Zinc in PDB 3gze: Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate

The structure of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate, PDB code: 3gze was solved by M.K.Koski, R.K.Wierenga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.60 / 1.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.250, 58.750, 105.160, 90.00, 102.21, 90.00
R / Rfree (%)	21.7 / 25.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate (pdb code 3gze). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate, PDB code: 3gze:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:9.5 occ:1.00 OXT A:ACY254 1.9 8.3 1.0 OD1 A:ASP145 2.0 10.9 1.0 NE2 A:HIS227 2.0 6.2 1.0 NE2 A:HIS143 2.1 4.8 1.0 C A:ACY254 2.6 8.7 1.0 O A:ACY254 2.6 11.2 1.0 CG A:ASP145 2.9 8.8 1.0 CE1 A:HIS227 2.9 10.2 1.0 CE1 A:HIS143 3.0 9.9 1.0 CD2 A:HIS143 3.0 10.1 1.0 CD2 A:HIS227 3.0 9.9 1.0 OD2 A:ASP145 3.1 3.9 1.0 ND1 A:HIS227 4.0 4.8 1.0 CH3 A:ACY254 4.0 8.3 1.0 CG A:HIS227 4.1 8.2 1.0 ND1 A:HIS143 4.1 9.1 1.0 CG A:HIS143 4.1 9.2 1.0 CG X:PRO6 4.1 8.7 1.0 CD X:PRO6 4.2 7.5 1.0 CB A:ASP145 4.3 9.8 1.0 CE2 A:TYR140 4.4 10.6 1.0 NE1 A:TRP243 4.5 8.7 1.0 CA A:ASP145 4.6 9.5 1.0 N A:ASP145 4.6 8.6 1.0 CZ A:TYR140 4.9 8.2 1.0 CZ2 A:TRP243 4.9 8.2 1.0 OH A:TYR140 4.9 12.8 1.0 CD2 A:TYR140 4.9 9.3 1.0 CZ A:PHE212 4.9 11.0 1.0 C A:TYR144 4.9 8.7 1.0 O A:HIS227 5.0 9.3 1.0

Zinc binding site 2 out of 14 in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5 b:12.6 occ:1.00 OD1 A:ASP236 2.0 8.9 1.0 ND1 A:HIS135 2.0 10.9 1.0 CG A:ASP236 2.9 9.9 1.0 CG A:HIS135 3.0 10.2 1.0 CE1 A:HIS135 3.1 7.2 1.0 OD2 A:ASP236 3.2 9.6 1.0 CB A:HIS135 3.3 9.8 1.0 OD2 A:ASP136 3.9 4.1 1.0 NE2 A:HIS133 4.0 2.6 1.0 NE2 A:HIS135 4.1 6.4 1.0 CD2 A:HIS135 4.2 8.4 1.0 CE1 A:HIS133 4.3 5.6 1.0 CB A:ASP236 4.3 10.4 1.0 CG A:ASP136 4.6 7.8 1.0 OD1 A:ASP136 4.7 9.0 1.0 CA A:ASP236 4.8 9.8 1.0 CA A:HIS135 4.8 9.6 1.0 O A:GLY235 5.0 11.1 1.0

Zinc binding site 3 out of 14 in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7 b:9.8 occ:0.50 OE1 A:GLU91 1.8 15.7 1.0 OE2 A:GLU141 1.9 10.5 1.0 CD A:GLU141 2.6 14.1 1.0 OE1 A:GLU141 2.7 17.6 1.0 CD A:GLU91 2.8 17.5 1.0 OE2 A:GLU91 3.2 13.2 1.0 O A:HOH291 3.5 40.5 1.0 NZ A:LYS139 4.0 13.5 1.0 CG A:GLU141 4.0 12.1 1.0 CD1 A:ILE92 4.2 20.8 1.0 CG A:GLU91 4.2 14.9 1.0 CA A:ILE92 4.3 12.7 1.0 O A:GLU91 4.3 11.1 1.0 N A:ILE92 4.4 12.5 1.0 C A:GLU91 4.4 12.4 1.0 CB A:GLU91 4.6 14.1 1.0 CG1 A:ILE92 4.7 15.9 1.0 CE A:LYS139 4.7 14.0 1.0

