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Zinc in PDB 4gkv: Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad

Enzymatic activity of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad

All present enzymatic activity of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad:
1.1.1.1;

Protein crystallography data

The structure of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad, PDB code: 4gkv was solved by P.A.Sims, L.M.Thomas, A.R.Harper, W.A.Miner, H.O.Ajufo, K.M.Branscrum, L.Kao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.69 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.160, 118.920, 97.870, 90.00, 106.41, 90.00
R / Rfree (%) 13.8 / 18.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad (pdb code 4gkv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad, PDB code: 4gkv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4gkv

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Zinc binding site 1 out of 8 in the Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:9.9
occ:1.00
 NE2 A:HIS58 2.2 3.6 1.0
O A:HOH509 2.2 5.6 1.0
SG A:CYS145 2.4 3.2 1.0
SG A:CYS37 2.5 7.1 1.0
CD2 A:HIS58 2.9 4.7 1.0
C5N A:NAD401 3.3 4.2 1.0
CB A:CYS37 3.3 4.3 1.0
CE1 A:HIS58 3.4 5.1 1.0
CB A:CYS145 3.4 3.3 1.0
OG1 A:THR39 3.7 6.8 1.0
CB A:THR39 3.8 6.6 1.0
C4N A:NAD401 4.0 9.2 1.0
C6N A:NAD401 4.0 6.1 1.0
CG A:HIS58 4.2 3.9 1.0
ND1 A:HIS58 4.3 5.8 1.0
CG2 A:THR39 4.7 4.3 1.0
CA A:CYS37 4.8 5.2 1.0
NH2 A:ARG329 4.8 6.4 1.0
CA A:CYS145 4.8 4.8 1.0
N A:THR39 4.9 3.4 1.0
O A:HOH517 5.0 3.9 1.0
CA A:THR39 5.0 4.4 1.0

Zinc binding site 2 out of 8 in 4gkv

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Zinc binding site 2 out of 8 in the Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:10.8
occ:1.00
 SG A:CYS95 2.4 6.3 1.0
SG A:CYS103 2.4 5.5 1.0
SG A:CYS92 2.5 5.7 1.0
SG A:CYS89 2.5 7.8 1.0
CB A:CYS103 3.2 4.1 1.0
CB A:CYS95 3.4 5.8 1.0
CB A:CYS89 3.5 12.4 1.0
CB A:CYS92 3.5 5.2 1.0
N A:CYS89 3.6 7.8 1.0
N A:GLY90 3.8 6.6 1.0
CA A:CYS89 3.9 8.3 1.0
CA A:CYS103 4.0 4.8 1.0
O A:HOH501 4.1 5.0 1.0
N A:CYS95 4.1 2.3 1.0
N A:CYS92 4.1 6.0 1.0
C A:CYS89 4.2 12.0 1.0
CA A:CYS95 4.4 7.0 1.0
N A:HIS91 4.4 5.9 1.0
CA A:CYS92 4.4 7.1 1.0
O A:HOH662 4.5 15.5 1.0
C A:HIS91 4.6 10.2 1.0
C A:GLY88 4.7 6.7 1.0
CA A:GLY90 4.8 6.7 1.0
C A:CYS103 4.9 5.0 1.0
N A:ARG104 5.0 6.0 1.0
C A:GLY90 5.0 8.1 1.0

Zinc binding site 3 out of 8 in 4gkv

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Zinc binding site 3 out of 8 in the Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:7.6
occ:1.00
 NE2 B:HIS58 2.2 1.9 1.0
O B:HOH932 2.3 3.1 1.0
SG B:CYS145 2.4 2.4 1.0
SG B:CYS37 2.4 3.7 1.0
CD2 B:HIS58 2.9 2.1 1.0
CB B:CYS37 3.3 5.6 1.0
C5N B:NAD401 3.3 1.6 1.0
CE1 B:HIS58 3.4 4.5 1.0
CB B:CYS145 3.4 2.0 1.0
OG1 B:THR39 3.8 4.8 1.0
CB B:THR39 3.8 6.6 1.0
C4N B:NAD401 4.0 6.0 1.0
C6N B:NAD401 4.0 3.7 1.0
CG B:HIS58 4.2 2.2 1.0
ND1 B:HIS58 4.3 2.4 1.0
O B:HOH947 4.4 17.4 1.0
CG2 B:THR39 4.6 4.0 1.0
CA B:CYS37 4.8 3.0 1.0
NH2 B:ARG329 4.8 3.7 1.0
CA B:CYS145 4.8 3.2 1.0
N B:THR39 4.9 4.1 1.0
CA B:THR39 5.0 4.7 1.0
OE2 B:GLU59 5.0 5.5 1.0

