Zinc in PDB 5c7e: Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide

The structure of Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide, PDB code: 5c7e was solved by J.Ke, H.Ma, X.Gu, J.S.Brunzelle, H.E.Xu, K.Melcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 3.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.668, 162.668, 157.250, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 22.9

The binding sites of Zinc atom in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide (pdb code 5c7e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide, PDB code: 5c7e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


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 the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:0.8 occ:0.50 NE2 A:HIS202 2.0 0.7 1.0 ND1 A:HIS183 2.0 0.9 1.0 SG A:CYS186 2.2 1.0 1.0 SG A:CYS204 2.3 0.4 1.0 CE1 A:HIS183 2.8 0.8 1.0 CD2 A:HIS202 3.0 0.0 1.0 CE1 A:HIS202 3.0 0.4 1.0 CG A:HIS183 3.1 0.3 1.0 CB A:HIS183 3.6 0.3 1.0 CB A:CYS204 3.7 0.5 1.0 CA A:HIS183 3.7 0.6 1.0 CB A:CYS186 3.9 0.8 1.0 O A:HIS183 3.9 0.6 1.0 N A:CYS204 4.0 0.8 1.0 NE2 A:HIS183 4.0 0.6 1.0 C A:THR203 4.1 0.9 1.0 ND1 A:HIS202 4.1 0.3 1.0 CG A:HIS202 4.1 0.8 1.0 CD2 A:HIS183 4.1 1.0 1.0 CG A:PRO193 4.2 0.1 1.0 C A:HIS183 4.3 0.0 1.0 CA A:CYS204 4.3 0.1 1.0 CA A:THR203 4.5 0.3 1.0 O A:THR203 4.5 0.5 1.0 CB A:PRO193 4.6 0.3 1.0 N A:HIS183 5.0 0.8 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


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 the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:0.7 occ:0.50 ND1 B:HIS183 1.9 0.9 1.0 SG B:CYS186 2.2 0.7 1.0 SG B:CYS204 2.2 0.9 1.0 NE2 B:HIS202 2.4 0.2 1.0 CE1 B:HIS183 2.6 0.4 1.0 CG B:HIS183 3.0 0.7 1.0 CB B:CYS186 3.1 0.4 1.0 CD2 B:HIS202 3.4 0.1 1.0 CE1 B:HIS202 3.4 0.1 1.0 CB B:CYS204 3.5 0.9 1.0 CB B:HIS183 3.6 0.1 1.0 O B:HIS183 3.7 0.2 1.0 NE2 B:HIS183 3.7 0.1 1.0 CA B:HIS183 3.7 0.9 1.0 CD2 B:HIS183 4.0 0.5 1.0 CB B:PRO193 4.0 0.7 1.0 N B:CYS204 4.1 0.6 1.0 C B:HIS183 4.2 0.9 1.0 CA B:CYS204 4.4 0.4 1.0 C B:THR203 4.4 0.9 1.0 ND1 B:HIS202 4.5 0.3 1.0 CG B:HIS202 4.5 0.3 1.0 CA B:CYS186 4.5 0.6 1.0 CB B:PRO189 4.6 0.8 1.0 CA B:PRO189 4.6 0.2 1.0 O B:THR203 4.8 0.6 1.0 CG B:PRO193 4.8 0.2 1.0 CA B:THR203 4.9 0.1 1.0 N B:HIS183 5.0 1.0 1.0 N B:CYS186 5.0 0.7 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


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 the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn400 b:84.8 occ:0.50 ND1 C:HIS183 1.9 0.0 1.0 SG C:CYS204 2.0 0.5 1.0 SG C:CYS186 2.2 99.8 1.0 NE2 C:HIS202 2.2 98.2 1.0 CE1 C:HIS183 2.6 0.0 1.0 CE1 C:HIS202 3.1 0.5 1.0 CG C:HIS183 3.1 97.7 1.0 CB C:CYS186 3.1 0.3 1.0 CD2 C:HIS202 3.2 98.3 1.0 CB C:CYS204 3.6 0.8 1.0 CB C:HIS183 3.7 93.1 1.0 NE2 C:HIS183 3.8 0.4 1.0 CA C:HIS183 3.8 90.5 1.0 CB C:PRO189 3.9 0.1 1.0 O C:HIS183 3.9 0.3 1.0 N C:CYS204 4.0 0.8 1.0 CB C:PRO193 4.0 0.1 1.0 CD2 C:HIS183 4.0 98.1 1.0 CA C:CYS204 4.2 0.1 1.0 ND1 C:HIS202 4.2 0.6 1.0 CG C:PRO189 4.2 0.9 1.0 CG C:HIS202 4.3 0.6 1.0 C C:HIS183 4.3 95.5 1.0 C C:THR203 4.5 0.0 1.0 CA C:CYS186 4.6 0.8 1.0 CG C:PRO193 4.7 0.8 1.0 CA C:THR203 4.9 0.9 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