Zinc binding site 4 out of 14 in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn8 b:36.4 occ:1.00 O A:HOH311 2.0 18.4 1.0 NE2 A:HIS148 2.3 9.1 1.0 OE1 A:GLU83 2.6 14.2 1.0 OE2 A:GLU83 2.7 20.3 1.0 CD A:GLU83 3.0 15.8 1.0 CD2 A:HIS148 3.2 12.8 1.0 CE1 A:HIS148 3.2 11.4 1.0 O A:HOH348 4.2 21.4 1.0 ND1 A:HIS148 4.3 14.1 1.0 CG A:HIS148 4.3 8.4 1.0 CG A:GLU83 4.5 14.8 1.0

Zinc binding site 5 out of 14 in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn10 b:29.5 occ:0.50 O A:HOH319 2.4 39.4 1.0 CE1 A:HIS157 3.0 26.8 1.0 NE2 A:HIS157 3.3 25.8 1.0 ND1 A:HIS157 4.0 23.5 1.0 CB A:GLU156 4.3 20.1 1.0 CD2 A:HIS157 4.4 22.3 1.0 CD A:GLU156 4.4 28.2 1.0 CG A:GLU156 4.5 22.5 1.0 OE1 A:GLU156 4.5 24.2 1.0 CG A:HIS157 4.7 20.8 1.0 OE2 A:GLU156 4.9 31.1 1.0 CG1 A:VAL151 5.0 11.4 1.0 O A:HOH349 5.0 31.1 1.0

Zinc binding site 6 out of 14 in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:10.1 occ:1.00 OD1 B:ASP145 2.0 9.6 1.0 O B:ACY254 2.0 15.4 1.0 NE2 B:HIS227 2.0 2.3 1.0 NE2 B:HIS143 2.2 12.7 1.0 C B:ACY254 2.7 13.1 1.0 OXT B:ACY254 2.8 12.1 1.0 CG B:ASP145 2.8 8.1 1.0 CE1 B:HIS227 2.8 2.0 1.0 OD2 B:ASP145 2.9 10.7 1.0 CD2 B:HIS143 3.0 10.7 1.0 CD2 B:HIS227 3.1 7.0 1.0 CE1 B:HIS143 3.1 10.5 1.0 ND1 B:HIS227 4.0 5.7 1.0 CG B:HIS143 4.1 11.5 1.0 ND1 B:HIS143 4.1 11.9 1.0 CG B:HIS227 4.1 5.2 1.0 CH3 B:ACY254 4.2 13.4 1.0 CB B:ASP145 4.2 7.2 1.0 NE1 B:TRP243 4.3 16.7 1.0 CZ2 B:TRP243 4.4 19.5 1.0 CA B:ASP145 4.6 6.9 1.0 CE2 B:TRP243 4.7 16.0 1.0 N B:ASP145 4.8 6.6 1.0 CZ B:PHE212 5.0 6.2 1.0

Zinc binding site 7 out of 14 in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn12 b:46.2 occ:1.00 OD1 B:ASP236 2.1 16.9 1.0 NE2 B:HIS133 2.2 11.4 1.0 CG B:ASP236 2.8 18.4 1.0 OD2 B:ASP236 2.8 23.4 1.0 CE1 B:HIS133 3.1 11.3 1.0 CD2 B:HIS133 3.3 14.1 1.0 O B:HOH334 3.5 43.6 1.0 CB B:ASP236 4.2 18.1 1.0 ND1 B:HIS133 4.2 14.3 1.0 CG B:HIS133 4.4 13.7 1.0 NE1 B:TRP238 4.4 14.7 1.0 CA B:ASP236 4.9 17.7 1.0

