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

Protein crystallography data

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

Zinc Binding Sites:

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 2jig

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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 2jig

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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 2jig

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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 2jig

Go back to Zinc Binding Sites List in 2jig
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

Reference:

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
Page generated: Thu Oct 17 01:14:26 2024

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