Zinc in PDB 6c2c: The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme

The structure of The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme, PDB code: 6c2c was solved by N.-S.Hong, C.J.Jackson, P.D.Carr, N.Tokuriki, F.Baier, G.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.38 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.600, 88.150, 119.800, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.4

The structure of The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme (pdb code 6c2c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme, PDB code: 6c2c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.8 occ:1.00 O A:HOH517 1.9 8.8 1.0 NE2 A:HIS119 2.1 7.4 1.0 OD2 A:ASP221 2.1 11.0 1.0 NE2 A:HIS268 2.2 9.3 1.0 OD2 A:ASP118 2.3 9.3 1.0 CG A:ASP221 2.9 13.6 1.0 OD1 A:ASP221 3.0 10.4 1.0 ZN A:ZN402 3.0 16.1 1.0 CD2 A:HIS119 3.0 8.1 1.0 CE1 A:HIS268 3.1 12.9 1.0 CG A:ASP118 3.1 10.5 1.0 CE1 A:HIS119 3.1 9.9 1.0 CD2 A:HIS268 3.2 9.5 1.0 OD1 A:ASP118 3.2 12.2 1.0 O A:HOH652 3.8 14.3 1.0 NE2 A:HIS114 3.8 9.3 1.0 CE1 A:HIS114 3.9 11.7 1.0 CG A:HIS119 4.2 8.5 1.0 ND1 A:HIS119 4.2 9.8 1.0 C1 A:PEG404 4.2 24.4 1.0 ND1 A:HIS268 4.2 9.0 1.0 CG A:HIS268 4.3 9.4 1.0 CB A:ASP221 4.3 12.4 1.0 O2 A:PEG404 4.4 43.3 1.0 CB A:ASP118 4.5 9.4 1.0 NE2 A:HIS224 4.7 12.8 1.0 CB A:HIS116 4.9 11.1 1.0 ND1 A:HIS116 4.9 11.2 1.0 C2 A:PEG404 5.0 34.9 1.0 CB A:ALA267 5.0 9.5 1.0 NE2 A:HIS200 5.0 12.3 1.0

Zinc binding site 2 out of 4 in the The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:16.1 occ:1.00 O A:HOH517 1.9 8.8 1.0 NE2 A:HIS114 2.1 9.3 1.0 OD2 A:ASP221 2.2 11.0 1.0 O A:HOH652 2.2 14.3 1.0 ND1 A:HIS116 2.3 11.2 1.0 NE2 A:HIS200 2.3 12.3 1.0 ZN A:ZN401 3.0 13.8 1.0 CD2 A:HIS114 3.1 10.4 1.0 CE1 A:HIS114 3.2 11.7 1.0 CE1 A:HIS116 3.2 14.8 1.0 CG A:ASP221 3.2 13.6 1.0 CD2 A:HIS200 3.2 11.4 1.0 CG A:HIS116 3.3 10.8 1.0 CE1 A:HIS200 3.3 11.2 1.0 CB A:HIS116 3.6 11.1 1.0 CB A:ASP221 3.8 12.4 1.0 NE2 A:HIS119 4.0 7.4 1.0 OD1 A:ASP221 4.1 10.4 1.0 NE2 A:HIS224 4.2 12.8 1.0 ND1 A:HIS114 4.3 10.8 1.0 CG A:HIS114 4.3 9.8 1.0 CD2 A:HIS119 4.3 8.1 1.0 NE2 A:HIS116 4.3 11.2 1.0 OD1 A:ASP118 4.3 12.2 1.0 CG A:HIS200 4.4 9.9 1.0 CD2 A:HIS116 4.4 12.6 1.0 ND1 A:HIS200 4.4 9.0 1.0 OD2 A:ASP118 4.8 9.3 1.0 NE2 A:HIS268 4.8 9.3 1.0 CE1 A:HIS224 4.8 13.8 1.0 C4 A:PEG404 4.8 30.6 1.0 O2 A:PEG404 4.9 43.3 1.0 CE1 A:HIS119 5.0 9.9 1.0

