Zinc in PDB 6p2k: Crystal Structure of AFV00434, An Ancestral GH74 Enzyme

The structure of Crystal Structure of AFV00434, An Ancestral GH74 Enzyme, PDB code: 6p2k was solved by P.J.Stogios, T.Skarina, G.Arnal, H.Brumer, A.Savchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.78 / 2.15
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	173.427, 173.427, 173.427, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 20.4

The structure of Crystal Structure of AFV00434, An Ancestral GH74 Enzyme also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of AFV00434, An Ancestral GH74 Enzyme (pdb code 6p2k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of AFV00434, An Ancestral GH74 Enzyme, PDB code: 6p2k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of AFV00434, An Ancestral GH74 Enzyme


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 AFV00434, An Ancestral GH74 Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:28.1 occ:0.25 OD1 A:ASP124 2.0 47.7 1.0 OE1 A:GLN16 2.1 45.4 1.0 OD2 A:ASP124 2.1 47.2 1.0 O A:HOH904 2.1 33.8 1.0 O A:HOH997 2.1 29.0 1.0 O A:HOH923 2.1 32.6 1.0 O A:HOH935 2.1 30.5 1.0 CG A:ASP124 2.3 43.3 1.0 CD A:GLN16 3.3 36.8 1.0 CB A:ASP124 3.7 30.9 1.0 NE2 A:GLN16 3.9 35.3 1.0 NE2 A:GLN18 4.0 32.2 1.0 OE1 A:GLN18 4.0 35.2 1.0 OD1 A:ASP123 4.3 24.6 1.0 NH1 A:ARG59 4.3 38.2 1.0 CA A:ASP124 4.3 23.9 1.0 CD A:GLN18 4.4 32.5 1.0 CG A:GLN16 4.4 32.9 1.0 OD2 A:ASP123 4.4 25.2 1.0 CG A:ASP123 4.6 25.8 1.0 OD2 A:ASP35 4.6 45.8 1.0 N A:ASP124 4.6 22.6 1.0 NH2 A:ARG334 4.7 19.2 1.0 C A:ASP123 5.0 22.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of AFV00434, An Ancestral GH74 Enzyme


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 AFV00434, An Ancestral GH74 Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:20.5 occ:0.30 OD2 A:ASP405 2.1 34.1 1.0 O A:HOH1370 2.1 35.2 1.0 OD1 A:ASP513 2.1 37.8 1.0 O A:HOH991 2.1 30.3 1.0 O A:HOH1047 2.1 31.2 1.0 O A:HOH995 2.1 28.3 1.0 O A:HOH939 2.1 34.4 1.0 CG A:ASP405 3.3 30.1 1.0 CG A:ASP513 3.3 35.6 1.0 OD2 A:ASP513 3.8 32.2 1.0 OD1 A:ASP405 3.9 29.5 1.0 CB A:ALA450 4.1 24.4 1.0 O A:VAL514 4.4 31.9 1.0 CB A:ASP405 4.4 25.9 1.0 CA A:ALA450 4.4 23.1 1.0 O A:VAL451 4.5 21.0 1.0 CB A:ASP513 4.5 30.9 1.0 O A:HOH1295 4.6 49.1 1.0 N A:VAL451 4.7 28.3 1.0 O A:HOH1131 4.8 34.4 1.0 N A:VAL514 4.9 27.9 1.0 CA A:ASP513 4.9 31.0 1.0 O A:HOH1152 4.9 39.4 1.0 O A:GLN449 4.9 26.9 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of AFV00434, An Ancestral GH74 Enzyme


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 AFV00434, An Ancestral GH74 Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn813 b:36.6 occ:0.50 OD2 A:ASP544 2.6 39.0 1.0 CG A:ASP544 3.2 39.1 1.0 CB A:ASP544 3.2 34.2 1.0 OD1 A:ASP544 4.3 38.6 1.0 NH1 A:ARG548 4.3 47.3 1.0 CG A:ARG541 4.6 46.3 1.0 CA A:ASP544 4.7 29.8 1.0 O A:HOH1059 4.8 54.5 1.0 NH2 A:ARG548 4.9 44.3 1.0 CZ2 A:TRP457 4.9 29.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of AFV00434, An Ancestral GH74 Enzyme


