Zinc in PDB 1kb4: Crystal Structure of Vdr Dna-Binding Domain Bound to A Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element

The structure of Crystal Structure of Vdr Dna-Binding Domain Bound to A Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element, PDB code: 1kb4 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 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.500, 61.500, 241.970, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 27.2

The binding sites of Zinc atom in the Crystal Structure of Vdr Dna-Binding Domain Bound to A Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element (pdb code 1kb4). 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 A Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element, PDB code: 1kb4:
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 A Canonical Direct Repeat with Three Base Pair Spacer (DR3) 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 A Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:60.5 occ:1.00 SG A:CYS24 2.2 58.0 1.0 SG A:CYS27 2.3 65.0 1.0 SG A:CYS44 2.4 60.0 1.0 SG A:CYS41 2.5 56.0 1.0 CB A:CYS44 3.2 57.6 1.0 CB A:CYS24 3.2 61.3 1.0 CB A:CYS27 3.5 60.1 1.0 CB A:CYS41 3.5 54.4 1.0 N A:CYS27 3.6 59.7 1.0 N A:CYS41 4.0 55.3 1.0 CB A:VAL26 4.1 55.5 1.0 CA A:CYS27 4.1 60.3 1.0 NH1 A:ARG73 4.2 63.5 1.0 N A:CYS44 4.2 58.2 1.0 CA A:CYS44 4.3 58.8 1.0 CA A:CYS41 4.4 55.4 1.0 C A:VAL26 4.5 58.5 1.0 CA A:CYS24 4.6 62.1 1.0 CA A:VAL26 4.6 56.7 1.0 N A:VAL26 4.6 55.8 1.0 CG1 A:VAL26 4.7 51.1 1.0 CB A:ASP29 4.7 67.1 1.0 C A:CYS27 4.8 60.8 1.0 O A:CYS41 4.9 58.1 1.0 CD A:ARG73 4.9 61.6 1.0 N A:GLY28 4.9 61.7 1.0 C A:CYS41 4.9 56.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to A Canonical Direct Repeat with Three Base Pair Spacer (DR3) 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 A Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn151 b:59.6 occ:1.00 SG A:CYS79 2.2 50.1 1.0 SG A:CYS76 2.2 64.2 1.0 SG A:CYS60 2.3 59.4 1.0 SG A:CYS66 2.4 54.8 1.0 CB A:CYS79 3.2 50.3 1.0 CB A:CYS60 3.3 58.8 1.0 CB A:CYS76 3.4 62.5 1.0 CB A:CYS66 3.4 56.3 1.0 N A:CYS66 4.0 57.6 1.0 N A:CYS79 4.1 50.8 1.0 CA A:CYS60 4.1 59.8 1.0 CA A:CYS79 4.2 50.3 1.0 O A:HOH612 4.3 49.0 1.0 CA A:CYS66 4.3 57.2 1.0 CA A:GLY64 4.3 59.5 1.0 N A:ASP65 4.5 59.1 1.0 CD2 A:PHE62 4.5 73.3 1.0 N A:GLY64 4.5 61.5 1.0 C A:GLY64 4.6 59.3 1.0 CA A:CYS76 4.7 61.8 1.0 CB A:ALA78 4.8 50.5 1.0 C A:CYS60 5.0 60.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to A Canonical Direct Repeat with Three Base Pair Spacer (DR3) 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 A Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn350 b:67.7 occ:1.00 SG B:CYS227 2.2 74.9 1.0 SG B:CYS224 2.2 76.0 1.0 SG B:CYS244 2.3 65.2 1.0 SG B:CYS241 2.5 69.2 1.0 CB B:CYS244 3.3 65.1 1.0 CB B:CYS224 3.4 78.5 1.0 CB B:CYS241 3.4 65.9 1.0 CB B:CYS227 3.5 75.2 1.0 N B:CYS227 3.6 74.5 1.0 N B:CYS241 4.0 65.2 1.0 N B:CYS244 4.1 65.3 1.0 CA B:CYS227 4.1 75.4 1.0 CB B:ASP229 4.1 80.7 1.0 CB B:VAL226 4.2 71.9 1.0 CA B:CYS244 4.3 65.1 1.0 CA B:CYS241 4.3 65.1 1.0 NH1 B:ARG273 4.5 68.7 1.0 N B:ASP229 4.7 79.3 1.0 C B:VAL226 4.7 74.3 1.0 CG1 B:VAL226 4.7 70.3 1.0 C B:CYS227 4.8 76.2 1.0 CA B:CYS224 4.8 79.5 1.0 N B:GLY228 4.8 76.4 1.0 CA B:VAL226 4.8 73.7 1.0 N B:VAL226 4.9 74.5 1.0 CD B:ARG273 4.9 73.8 1.0 C B:CYS241 4.9 65.5 1.0 O B:CYS241 5.0 66.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vdr Dna-Binding Domain Bound to A Canonical Direct Repeat with Three Base Pair Spacer (DR3) 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 A Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn351 b:75.8 occ:1.00 SG B:CYS260 2.2 79.9 1.0 SG B:CYS279 2.3 77.3 1.0 SG B:CYS266 2.4 84.1 1.0 SG B:CYS276 2.5 77.4 1.0 CB B:CYS276 3.4 79.0 1.0 CB B:CYS279 3.4 73.8 1.0 CB B:CYS266 3.4 85.3 1.0 CB B:CYS260 3.4 79.4 1.0 N B:CYS266 3.9 87.6 1.0 CA B:CYS266 4.2 86.7 1.0 CA B:CYS260 4.3 80.7 1.0 CD1 B:PHE262 4.3 91.2 1.0 CA B:GLY264 4.4 88.7 1.0 N B:ASP265 4.5 88.5 1.0 N B:CYS279 4.5 72.8 1.0 CA B:CYS279 4.5 72.9 1.0 CD B:PRO261 4.5 83.3 1.0 N B:GLY264 4.5 89.5 1.0 C B:GLY264 4.7 88.6 1.0 CA B:CYS276 4.8 79.6 1.0 N B:PRO261 4.9 83.2 1.0 C B:CYS260 5.0 81.9 1.0 N B:PHE262 5.0 86.3 1.0 C B:ASP265 5.0 88.6 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