Zinc in PDB 5j9k: Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Topless Domain (1-209) in Complex with Rice D53 Repressor Ear Peptide Motif

The structure of Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Topless Domain (1-209) in Complex with Rice D53 Repressor Ear Peptide Motif, PDB code: 5j9k 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)	34.38 / 2.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.718, 59.638, 171.183, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.3

The binding sites of Zinc atom in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Topless Domain (1-209) in Complex with Rice D53 Repressor Ear Peptide Motif (pdb code 5j9k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Topless Domain (1-209) in Complex with Rice D53 Repressor Ear Peptide Motif, PDB code: 5j9k:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Topless Domain (1-209) in Complex with Rice D53 Repressor Ear Peptide Motif


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 Topless Domain (1-209) in Complex with Rice D53 Repressor Ear Peptide Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:83.8 occ:1.00 ND1 A:HIS183 2.1 71.5 1.0 NE2 A:HIS202 2.3 73.5 1.0 SG A:CYS186 2.5 79.5 1.0 CE1 A:HIS183 2.8 72.1 1.0 SG A:CYS204 2.8 96.4 1.0 CB A:CYS186 3.1 80.0 1.0 CG A:HIS183 3.2 74.5 1.0 CD2 A:HIS202 3.2 73.6 1.0 CE1 A:HIS202 3.3 78.2 1.0 CB A:CYS204 3.4 96.0 1.0 O A:HIS183 3.7 68.6 1.0 CA A:HIS183 3.7 63.4 1.0 CB A:HIS183 3.8 68.8 1.0 N A:CYS204 3.9 89.5 1.0 NE2 A:HIS183 3.9 78.6 1.0 C A:HIS183 4.1 66.6 1.0 CD2 A:HIS183 4.1 73.6 1.0 CA A:CYS204 4.2 99.5 1.0 C A:THR203 4.3 81.3 1.0 ND1 A:HIS202 4.4 78.0 1.0 CG A:HIS202 4.4 78.9 1.0 CA A:CYS186 4.6 82.2 1.0 CB A:PRO193 4.6 91.8 1.0 O A:THR203 4.7 84.0 1.0 CA A:THR203 4.9 83.7 1.0 O A:ASN188 4.9 0.3 1.0 N A:HIS183 4.9 63.1 1.0 N A:CYS186 5.0 81.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Topless Domain (1-209) in Complex with Rice D53 Repressor Ear Peptide Motif


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 Topless Domain (1-209) in Complex with Rice D53 Repressor Ear Peptide Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:0.3 occ:1.00 ND1 B:HIS183 2.1 0.3 1.0 SG B:CYS186 2.3 0.4 1.0 NE2 B:HIS202 2.3 0.6 1.0 SG B:CYS204 2.3 0.4 1.0 CE1 B:HIS183 2.5 0.2 1.0 CE1 B:HIS202 2.8 0.9 1.0 CB B:CYS204 3.0 0.1 1.0 CB B:CYS186 3.1 0.2 1.0 CG B:HIS183 3.5 0.7 1.0 CD2 B:HIS202 3.6 0.3 1.0 NE2 B:HIS183 3.8 0.0 1.0 N B:CYS204 4.0 0.7 1.0 CA B:CYS204 4.0 0.6 1.0 O B:HIS183 4.1 0.1 1.0 ND1 B:HIS202 4.1 0.4 1.0 CA B:HIS183 4.2 0.7 1.0 CD2 B:HIS183 4.3 0.9 1.0 CB B:HIS183 4.3 0.6 1.0 C B:THR203 4.4 0.9 1.0 CG B:HIS202 4.5 0.9 1.0 CA B:CYS186 4.6 0.5 1.0 CD B:PRO193 4.6 0.3 1.0 C B:HIS183 4.6 0.1 1.0 O B:THR203 4.7 0.4 1.0 N B:PRO193 4.7 0.6 1.0 CA B:PRO189 4.8 0.8 1.0 CB B:PRO189 4.8 0.8 1.0 O B:ASN188 4.9 0.0 1.0

H.Ma, J.Duan, J.Ke, Y.He, X.Gu, T.H.Xu, H.Yu, Y.Wang, J.S.Brunzelle, Y.Jiang, S.B.Rothbart, H.E.Xu, J.Li, K.Melcher. A D53 Repression Motif Induces Oligomerization of Topless Corepressors and Promotes Assembly of A Corepressor-Nucleosome Complex. Sci Adv V. 3 01217 2017.
ISSN: ESSN 2375-2548
PubMed: 28630893
DOI: 10.1126/SCIADV.1601217