Zinc in PDB 1kb6: Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element

The structure of Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element, PDB code: 1kb6 was solved by P.L.Shaffer, D.T.Gewirth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.150, 61.150, 241.800, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 27.5

The binding sites of Zinc atom in the Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element (pdb code 1kb6). 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 Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element, PDB code: 1kb6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element


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 Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:58.0 occ:1.00 SG A:CYS24 2.2 59.0 1.0 SG A:CYS27 2.3 57.1 1.0 SG A:CYS44 2.3 55.9 1.0 SG A:CYS41 2.4 57.2 1.0 CB A:CYS24 3.2 61.2 1.0 CB A:CYS44 3.3 56.5 1.0 CB A:CYS27 3.4 59.1 1.0 CB A:CYS41 3.4 57.3 1.0 N A:CYS27 3.5 58.7 1.0 CA A:CYS27 4.0 60.2 1.0 NH1 A:ARG73 4.0 70.4 1.0 N A:CYS41 4.0 57.8 1.0 N A:CYS44 4.2 57.8 1.0 CB A:VAL26 4.2 57.2 1.0 CA A:CYS41 4.3 58.4 1.0 CA A:CYS44 4.4 57.5 1.0 CB A:ASP29 4.5 71.8 1.0 N A:GLY28 4.5 63.5 1.0 C A:VAL26 4.6 57.8 1.0 C A:CYS27 4.6 62.0 1.0 CA A:CYS24 4.7 61.4 1.0 N A:ASP29 4.7 68.6 1.0 CA A:VAL26 4.8 57.7 1.0 N A:VAL26 4.8 56.3 1.0 NH2 A:ARG80 4.8 42.2 1.0 CG1 A:VAL26 4.8 55.7 1.0 CD A:ARG73 5.0 67.0 1.0 C A:CYS41 5.0 60.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element


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 Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn151 b:57.9 occ:1.00 SG A:CYS60 2.2 59.3 1.0 SG A:CYS79 2.2 50.7 1.0 SG A:CYS76 2.3 57.8 1.0 SG A:CYS66 2.3 57.2 1.0 CB A:CYS79 3.2 50.5 1.0 CB A:CYS66 3.4 54.5 1.0 CB A:CYS76 3.4 61.6 1.0 CB A:CYS60 3.4 61.2 1.0 N A:CYS66 4.0 53.6 1.0 CA A:CYS60 4.1 62.8 1.0 N A:CYS79 4.2 51.0 1.0 CA A:GLY64 4.2 58.5 1.0 N A:GLY64 4.2 60.2 1.0 CA A:CYS79 4.3 50.0 1.0 CA A:CYS66 4.3 54.7 1.0 N A:ASP65 4.4 57.6 1.0 CD A:PRO61 4.7 61.1 1.0 C A:GLY64 4.7 58.0 1.0 CA A:CYS76 4.8 62.5 1.0 CB A:PHE62 4.9 64.0 1.0 CD2 A:PHE62 5.0 65.8 1.0 CB A:ALA78 5.0 50.7 1.0 C A:CYS60 5.0 62.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element


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 Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn350 b:68.6 occ:1.00 SG B:CYS227 2.2 85.3 1.0 SG B:CYS224 2.2 82.0 1.0 SG B:CYS241 2.4 71.7 1.0 SG B:CYS244 2.4 71.0 1.0 CB B:CYS227 2.9 83.5 1.0 CB B:CYS241 3.1 70.3 1.0 CB B:CYS224 3.2 84.5 1.0 CB B:CYS244 3.4 67.4 1.0 N B:CYS227 3.5 82.5 1.0 N B:CYS241 3.8 68.3 1.0 CA B:CYS227 3.8 83.1 1.0 CA B:CYS241 4.0 70.5 1.0 NH1 B:ARG273 4.2 79.6 1.0 N B:CYS244 4.2 67.7 1.0 CB B:ASP229 4.3 84.7 1.0 CA B:CYS244 4.4 67.6 1.0 C B:CYS227 4.5 82.5 1.0 CD B:ARG273 4.6 84.9 1.0 O B:CYS241 4.6 72.8 1.0 C B:VAL226 4.7 81.8 1.0 CB B:VAL226 4.7 80.7 1.0 N B:GLY228 4.7 82.0 1.0 C B:CYS241 4.7 71.4 1.0 CA B:CYS224 4.7 85.5 1.0 N B:ASP229 4.8 83.2 1.0 C B:THR240 4.9 66.7 1.0 N B:VAL226 5.0 81.8 1.0 CZ B:ARG273 5.0 81.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element


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 Vdr Dna-Binding Domain Bound to Rat Osteocalcin (Oc) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn351 b:80.5 occ:1.00 SG B:CYS260 2.3 81.7 1.0 SG B:CYS276 2.4 77.6 1.0 SG B:CYS279 2.4 77.8 1.0 SG B:CYS266 2.4 79.7 1.0 CB B:CYS260 3.2 81.0 1.0 CB B:CYS279 3.3 74.8 1.0 CB B:CYS276 3.4 81.7 1.0 CB B:CYS266 3.4 82.7 1.0 CA B:CYS260 4.1 82.0 1.0 N B:CYS266 4.2 86.0 1.0 N B:CYS279 4.2 73.4 1.0 CD1 B:PHE262 4.3 89.7 1.0 CA B:CYS279 4.4 73.2 1.0 CA B:CYS266 4.4 84.9 1.0 N B:GLY264 4.5 91.1 1.0 CA B:GLY264 4.6 89.9 1.0 CD B:PRO261 4.7 86.5 1.0 C B:CYS260 4.7 84.2 1.0 CB B:PHE262 4.8 89.3 1.0 N B:PRO261 4.8 86.3 1.0 N B:PHE262 4.8 88.5 1.0 N B:ASP265 4.8 88.8 1.0 CA B:CYS276 4.9 82.9 1.0 CG B:PHE262 5.0 89.4 1.0 C B:GLY264 5.0 89.0 1.0

P.L.Shaffer, D.T.Gewirth. Structural Basis of Vdr-Dna Interactions on Direct Repeat Response Elements. Embo J. V. 21 2242 2002.
ISSN: ISSN 0261-4189
PubMed: 11980721
DOI: 10.1093/EMBOJ/21.9.2242