Zinc binding site 3 out of 4 in the The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:14.4 occ:1.00 O B:HOH514 1.9 8.5 1.0 NE2 B:HIS119 2.1 10.2 1.0 NE2 B:HIS268 2.1 10.4 1.0 OD2 B:ASP221 2.2 10.4 1.0 OD2 B:ASP118 2.3 13.7 1.0 CG B:ASP221 2.9 15.7 1.0 OD1 B:ASP221 3.0 12.4 1.0 ZN B:ZN402 3.0 17.7 1.0 CD2 B:HIS119 3.0 10.8 1.0 CE1 B:HIS268 3.1 13.5 1.0 CG B:ASP118 3.1 14.4 1.0 CD2 B:HIS268 3.1 12.5 1.0 CE1 B:HIS119 3.1 9.7 1.0 OD1 B:ASP118 3.2 14.5 1.0 O B:HOH581 3.7 15.6 1.0 NE2 B:HIS114 3.9 10.9 1.0 CE1 B:HIS114 4.0 9.7 1.0 C4 B:PEG404 4.1 28.6 1.0 CG B:HIS119 4.2 10.8 1.0 ND1 B:HIS268 4.2 10.7 1.0 ND1 B:HIS119 4.2 9.6 1.0 O2 B:PEG404 4.2 42.7 1.0 CG B:HIS268 4.3 10.5 1.0 CB B:ASP221 4.3 13.2 1.0 CB B:ASP118 4.5 12.1 1.0 NE2 B:HIS224 4.7 13.7 1.0 C3 B:PEG404 4.7 30.6 1.0 ND1 B:HIS116 4.9 9.4 1.0 CB B:HIS116 4.9 13.9 1.0 CB B:ALA267 5.0 10.3 1.0

Zinc binding site 4 out of 4 in the The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:17.7 occ:1.00 O B:HOH514 1.9 8.5 1.0 OD2 B:ASP221 2.0 10.4 1.0 NE2 B:HIS114 2.2 10.9 1.0 O B:HOH581 2.2 15.6 1.0 NE2 B:HIS200 2.3 10.3 1.0 ND1 B:HIS116 2.3 9.4 1.0 ZN B:ZN401 3.0 14.4 1.0 CG B:ASP221 3.0 15.7 1.0 CE1 B:HIS114 3.2 9.7 1.0 CD2 B:HIS114 3.2 11.8 1.0 CE1 B:HIS200 3.2 11.5 1.0 CE1 B:HIS116 3.2 14.7 1.0 CD2 B:HIS200 3.3 11.9 1.0 CG B:HIS116 3.4 13.6 1.0 CB B:ASP221 3.7 13.2 1.0 CB B:HIS116 3.7 13.9 1.0 NE2 B:HIS119 3.9 10.2 1.0 OD1 B:ASP221 4.0 12.4 1.0 NE2 B:HIS224 4.1 13.7 1.0 CD2 B:HIS119 4.3 10.8 1.0 ND1 B:HIS114 4.3 11.0 1.0 CG B:HIS114 4.3 11.2 1.0 ND1 B:HIS200 4.3 9.2 1.0 OD1 B:ASP118 4.3 14.5 1.0 NE2 B:HIS116 4.4 14.1 1.0 CG B:HIS200 4.4 11.1 1.0 O1 B:PEG404 4.4 54.9 1.0 CD2 B:HIS116 4.5 16.3 1.0 NE2 B:HIS268 4.7 10.4 1.0 OD2 B:ASP118 4.7 13.7 1.0 CE1 B:HIS224 4.8 13.7 1.0 CE1 B:HIS119 4.9 9.7 1.0 O2 B:PEG404 4.9 42.7 1.0 C1 B:PEG404 4.9 33.0 1.0

G.Yang, D.W.Anderson, F.Baier, E.Dohmen, N.Hong, P.D.Carr, S.C.L.Kamerlin, C.J.Jackson, E.Bornberg-Bauer, N.Tokuriki. Higher-Order Epistasis Shapes the Fitness Landscape of A Xenobiotic-Degrading Enzyme. Nat.Chem.Biol. V. 15 1120 2019.
ISSN: ESSN 1552-4469
PubMed: 31636435
DOI: 10.1038/S41589-019-0386-3