1.0
C1 C:B7F404 2.8 21.9 0.4
CD2 C:HIS67 3.1 14.7 1.0
CE1 C:HIS67 3.1 14.3 1.0
C1 C:B7F404 3.2 27.5 0.6
CB C:CYS46 3.2 16.1 1.0
CB C:CYS174 3.4 13.4 1.0
C5N C:NAI403 3.5 13.6 1.0
OG C:SER48 3.9 13.7 1.0
C6N C:NAI403 3.9 14.8 1.0
CB C:SER48 4.0 13.3 1.0
C4N C:NAI403 4.0 12.4 1.0
C2 C:B7F404 4.2 22.1 0.4
ND1 C:HIS67 4.2 13.5 1.0
CG C:HIS67 4.2 11.0 1.0
F2 C:B7F404 4.4 24.4 0.4
F1 C:B7F404 4.5 24.4 0.4
C2 C:B7F404 4.5 29.2 0.6
NH2 C:ARG369 4.6 17.7 1.0
CA C:CYS174 4.7 13.2 1.0
F4 C:B7F404 4.7 33.1 0.6
CA C:CYS46 4.7 16.7 1.0
OE2 C:GLU68 4.7 17.9 1.0
F1 C:B7F404 4.7 23.9 0.6
N C:SER48 4.9 13.8 1.0
CE2 C:PHE93 5.0 14.4 1.0

Zinc binding site 6 out of 8 in 6xt2

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Zinc binding site 6 out of 8 in the Eqadh-Nadh-Heptafluorobutanol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Eqadh-Nadh-Heptafluorobutanol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:19.8
occ:1.00
 SG C:CYS103 2.3 19.9 1.0
SG C:CYS100 2.3 19.7 1.0
SG C:CYS97 2.3 21.5 1.0
SG C:CYS111 2.4 19.6 1.0
CB C:CYS111 3.3 19.6 1.0
CB C:CYS103 3.4 17.2 1.0
CB C:CYS97 3.4 19.9 1.0
CB C:CYS100 3.5 21.6 1.0
N C:CYS97 3.6 19.3 1.0
CA C:CYS111 3.7 18.8 1.0
N C:CYS100 3.8 27.0 1.0
CA C:CYS97 3.9 20.5 1.0
N C:LEU112 4.0 19.2 1.0
N C:GLY98 4.0 23.3 1.0
CA C:CYS100 4.2 25.0 1.0
N C:CYS103 4.2 18.5 1.0
C C:CYS111 4.3 20.0 1.0
C C:CYS97 4.3 22.1 1.0
CA C:CYS103 4.3 17.0 1.0
N C:LYS99 4.5 25.1 1.0
C C:GLN96 4.7 19.2 1.0
O C:HOH766 4.7 41.8 1.0
C C:CYS100 4.9 22.7 1.0
N C:LYS113 4.9 17.3 1.0
CG C:LYS113 4.9 24.1 1.0
O C:CYS100 4.9 20.8 1.0
C C:LYS99 5.0 28.5 1.0
CA C:GLN96 5.0 17.2 1.0

Zinc binding site 7 out of 8 in 6xt2

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Zinc binding site 7 out of 8 in the Eqadh-Nadh-Heptafluorobutanol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Eqadh-Nadh-Heptafluorobutanol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:19.4
occ:1.00
 NE2 D:HIS67 2.0 16.9 1.0
O1 D:B7F404 2.1 20.6 0.8
O1 D:B7F404 2.1 17.9 0.2
SG D:CYS46 2.3 17.6 1.0
SG D:CYS174 2.3 17.5 1.0
C1 D:B7F404 3.0 27.0 0.8
CD2 D:HIS67 3.0 16.5 1.0
CE1 D:HIS67 3.0 17.7 1.0
CB D:CYS46 3.3 16.6 1.0
C5N D:NAI403 3.4 16.5 1.0
CB D:CYS174 3.4 17.2 1.0
C1 D:B7F404 3.5 17.5 0.2
OG D:SER48 3.8 15.9 1.0
C6N D:NAI403 4.0 15.7 1.0
C4N D:NAI403 4.0 14.6 1.0
CB D:SER48 4.1 16.1 1.0
ND1 D:HIS67 4.1 14.9 1.0
CG D:HIS67 4.2 16.0 1.0
F4 D:B7F404 4.4 29.2 0.8
C2 D:B7F404 4.5 28.4 0.8
NH2 D:ARG369 4.5 19.2 1.0
C2 D:B7F404 4.7 22.6 0.2
F2 D:B7F404 4.7 27.6 0.2
CA D:CYS174 4.7 16.6 1.0
CA D:CYS46 4.7 16.2 1.0
CE2 D:PHE93 4.9 18.1 1.0
OE2 D:GLU68 4.9 19.5 1.0
F1 D:B7F404 4.9 25.6 0.8
N D:SER48 4.9 14.1 1.0

Zinc binding site 8 out of 8 in 6xt2

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Zinc binding site 8 out of 8 in the Eqadh-Nadh-Heptafluorobutanol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Eqadh-Nadh-Heptafluorobutanol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:18.0
occ:1.00
 SG D:CYS100 2.3 17.6 1.0
SG D:CYS103 2.3 18.3 1.0
SG D:CYS111 2.3 16.9 1.0
SG D:CYS97 2.4 19.9 1.0
CB D:CYS103 3.3 18.5 1.0
CB D:CYS111 3.3 16.4 1.0
CB D:CYS100 3.4 20.8 1.0
CB D:CYS97 3.4 17.9 1.0
N D:CYS97 3.6 17.8 1.0
CA D:CYS111 3.7 15.5 1.0
N D:CYS100 3.9 20.3 1.0
CA D:CYS97 3.9 17.2 1.0
N D:GLY98 4.0 18.1 1.0
N D:LEU112 4.0 16.7 1.0
CA D:CYS100 4.2 20.2 1.0
N D:CYS103 4.2 14.2 1.0
C D:CYS111 4.3 14.9 1.0
CA D:CYS103 4.3 16.9 1.0
C D:CYS97 4.3 18.3 1.0
N D:LYS99 4.5 21.9 1.0
C D:GLN96 4.7 15.4 1.0
C D:CYS100 4.9 19.9 1.0
N D:LYS113 4.9 18.6 1.0
CA D:GLN96 4.9 17.3 1.0
O D:CYS100 4.9 19.7 1.0
CA D:GLY98 5.0 20.4 1.0
O D:HOH733 5.0 35.7 1.0

Reference:

B.V.Plapp, S.Ramaswamy. Alternative Binding Modes in Abortive Nadh and Alcohol Complexes of Horse Liver Alcohol Dehydrogenase To Be Published.
Page generated: Wed Dec 16 13:11:46 2020

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