Zinc in PDB 2jig: Crystal Structure of Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate

The structure of Crystal Structure of Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate, PDB code: 2jig was solved by M.K.Koski, R.Hieta, C.Bollner, K.I.Kivirikko, J.Myllyharju, R.K.Wierenga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.17 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.920, 60.250, 116.850, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.8

The binding sites of Zinc atom in the Crystal Structure of Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate (pdb code 2jig). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate, PDB code: 2jig:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate


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 Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1252 b:20.5 occ:1.00 O22 A:PD21254 2.1 13.6 1.0 OD1 A:ASP145 2.1 21.4 1.0 NE2 A:HIS143 2.1 20.0 1.0 NE2 A:HIS227 2.1 16.2 1.0 N1 A:PD21254 2.2 13.0 1.0 C21 A:PD21254 2.9 15.5 1.0 C2 A:PD21254 2.9 12.9 1.0 CG A:ASP145 2.9 19.2 1.0 CD2 A:HIS143 3.0 19.2 1.0 CD2 A:HIS227 3.0 14.6 1.0 CE1 A:HIS143 3.1 19.0 1.0 OD2 A:ASP145 3.1 20.2 1.0 CE1 A:HIS227 3.1 18.8 1.0 C6 A:PD21254 3.3 12.1 1.0 O A:HOH2151 3.8 14.8 1.0 O21 A:PD21254 4.1 16.7 1.0 ND1 A:HIS143 4.2 19.5 1.0 CG A:HIS227 4.2 16.3 1.0 CG A:HIS143 4.2 20.5 1.0 ND1 A:HIS227 4.2 17.2 1.0 C3 A:PD21254 4.3 11.8 1.0 CB A:ASP145 4.4 19.0 1.0 C5 A:PD21254 4.5 13.3 1.0 NE1 A:TRP243 4.5 18.0 1.0 CE2 A:TYR140 4.6 18.3 1.0 CZ A:PHE212 4.7 17.5 1.0 O A:HIS227 4.8 18.6 1.0 CA A:ASP145 4.9 18.7 1.0 N A:ASP145 4.9 17.8 1.0 O A:HOH2142 4.9 19.8 1.0 C4 A:PD21254 4.9 13.1 1.0 CD2 A:TYR140 5.0 17.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate


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 Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1253 b:21.3 occ:1.00 ND1 A:HIS135 2.0 17.2 1.0 OD1 A:ASP236 2.0 18.9 1.0 O A:HOH2244 2.1 21.3 1.0 O A:HOH2245 2.5 33.9 1.0 CG A:ASP236 2.8 17.7 1.0 CE1 A:HIS135 2.9 20.7 1.0 OD2 A:ASP236 3.0 18.0 1.0 CG A:HIS135 3.0 16.0 1.0 O A:HOH2135 3.3 28.9 1.0 CB A:HIS135 3.3 16.9 1.0 NE2 A:HIS135 4.1 20.1 1.0 O A:GLY235 4.1 17.5 1.0 CD2 A:HIS135 4.1 19.1 1.0 NE2 A:HIS133 4.1 17.9 1.0 CB A:ASP236 4.2 16.9 1.0 CE1 A:HIS133 4.4 19.9 1.0 OD1 A:ASP136 4.5 25.9 1.0 OD2 A:ASP136 4.7 23.1 1.0 CA A:ASP236 4.8 17.1 1.0 C A:GLY235 4.8 17.7 1.0 CA A:HIS135 4.9 16.5 1.0 CG A:ASP136 4.9 20.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate


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 Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1252 b:23.5 occ:1.00 NE2 B:HIS143 1.9 21.8 1.0 NE2 B:HIS227 2.0 21.0 1.0 OD1 B:ASP145 2.0 20.8 1.0 O B:HOH2187 2.2 19.1 1.0 CD2 B:HIS143 2.8 21.3 1.0 CG B:ASP145 2.9 18.9 1.0 CE1 B:HIS143 3.0 22.9 1.0 CD2 B:HIS227 3.0 20.7 1.0 CE1 B:HIS227 3.0 21.2 1.0 OD2 B:ASP145 3.0 21.6 1.0 CG B:HIS143 4.0 21.8 1.0 ND1 B:HIS143 4.0 22.1 1.0 ND1 B:HIS227 4.1 21.1 1.0 CG B:HIS227 4.1 20.4 1.0 CB B:ASP145 4.3 18.7 1.0 CZ B:PHE212 4.6 19.1 1.0 CA B:ASP145 4.7 19.7 1.0 N B:ASP145 4.7 18.8 1.0 CZ2 B:TRP243 4.9 18.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate


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 Chlamydomonas Reinhardtii Prolyl-4 Hydroxylase Type I Complexed with Zinc and Pyridine-2,4-Dicarboxylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1253 b:53.4 occ:0.50 ND1 B:HIS133 2.3 26.1 1.0 NE2 B:HIS135 2.9 36.5 1.0 CE1 B:HIS133 3.1 26.6 1.0 CG B:HIS133 3.3 25.9 1.0 CE1 B:HIS135 3.6 37.0 1.0 CB B:HIS133 3.7 25.6 1.0 CD2 B:HIS135 4.0 36.0 1.0 NE2 B:HIS133 4.2 25.8 1.0 OG1 B:THR96 4.3 33.5 1.0 CB B:THR96 4.3 31.6 1.0 CD2 B:HIS133 4.4 26.4 1.0 CZ2 B:TRP238 4.7 23.7 1.0 O B:HIS133 4.8 26.6 1.0 SD B:MET74 4.9 35.4 1.0 CH2 B:TRP238 4.9 22.9 1.0 ND1 B:HIS135 4.9 36.1 1.0 CA B:HIS133 5.0 25.6 1.0

M.K.Koski, R.Hieta, C.Bollner, K.I.Kivirikko, J.Myllyharju, R.K.Wierenga. The Active Site of An Algal Prolyl 4-Hydroxylase Has A Large Structural Plasticity. J.Biol.Chem. V. 282 37112 2007.
ISSN: ISSN 0021-9258
PubMed: 17940281
DOI: 10.1074/JBC.M706554200