Zinc in PDB 1kb2: Crystal Structure of Vdr Dna-Binding Domain Bound to Mouse Osteopontin (Spp) Response Element

The structure of Crystal Structure of Vdr Dna-Binding Domain Bound to Mouse Osteopontin (Spp) Response Element, PDB code: 1kb2 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 (°)	62.140, 62.140, 241.750, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 28.9

The binding sites of Zinc atom in the Crystal Structure of Vdr Dna-Binding Domain Bound to Mouse Osteopontin (Spp) Response Element (pdb code 1kb2). 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 Mouse Osteopontin (Spp) Response Element, PDB code: 1kb2:
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 Mouse Osteopontin (Spp) 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 Mouse Osteopontin (Spp) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:58.7 occ:1.00 SG A:CYS24 2.3 65.6 1.0 SG A:CYS27 2.3 66.5 1.0 SG A:CYS44 2.4 63.0 1.0 SG A:CYS41 2.4 62.4 1.0 CB A:CYS44 3.2 59.2 1.0 CB A:CYS24 3.3 66.5 1.0 CB A:CYS27 3.4 65.2 1.0 CB A:CYS41 3.6 60.0 1.0 N A:CYS27 3.6 64.3 1.0 N A:CYS41 3.9 58.0 1.0 CA A:CYS27 4.0 65.7 1.0 N A:CYS44 4.2 57.9 1.0 NH1 A:ARG73 4.3 54.5 1.0 CA A:CYS44 4.3 58.6 1.0 CB A:VAL26 4.3 62.0 1.0 CA A:CYS41 4.3 58.9 1.0 C A:VAL26 4.6 64.1 1.0 CB A:ASP29 4.6 79.0 1.0 CG1 A:VAL26 4.7 58.6 1.0 CA A:CYS24 4.7 65.9 1.0 C A:CYS27 4.8 67.7 1.0 CA A:VAL26 4.8 62.9 1.0 N A:VAL26 4.8 63.0 1.0 CD A:ARG73 4.9 60.1 1.0 N A:GLY28 4.9 70.1 1.0 C A:CYS41 4.9 59.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Mouse Osteopontin (Spp) 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 Mouse Osteopontin (Spp) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn151 b:58.1 occ:1.00 SG A:CYS66 2.2 57.4 1.0 SG A:CYS76 2.2 57.9 1.0 SG A:CYS60 2.2 56.8 1.0 SG A:CYS79 2.3 58.2 1.0 CB A:CYS66 3.1 55.2 1.0 CB A:CYS79 3.2 55.5 1.0 CB A:CYS76 3.2 59.8 1.0 CB A:CYS60 3.4 56.5 1.0 N A:CYS66 4.0 55.3 1.0 CA A:CYS60 4.1 58.1 1.0 O A:HOH607 4.1 60.2 1.0 N A:CYS79 4.1 54.4 1.0 CA A:CYS66 4.1 55.1 1.0 CA A:CYS79 4.2 55.0 1.0 CD A:PRO61 4.4 60.4 1.0 N A:GLY64 4.5 63.0 1.0 CA A:GLY64 4.6 60.9 1.0 CA A:CYS76 4.6 60.3 1.0 CD2 A:PHE62 4.6 72.5 1.0 N A:ASP65 4.8 58.6 1.0 C A:GLY64 4.8 59.9 1.0 C A:CYS60 4.9 59.1 1.0 N A:PRO61 4.9 60.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Mouse Osteopontin (Spp) 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 Mouse Osteopontin (Spp) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn350 b:71.1 occ:1.00 SG B:CYS244 2.3 71.9 1.0 SG B:CYS224 2.3 81.1 1.0 SG B:CYS227 2.4 76.3 1.0 SG B:CYS241 2.5 68.2 1.0 CB B:CYS244 3.1 70.6 1.0 CB B:CYS241 3.3 68.3 1.0 CB B:CYS227 3.4 78.4 1.0 CB B:CYS224 3.5 80.7 1.0 N B:CYS227 3.5 78.8 1.0 N B:CYS241 3.9 66.4 1.0 CA B:CYS227 4.1 78.1 1.0 N B:CYS244 4.1 70.1 1.0 CA B:CYS244 4.2 69.9 1.0 CA B:CYS241 4.2 67.3 1.0 CB B:VAL226 4.3 80.2 1.0 CB B:ASP229 4.4 84.0 1.0 C B:VAL226 4.6 79.8 1.0 CD B:ARG273 4.6 80.7 1.0 NH1 B:ARG273 4.6 73.3 1.0 N B:VAL226 4.7 79.9 1.0 CA B:VAL226 4.8 80.0 1.0 CG1 B:VAL226 4.8 79.7 1.0 C B:CYS227 4.8 77.8 1.0 CA B:CYS224 4.8 81.3 1.0 C B:CYS241 4.8 68.0 1.0 N B:GLY228 4.9 78.2 1.0 N B:ASP229 4.9 81.3 1.0 O B:CYS241 4.9 67.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to Mouse Osteopontin (Spp) 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 Mouse Osteopontin (Spp) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn351 b:81.5 occ:1.00 SG B:CYS260 2.3 82.3 1.0 SG B:CYS266 2.3 80.4 1.0 SG B:CYS279 2.4 83.0 1.0 SG B:CYS276 2.5 79.8 1.0 CB B:CYS260 3.1 84.2 1.0 CB B:CYS279 3.3 80.1 1.0 CB B:CYS276 3.7 81.6 1.0 CB B:CYS266 3.8 82.8 1.0 N B:CYS266 4.0 85.4 1.0 CA B:CYS260 4.2 86.1 1.0 CD1 B:PHE262 4.2 91.1 1.0 N B:CYS279 4.3 77.3 1.0 CA B:CYS279 4.4 77.8 1.0 N B:ASP265 4.5 88.7 1.0 CA B:CYS266 4.5 84.1 1.0 CA B:GLY264 4.5 89.7 1.0 N B:GLY264 4.5 90.5 1.0 C B:CYS260 4.8 86.7 1.0 C B:GLY264 4.8 89.2 1.0 CE1 B:PHE262 4.9 90.4 1.0 N B:PRO261 4.9 87.2 1.0 CD B:PRO261 5.0 86.7 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