Zinc in PDB 5c5t: The Crystal Structure of Viral Collagen Prolyl Hydroxylase Vcph From Paramecium Bursaria Chlorella Virus-1 - 2OG Complex

The structure of The Crystal Structure of Viral Collagen Prolyl Hydroxylase Vcph From Paramecium Bursaria Chlorella Virus-1 - 2OG Complex, PDB code: 5c5t was solved by C.W.Levy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.43 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.790, 156.950, 41.240, 90.00, 90.02, 90.00
R / Rfree (%)	17.8 / 21.1

The structure of The Crystal Structure of Viral Collagen Prolyl Hydroxylase Vcph From Paramecium Bursaria Chlorella Virus-1 - 2OG Complex also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Zinc atom in the The Crystal Structure of Viral Collagen Prolyl Hydroxylase Vcph From Paramecium Bursaria Chlorella Virus-1 - 2OG Complex (pdb code 5c5t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of Viral Collagen Prolyl Hydroxylase Vcph From Paramecium Bursaria Chlorella Virus-1 - 2OG Complex, PDB code: 5c5t:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Crystal Structure of Viral Collagen Prolyl Hydroxylase Vcph From Paramecium Bursaria Chlorella Virus-1 - 2OG Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Viral Collagen Prolyl Hydroxylase Vcph From Paramecium Bursaria Chlorella Virus-1 - 2OG Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.5 occ:1.00 OD1 A:ASP140 2.0 11.6 1.0 NE2 A:HIS138 2.1 11.0 1.0 NE2 A:HIS207 2.1 11.0 1.0 O2 A:AKG301 2.1 15.5 1.0 O5 A:AKG301 2.2 13.6 1.0 C1 A:AKG301 2.8 16.2 1.0 C2 A:AKG301 2.9 14.2 1.0 CG A:ASP140 2.9 12.6 1.0 CE1 A:HIS138 3.0 11.1 1.0 CE1 A:HIS207 3.0 12.9 1.0 CD2 A:HIS207 3.1 10.4 1.0 CD2 A:HIS138 3.1 11.4 1.0 OD2 A:ASP140 3.2 12.3 1.0 O A:HOH519 3.7 29.7 1.0 O A:HOH430 4.1 25.9 1.0 O1 A:AKG301 4.1 13.9 1.0 ND1 A:HIS207 4.1 10.8 1.0 ND1 A:HIS138 4.1 11.5 1.0 O A:HOH459 4.2 36.4 1.0 CG A:HIS138 4.2 11.7 1.0 CG A:HIS207 4.2 10.6 1.0 CB A:ASP140 4.3 10.9 1.0 CE2 A:TYR135 4.4 12.7 1.0 C3 A:AKG301 4.4 13.9 1.0 CA A:ASP140 4.7 11.3 1.0 CZ A:TYR135 4.8 13.4 1.0 CD2 A:TYR135 4.8 14.8 1.0 CZ A:PHE191 4.8 12.1 1.0 N A:ASP140 4.9 12.7 1.0 C4 A:AKG301 5.0 15.2 1.0 OH A:TYR135 5.0 19.4 1.0

Zinc binding site 2 out of 2 in the The Crystal Structure of Viral Collagen Prolyl Hydroxylase Vcph From Paramecium Bursaria Chlorella Virus-1 - 2OG Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Viral Collagen Prolyl Hydroxylase Vcph From Paramecium Bursaria Chlorella Virus-1 - 2OG Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:12.4 occ:1.00 OD1 B:ASP140 2.0 11.5 1.0 O1 B:AKG301 2.0 13.8 1.0 NE2 B:HIS207 2.0 11.2 1.0 NE2 B:HIS138 2.1 11.1 1.0 O5 B:AKG301 2.3 15.0 1.0 C1 B:AKG301 2.8 13.1 1.0 CG B:ASP140 2.9 14.1 1.0 C2 B:AKG301 2.9 14.8 1.0 CE1 B:HIS207 3.0 15.1 1.0 CE1 B:HIS138 3.0 11.1 1.0 CD2 B:HIS138 3.1 12.4 1.0 CD2 B:HIS207 3.1 12.8 1.0 OD2 B:ASP140 3.1 13.9 1.0 O B:HOH488 3.8 26.8 1.0 O2 B:AKG301 4.0 14.0 1.0 O B:HOH441 4.1 25.5 1.0 ND1 B:HIS207 4.1 11.4 1.0 ND1 B:HIS138 4.1 11.5 1.0 CG B:HIS207 4.2 11.0 1.0 CG B:HIS138 4.2 12.4 1.0 CB B:ASP140 4.3 13.3 1.0 C3 B:AKG301 4.4 15.8 1.0 CE2 B:TYR135 4.4 16.8 1.0 O B:HOH507 4.7 44.5 1.0 CA B:ASP140 4.7 15.3 1.0 CZ B:TYR135 4.8 15.0 1.0 CZ B:PHE191 4.8 13.3 1.0 CD2 B:TYR135 4.8 18.4 1.0 N B:ASP140 4.8 16.2 1.0 C4 B:AKG301 5.0 14.9 1.0 OH B:TYR135 5.0 20.2 1.0

J.E.Longbotham, C.Levy, L.O.Johannissen, H.Tarhonskaya, S.Jiang, C.Loenarz, E.Flashman, S.Hay, C.J.Schofield, N.S.Scrutton. Structure and Mechanism of A Viral Collagen Prolyl Hydroxylase. Biochemistry V. 54 6093 2015.
ISSN: ISSN 0006-2960
PubMed: 26368022
DOI: 10.1021/ACS.BIOCHEM.5B00789