Zinc binding site 8 out of 14 in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn14 b:31.4 occ:1.00 O B:ACY5 1.9 7.8 1.0 NE2 B:HIS148 2.0 13.5 1.0 NE2 D:HIS148 2.1 12.2 1.0 OXT B:ACY5 2.1 6.8 1.0 C B:ACY5 2.3 8.4 1.0 CE1 B:HIS148 2.5 15.4 1.0 CE1 D:HIS148 2.5 16.9 1.0 CD2 B:HIS148 3.3 16.9 1.0 CD2 D:HIS148 3.4 15.6 1.0 ND1 B:HIS148 3.8 10.2 1.0 ND1 D:HIS148 3.8 13.2 1.0 CH3 B:ACY5 3.8 8.1 1.0 CG B:HIS148 4.2 15.1 1.0 CG D:HIS148 4.2 15.2 1.0 CD1 D:TYR144 4.6 4.1 1.0 CD1 B:TYR144 4.6 6.8 1.0 O B:HOH372 4.7 24.5 1.0 N B:TYR144 4.7 7.1 1.0 O B:TYR144 4.8 6.6 1.0 N D:TYR144 4.9 7.9 1.0 CB B:HIS143 5.0 8.4 1.0

Zinc binding site 9 out of 14 in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3 b:10.1 occ:1.00 O C:ACY254 2.0 10.0 1.0 OD1 C:ASP145 2.1 14.7 1.0 NE2 C:HIS143 2.1 12.4 1.0 NE2 C:HIS227 2.1 9.0 1.0 OXT C:ACY254 2.5 9.7 1.0 C C:ACY254 2.6 10.8 1.0 CG C:ASP145 3.0 10.3 1.0 CE1 C:HIS143 3.0 15.3 1.0 CE1 C:HIS227 3.1 14.1 1.0 CD2 C:HIS227 3.1 9.8 1.0 CD2 C:HIS143 3.1 12.7 1.0 OD2 C:ASP145 3.2 11.4 1.0 CH3 C:ACY254 4.0 10.3 1.0 CG Y:PRO6 4.0 10.8 1.0 ND1 C:HIS143 4.1 10.3 1.0 ND1 C:HIS227 4.2 9.8 1.0 CG C:HIS227 4.2 11.0 1.0 CD Y:PRO6 4.2 12.4 1.0 CG C:HIS143 4.2 9.7 1.0 CB C:ASP145 4.3 9.0 1.0 CE2 C:TYR140 4.4 8.5 1.0 NE1 C:TRP243 4.4 12.6 1.0 CA C:ASP145 4.6 9.3 1.0 N C:ASP145 4.7 8.0 1.0 CZ2 C:TRP243 4.8 13.0 1.0 CD2 C:TYR140 4.8 7.9 1.0 CZ C:PHE212 4.9 9.3 1.0 C C:TYR144 5.0 8.3 1.0 CE2 C:TRP243 5.0 11.0 1.0

Zinc binding site 10 out of 14 in the Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Algal Prolyl 4-Hydroxylase Complexed with Zinc and (Ser-Pro)5 Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn6 b:15.2 occ:1.00 OD1 C:ASP236 2.1 9.1 1.0 ND1 C:HIS135 2.1 9.6 1.0 CG C:ASP236 3.0 11.0 1.0 CG C:HIS135 3.0 10.6 1.0 OD2 C:ASP236 3.2 11.0 1.0 CB C:HIS135 3.2 9.5 1.0 CE1 C:HIS135 3.2 9.2 1.0 OD2 C:ASP136 3.9 3.8 1.0 NE2 C:HIS133 4.0 8.4 1.0 CD2 C:HIS135 4.2 9.8 1.0 NE2 C:HIS135 4.2 10.7 1.0 CE1 C:HIS133 4.3 10.9 1.0 CB C:ASP236 4.3 9.4 1.0 CG C:ASP136 4.6 8.0 1.0 CA C:HIS135 4.7 10.8 1.0 OD1 C:ASP136 4.7 6.9 1.0 CA C:ASP236 4.8 9.9 1.0 O C:GLY235 4.9 12.0 1.0

M.K.Koski, R.Hieta, M.Hirsila, A.Ronka, J.Myllyharju, R.K.Wierenga. The Crystal Structure of An Algal Prolyl 4-Hydroxylase Complexed with A Proline-Rich Peptide Reveals A Novel Buried Tripeptide Binding Motif J.Biol.Chem. V. 284 25290 2009.
ISSN: ISSN 0021-9258
PubMed: 19553701
DOI: 10.1074/JBC.M109.014050