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 the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn400 b:0.7 occ:0.50 ND1 D:HIS183 1.9 0.6 1.0 NE2 D:HIS202 2.0 0.9 1.0 SG D:CYS204 2.1 0.4 1.0 SG D:CYS186 2.3 94.6 1.0 CE1 D:HIS183 2.5 0.9 1.0 CE1 D:HIS202 2.9 0.8 1.0 CG D:HIS183 3.1 0.4 1.0 CD2 D:HIS202 3.1 0.8 1.0 CB D:CYS204 3.2 0.8 1.0 CB D:CYS186 3.5 0.7 1.0 CB D:HIS183 3.7 0.1 1.0 NE2 D:HIS183 3.7 0.4 1.0 N D:CYS204 3.8 0.5 1.0 CB D:PRO193 3.8 0.2 1.0 CA D:HIS183 3.9 0.9 1.0 CA D:CYS204 4.0 0.2 1.0 CD2 D:HIS183 4.0 0.2 1.0 O D:HIS183 4.0 0.6 1.0 ND1 D:HIS202 4.1 0.0 1.0 C D:THR203 4.1 0.4 1.0 CG D:HIS202 4.2 0.5 1.0 C D:HIS183 4.5 0.3 1.0 CA D:PRO189 4.5 0.5 1.0 O D:THR203 4.6 0.6 1.0 CA D:THR203 4.6 0.2 1.0 CB D:PRO189 4.7 0.1 1.0 CG D:PRO193 4.8 0.9 1.0 N D:ARG190 4.9 0.7 1.0 CA D:CYS186 5.0 0.9 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn400 b:0.0 occ:0.50 ND1 E:HIS183 1.9 0.1 1.0 SG E:CYS204 2.1 1.0 1.0 NE2 E:HIS202 2.2 0.5 1.0 SG E:CYS186 2.2 0.8 1.0 CE1 E:HIS183 2.8 0.8 1.0 CG E:HIS183 2.9 0.4 1.0 CD2 E:HIS202 3.0 0.8 1.0 CB E:CYS186 3.2 0.3 1.0 CE1 E:HIS202 3.3 0.4 1.0 CB E:HIS183 3.3 0.3 1.0 CA E:HIS183 3.4 0.0 1.0 O E:HIS183 3.5 0.7 1.0 CB E:CYS204 3.7 0.3 1.0 NE2 E:HIS183 3.8 0.3 1.0 CD2 E:HIS183 3.9 0.3 1.0 C E:HIS183 3.9 0.7 1.0 CB E:PRO193 4.1 0.6 1.0 CG E:HIS202 4.2 0.7 1.0 N E:CYS204 4.2 0.9 1.0 ND1 E:HIS202 4.3 0.5 1.0 C E:THR203 4.4 0.3 1.0 CA E:CYS204 4.4 0.4 1.0 CG E:PRO193 4.5 0.5 1.0 N E:HIS183 4.6 0.1 1.0 CA E:CYS186 4.6 0.8 1.0 O E:THR203 4.6 0.1 1.0 CA E:THR203 4.8 0.9 1.0 O E:GLN182 4.9 0.6 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn400 b:0.0 occ:0.50 ND1 F:HIS183 1.9 0.6 1.0 NE2 F:HIS202 2.2 0.5 1.0 SG F:CYS186 2.2 0.3 1.0 SG F:CYS204 2.3 0.9 1.0 CE1 F:HIS183 2.7 0.8 1.0 CG F:HIS183 2.9 0.8 1.0 CE1 F:HIS202 3.1 0.4 1.0 CD2 F:HIS202 3.1 0.4 1.0 CB F:CYS186 3.5 0.0 1.0 CB F:HIS183 3.5 0.3 1.0 CA F:HIS183 3.6 1.0 1.0 O F:HIS183 3.7 0.0 1.0 CB F:CYS204 3.7 0.3 1.0 NE2 F:HIS183 3.8 0.1 1.0 CD2 F:HIS183 3.9 0.2 1.0 C F:HIS183 4.1 0.4 1.0 ND1 F:HIS202 4.2 0.1 1.0 CG F:HIS202 4.3 0.2 1.0 N F:CYS204 4.3 0.5 1.0 C F:THR203 4.6 0.3 1.0 CA F:CYS204 4.6 0.4 1.0 N F:HIS183 4.8 0.8 1.0 CA F:CYS186 4.8 0.2 1.0

J.Ke, H.Ma, X.Gu, A.Thelen, J.S.Brunzelle, J.Li, H.E.Xu, K.Melcher. Structural Basis For Recognition of Diverse Transcriptional Repressors By the Topless Family of Corepressors. Sci Adv V. 1 00107 2015.
ISSN: ESSN 2375-2548
PubMed: 26601214
DOI: 10.1126/SCIADV.1500107