Zinc binding site 4 out of 8 in 4gkv

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Zinc binding site 4 out of 8 in the Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:9.0
occ:1.00
 SG B:CYS89 2.4 4.8 1.0
SG B:CYS92 2.4 4.9 1.0
SG B:CYS103 2.4 4.6 1.0
SG B:CYS95 2.4 5.2 1.0
CB B:CYS103 3.3 3.8 1.0
CB B:CYS89 3.4 7.7 1.0
CB B:CYS95 3.4 5.1 1.0
CB B:CYS92 3.5 7.7 1.0
N B:CYS89 3.6 4.0 1.0
CA B:CYS89 3.8 7.3 1.0
N B:GLY90 3.9 5.8 1.0
O B:HOH533 3.9 5.4 1.0
CA B:CYS103 4.1 5.0 1.0
N B:CYS92 4.1 8.5 1.0
N B:CYS95 4.2 3.4 1.0
C B:CYS89 4.2 8.9 1.0
O B:HOH618 4.2 13.7 1.0
N B:HIS91 4.4 6.9 1.0
CA B:CYS95 4.4 7.2 1.0
CA B:CYS92 4.4 6.5 1.0
C B:HIS91 4.6 9.2 1.0
C B:GLY88 4.7 5.8 1.0
O B:HOH780 4.7 27.2 1.0
CA B:GLY90 4.9 7.1 1.0
C B:CYS103 4.9 4.6 1.0
O B:HIS91 5.0 10.9 1.0

Zinc binding site 5 out of 8 in 4gkv

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Zinc binding site 5 out of 8 in the Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:6.6
occ:1.00
 NE2 C:HIS58 2.2 2.3 1.0
O C:HOH901 2.3 1.9 1.0
SG C:CYS145 2.4 2.6 1.0
SG C:CYS37 2.4 4.8 1.0
CD2 C:HIS58 3.0 2.6 1.0
CB C:CYS37 3.2 7.2 1.0
C5N C:NAD401 3.3 2.3 1.0
CE1 C:HIS58 3.3 2.7 1.0
CB C:CYS145 3.4 2.7 1.0
OG1 C:THR39 3.7 5.8 1.0
CB C:THR39 3.8 4.0 1.0
C4N C:NAD401 4.0 4.7 1.0
C6N C:NAD401 4.0 2.9 1.0
CG C:HIS58 4.2 2.4 1.0
ND1 C:HIS58 4.3 3.3 1.0
CG2 C:THR39 4.6 4.3 1.0
O C:HOH893 4.6 15.8 1.0
CA C:CYS37 4.7 4.6 1.0
NH2 C:ARG329 4.8 2.3 1.0
CA C:CYS145 4.8 3.8 1.0
N C:THR39 4.9 3.0 1.0
CA C:THR39 5.0 3.3 1.0

