Zinc in PDB 5b3h: The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex

The structure of The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex, PDB code: 5b3h was solved by Y.Hirano, T.Suyama, M.Nakagawa, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.44 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.668, 203.389, 88.451, 90.00, 90.46, 90.00
R / Rfree (%)	20.8 / 24.6

The binding sites of Zinc atom in the The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex (pdb code 5b3h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex, PDB code: 5b3h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:0.6 occ:1.00 SG C:CYS207 2.2 0.8 1.0 SG C:CYS190 2.2 0.2 1.0 NE2 C:HIS203 2.4 0.1 1.0 CB C:CYS190 2.5 0.5 1.0 SG C:CYS188 2.5 0.6 1.0 CD2 C:HIS203 2.8 0.2 1.0 CB C:CYS207 2.9 0.6 1.0 N C:CYS190 3.3 0.0 1.0 CA C:CYS190 3.4 0.3 1.0 CE1 C:HIS203 3.6 0.3 1.0 CB C:CYS188 3.8 0.2 1.0 CG C:HIS203 4.0 0.1 1.0 CA C:CYS207 4.1 0.7 1.0 ND1 C:HIS203 4.4 0.2 1.0 C C:CYS190 4.4 0.7 1.0 N C:GLY191 4.5 0.5 1.0 C C:ASP189 4.5 0.8 1.0 N C:ASP189 4.6 0.2 1.0 N C:CYS207 4.9 0.8 1.0 O C:HIS203 4.9 88.0 1.0 C C:CYS188 4.9 0.4 1.0

Zinc binding site 2 out of 4 in the The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:0.6 occ:1.00 SG C:CYS181 2.1 0.1 1.0 NE2 C:HIS177 2.3 0.7 1.0 SG C:CYS164 2.3 0.1 1.0 SG C:CYS161 2.4 0.1 1.0 CB C:CYS164 2.6 0.4 1.0 N C:CYS164 3.0 0.3 1.0 CE1 C:HIS177 3.0 0.8 1.0 CA C:CYS164 3.4 0.4 1.0 CD2 C:HIS177 3.5 0.1 1.0 CB C:CYS161 3.5 0.9 1.0 CB C:CYS181 3.8 0.5 1.0 CG C:LYS166 4.1 0.3 1.0 C C:LYS163 4.2 0.7 1.0 ND1 C:HIS177 4.2 0.4 1.0 C C:CYS164 4.3 0.5 1.0 N C:SER165 4.3 0.6 1.0 CG C:HIS177 4.5 0.5 1.0 CB C:LYS163 4.6 0.2 1.0 CB C:LYS166 4.6 0.3 1.0 N C:LYS166 4.7 0.4 1.0 CA C:LYS163 4.7 0.2 1.0 CA C:CYS181 4.9 0.6 1.0 N C:LYS163 4.9 0.7 1.0 CA C:CYS161 4.9 0.9 1.0 CD C:LYS166 5.0 97.0 1.0

Zinc binding site 3 out of 4 in the The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:0.5 occ:1.00 CB F:CYS190 2.1 0.4 1.0 SG F:CYS207 2.3 0.2 1.0 SG F:CYS190 2.3 0.7 1.0 NE2 F:HIS203 2.5 0.3 1.0 SG F:CYS188 2.7 0.3 1.0 CB F:CYS207 2.8 0.0 1.0 CD2 F:HIS203 3.2 0.8 1.0 CA F:CYS190 3.2 0.3 1.0 N F:CYS190 3.3 0.3 1.0 CE1 F:HIS203 3.7 97.5 1.0 CA F:CYS207 4.0 0.8 1.0 CB F:CYS188 4.1 0.0 1.0 C F:CYS190 4.4 0.6 1.0 CG F:HIS203 4.4 0.9 1.0 C F:ASP189 4.6 0.4 1.0 N F:GLY191 4.6 0.0 1.0 ND1 F:HIS203 4.6 97.4 1.0 N F:CYS207 4.8 0.5 1.0 N F:ASP189 4.8 0.5 1.0 OG1 F:THR192 4.8 0.1 1.0 C F:CYS188 4.9 0.4 1.0

Zinc binding site 4 out of 4 in the The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of the Jackdaw/IDD10 Bound to the Heterodimeric Shr-Scr Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn302 b:0.7 occ:1.00 NE2 F:HIS177 2.3 0.2 1.0 SG F:CYS164 2.3 0.7 1.0 SG F:CYS161 2.6 0.3 1.0 SG F:CYS181 2.6 0.1 1.0 CB F:CYS164 2.8 0.6 1.0 CB F:CYS181 2.9 0.2 1.0 CD2 F:HIS177 3.2 0.6 1.0 CE1 F:HIS177 3.3 1.0 1.0 N F:CYS164 3.6 0.7 1.0 CA F:CYS164 3.8 1.0 1.0 CB F:CYS161 3.8 0.5 1.0 CG F:HIS177 4.3 0.1 1.0 ND1 F:HIS177 4.3 0.7 1.0 CA F:CYS181 4.4 0.6 1.0 C F:CYS164 4.5 0.1 1.0 CB F:LYS166 4.6 0.1 1.0 C F:LYS163 4.6 0.8 1.0

Y.Hirano, M.Nakagawa, T.Suyama, K.Murase, M.Shirakawa, S.Takayama, T.P.Sun, T.Hakoshima. Structure of the Shr-Scr Heterodimer Bound to the Bird/Idd Transcriptional Factor Jkd Nat Plants V. 3 17010 2017.
ISSN: ESSN 2055-0278
PubMed: 28211915
DOI: 10.1038/NPLANTS.2017.10