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 AFV00434, An Ancestral GH74 Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:17.7 occ:0.70 OD2 B:ASP562 1.9 30.0 1.0 OE1 B:GLU559 2.0 28.4 1.0 OD2 B:ASP566 2.0 28.2 1.0 O B:HOH1007 2.1 17.5 1.0 OD1 B:ASP566 2.2 31.6 1.0 OE2 B:GLU559 2.2 31.6 1.0 CB B:ASP562 2.3 33.2 1.0 CG B:ASP566 2.4 26.8 1.0 CD B:GLU559 2.4 27.9 1.0 CG B:ASP562 2.4 31.3 1.0 CA B:ASP562 3.6 26.9 1.0 OD1 B:ASP562 3.7 28.6 1.0 N B:ASP562 3.7 22.2 1.0 CB B:ASP566 3.9 24.0 1.0 CG B:GLU559 4.0 28.2 1.0 O B:HOH1125 4.0 20.1 1.0 O B:GLU559 4.3 24.9 1.0 N B:LEU561 4.3 24.2 1.0 C B:LEU561 4.5 25.8 1.0 O B:ASP562 4.5 27.1 1.0 C B:ASP562 4.6 26.6 1.0 C B:GLU559 4.8 24.2 1.0 CA B:LEU561 4.8 25.3 1.0 N B:ASP566 4.8 22.9 1.0 CB B:ASN565 4.8 34.1 1.0 CA B:ASP566 4.9 22.8 1.0 CB B:GLU559 4.9 25.1 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of AFV00434, An Ancestral GH74 Enzyme


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 AFV00434, An Ancestral GH74 Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:69.0 occ:0.76 OD1 B:ASP124 2.0 79.7 1.0 OE1 B:GLN16 2.1 80.1 1.0 O B:HOH1265 2.1 68.2 1.0 O B:HOH1120 2.1 70.3 1.0 O B:HOH910 2.1 65.7 1.0 CG B:ASP124 3.1 68.7 1.0 CD B:GLN16 3.3 59.0 1.0 OD2 B:ASP124 3.6 72.9 1.0 O B:HOH1006 3.8 51.4 1.0 NE2 B:GLN16 4.0 54.0 1.0 NE2 B:GLN18 4.1 44.5 1.0 OD1 B:ASP123 4.3 41.6 1.0 OD2 B:ASP123 4.3 39.1 1.0 CB B:ASP124 4.3 58.6 1.0 CG B:GLN16 4.4 47.4 1.0 OE1 B:GLN18 4.4 42.2 1.0 CA B:ASP124 4.5 48.8 1.0 CG B:ASP123 4.5 40.1 1.0 NH2 B:ARG334 4.7 27.4 1.0 NH1 B:ARG59 4.7 46.6 1.0 CD B:GLN18 4.7 41.2 1.0 OD2 B:ASP35 4.7 62.1 1.0 N B:ASP124 4.7 43.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of AFV00434, An Ancestral GH74 Enzyme


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 AFV00434, An Ancestral GH74 Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn803 b:11.2 occ:0.40 O B:HOH1063 2.1 17.1 1.0 O B:HOH1035 2.1 15.6 1.0 O B:HOH963 2.1 23.4 1.0 O B:HOH1011 2.1 24.7 1.0 OD1 B:ASP513 2.1 21.7 1.0 O B:HOH1008 2.2 18.3 1.0 OD2 B:ASP405 2.2 21.3 1.0 CG B:ASP513 3.2 25.0 1.0 CG B:ASP405 3.3 21.8 1.0 OD2 B:ASP513 3.6 23.5 1.0 OD1 B:ASP405 3.9 16.1 1.0 NH2 B:ARG747 3.9 45.4 1.0 O B:HOH1133 4.1 45.8 1.0 CB B:ALA450 4.2 13.6 1.0 O B:VAL514 4.3 23.4 1.0 O B:HOH1111 4.4 30.3 1.0 CB B:ASP405 4.4 17.6 1.0 O B:HOH940 4.4 23.5 1.0 CA B:ALA450 4.5 16.9 1.0 CB B:ASP513 4.5 22.6 1.0 O B:VAL451 4.5 15.2 1.0 O B:HOH1112 4.6 24.3 1.0 N B:VAL451 4.8 12.6 1.0 O B:HOH1334 4.9 41.9 1.0 O B:GLN449 4.9 20.1 1.0 N B:VAL514 5.0 22.9 1.0 CA B:ASP513 5.0 22.1 1.0

G.Arnal, P.J.Stogios, J.Asohan, M.A.Attia, T.Skarina, A.H.Viborg, B.Henrissat, A.Savchenko, H.Brumer. Substrate Specificity, Regiospecificity, and Processivity in Glycoside Hydrolase Family 74. J.Biol.Chem. V. 294 13233 2019.
ISSN: ESSN 1083-351X
PubMed: 31324716
DOI: 10.1074/JBC.RA119.009861