Zinc binding site 6 out of 8 in 4gkv

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Zinc binding site 6 out of 8 in the Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:8.7
occ:1.00
 SG C:CYS89 2.4 4.6 1.0
SG C:CYS103 2.4 5.8 1.0
SG C:CYS92 2.5 6.7 1.0
SG C:CYS95 2.5 6.5 1.0
CB C:CYS103 3.3 2.4 1.0
CB C:CYS89 3.3 10.8 1.0
CB C:CYS95 3.4 5.5 1.0
CB C:CYS92 3.4 6.8 1.0
N C:CYS89 3.6 10.2 1.0
CA C:CYS89 3.8 7.8 1.0
N C:GLY90 3.8 7.3 1.0
O C:HOH512 4.0 4.0 1.0
CA C:CYS103 4.1 4.9 1.0
N C:CYS95 4.1 4.3 1.0
C C:CYS89 4.2 9.4 1.0
N C:CYS92 4.2 6.0 1.0
O C:HOH653 4.3 15.1 1.0
N C:HIS91 4.3 7.1 1.0
CA C:CYS95 4.4 4.1 1.0
CA C:CYS92 4.4 5.3 1.0
C C:HIS91 4.6 9.5 1.0
C C:GLY88 4.7 6.4 1.0
O C:HOH691 4.7 21.9 1.0
CA C:GLY90 4.9 4.2 1.0
C C:CYS103 4.9 3.6 1.0
O C:HIS91 4.9 10.1 1.0
N C:ARG104 5.0 2.9 1.0

Zinc binding site 7 out of 8 in 4gkv

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Zinc binding site 7 out of 8 in the Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:12.5
occ:1.00
 NE2 D:HIS58 2.2 6.9 1.0
O D:HOH512 2.4 9.4 1.0
SG D:CYS145 2.4 8.2 1.0
SG D:CYS37 2.5 7.2 1.0
CD2 D:HIS58 2.9 7.1 1.0
CB D:CYS37 3.3 7.0 1.0
C5N D:NAD401 3.3 7.1 1.0
CE1 D:HIS58 3.4 8.3 1.0
CB D:CYS145 3.5 10.7 1.0
OG1 D:THR39 3.7 9.6 1.0
CB D:THR39 3.8 12.8 1.0
C6N D:NAD401 4.0 12.6 1.0
C4N D:NAD401 4.0 8.2 1.0
CG D:HIS58 4.2 9.3 1.0
ND1 D:HIS58 4.4 7.8 1.0
O D:HOH841 4.5 25.4 1.0
CG2 D:THR39 4.6 8.1 1.0
NH2 D:ARG329 4.8 7.8 1.0
CA D:CYS37 4.8 6.7 1.0
CA D:CYS145 4.8 5.7 1.0
N D:THR39 4.9 5.9 1.0
CA D:THR39 4.9 6.9 1.0

Zinc binding site 8 out of 8 in 4gkv

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Zinc binding site 8 out of 8 in the Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:12.0
occ:1.00
 SG D:CYS95 2.4 4.8 1.0
SG D:CYS103 2.4 6.0 1.0
SG D:CYS92 2.5 6.5 1.0
SG D:CYS89 2.5 7.1 1.0
CB D:CYS103 3.2 4.3 1.0
CB D:CYS89 3.4 10.4 1.0
CB D:CYS95 3.4 5.8 1.0
CB D:CYS92 3.4 4.5 1.0
N D:CYS89 3.6 6.2 1.0
N D:GLY90 3.8 7.8 1.0
CA D:CYS89 3.9 7.1 1.0
CA D:CYS103 4.0 6.3 1.0
O D:HOH510 4.0 7.2 1.0
N D:CYS95 4.2 6.1 1.0
C D:CYS89 4.2 11.6 1.0
N D:CYS92 4.3 9.4 1.0
O D:HOH546 4.3 12.7 1.0
CA D:CYS95 4.4 7.0 1.0
CA D:CYS92 4.4 9.6 1.0
N D:HIS91 4.4 10.2 1.0
C D:HIS91 4.6 11.6 1.0
O D:HOH857 4.6 25.1 1.0
C D:GLY88 4.7 5.3 1.0
CA D:GLY90 4.8 7.7 1.0
C D:CYS103 4.9 5.8 1.0
C D:GLY90 5.0 12.1 1.0
N D:ARG104 5.0 5.5 1.0
O D:HIS91 5.0 13.5 1.0

Reference:

L.M.Thomas, A.R.Harper, W.A.Miner, H.O.Ajufo, K.M.Branscum, L.Kao, P.A.Sims. Structure of Escherichia Coli Adhp (Ethanol-Inducible Dehydrogenase) with Bound Nad. Acta Crystallogr.,Sect.F V. 69 730 2013.
ISSN: ESSN 1744-3091
PubMed: 23832197
DOI: 10.1107/S1744309113015170
Page generated: Wed Dec 16 05:20:01 2020

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