Zinc in PDB 3r68: Molecular Analysis of the PDZ3 Domain of PDZK1

The structure of Molecular Analysis of the PDZ3 Domain of PDZK1, PDB code: 3r68 was solved by O.Kocher, G.Birrane, M.Krieger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.15 / 1.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.910, 69.910, 37.659, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 15.7

The structure of Molecular Analysis of the PDZ3 Domain of PDZK1 also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Molecular Analysis of the PDZ3 Domain of PDZK1 (pdb code 3r68). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Molecular Analysis of the PDZ3 Domain of PDZK1, PDB code: 3r68:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Molecular Analysis of the PDZ3 Domain of PDZK1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Molecular Analysis of the PDZ3 Domain of PDZK1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4 b:11.9 occ:1.00 OE2 A:GLU297 2.0 15.7 1.0 CD A:GLU297 2.9 17.0 1.0 OE1 A:GLU297 3.2 24.5 1.0 CG A:GLU297 4.2 16.8 1.0 CG1 A:VAL289 4.3 12.3 1.0 CB A:VAL289 4.6 9.9 1.0

Zinc binding site 2 out of 4 in the Molecular Analysis of the PDZ3 Domain of PDZK1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Molecular Analysis of the PDZ3 Domain of PDZK1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5 b:11.0 occ:1.00 O A:HOH108 2.0 9.5 1.0 OD1 A:ASP302 2.0 10.2 1.0 CG A:ASP302 2.8 11.4 1.0 OD2 A:ASP302 2.9 15.2 1.0 ZN A:ZN6 3.3 9.9 1.0 O A:HOH332 3.8 10.9 1.0 O A:HOH23 4.1 13.8 1.0 O A:HOH40 4.1 9.4 1.0 CB A:ASP302 4.2 10.6 1.0 CD2 A:HIS301 4.7 8.7 1.0 O A:HOH34 4.7 17.2 1.0 CA A:ASP302 4.8 9.9 1.0 N A:ASP302 5.0 9.8 1.0

Zinc binding site 3 out of 4 in the Molecular Analysis of the PDZ3 Domain of PDZK1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Molecular Analysis of the PDZ3 Domain of PDZK1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn6 b:9.9 occ:1.00 O A:HOH108 1.6 9.5 1.0 O A:HOH40 1.7 9.4 1.0 O A:HOH34 1.9 17.2 1.0 ZN A:ZN7 3.3 9.0 1.0 ZN A:ZN5 3.3 11.0 1.0 O A:HOH332 3.7 10.9 1.0 CD2 A:HIS301 4.1 8.7 1.0 NE2 A:HIS301 4.2 8.7 1.0 OD1 A:ASP302 4.3 10.2 1.0 O A:HOH109 4.7 7.4 0.5

Zinc binding site 4 out of 4 in the Molecular Analysis of the PDZ3 Domain of PDZK1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Molecular Analysis of the PDZ3 Domain of PDZK1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7 b:9.0 occ:1.00 O A:HOH40 2.0 9.4 1.0 O A:HOH109 2.0 7.4 0.5 NE2 A:HIS301 2.1 8.7 1.0 CE1 A:HIS301 3.0 8.5 1.0 CD2 A:HIS301 3.1 8.7 1.0 ZN A:ZN6 3.3 9.9 1.0 O A:HOH34 3.7 17.2 1.0 CL A:CL10 3.9 9.8 1.0 O A:HOH332 4.0 10.9 1.0 ND1 A:HIS301 4.1 9.4 1.0 CG A:HIS301 4.2 9.0 1.0 CG2 A:VAL305 4.2 10.3 1.0 O A:HOH108 4.2 9.5 1.0 NH1 A:ARG258 4.9 10.3 0.5

O.Kocher, G.Birrane, A.Yesilaltay, S.Shechter, R.Pal, K.Daniels, M.Krieger. Identification of the PDZ3 Domain of the Adaptor Protein PDZK1 As A Second, Physiologically Functional Binding Site For the C Terminus of the High Density Lipoprotein Receptor Scavenger Receptor Class B Type I. J.Biol.Chem. V. 286 25171 2011.
ISSN: ISSN 0021-9258
PubMed: 21602281
DOI: 10.1074/JBC.M111.242362