Nickel in PDB 5zyp: Structure of the Yeast CTR9/PAF1 Complex

The structure of Structure of the Yeast CTR9/PAF1 Complex, PDB code: 5zyp was solved by Y.Xie, M.Zheng, H.Zhou, J.Long, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.98 / 2.53
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.953, 95.953, 115.498, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 24.3

The binding sites of Nickel atom in the Structure of the Yeast CTR9/PAF1 Complex (pdb code 5zyp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Structure of the Yeast CTR9/PAF1 Complex, PDB code: 5zyp:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Structure of the Yeast CTR9/PAF1 Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the Yeast CTR9/PAF1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni801 b:80.8 occ:1.00 NE2 A:HIS169 2.0 72.0 1.0 O A:HOH954 2.2 47.1 1.0 NE2 A:HIS173 2.5 80.4 1.0 O A:HOH964 2.7 45.4 1.0 CE1 A:HIS169 2.9 66.8 1.0 CE1 A:HIS173 3.0 81.2 1.0 CD2 A:HIS169 3.1 61.2 1.0 CD2 A:HIS173 3.6 76.8 1.0 ND1 A:HIS169 4.0 57.3 1.0 ND1 A:HIS173 4.1 78.5 1.0 CG A:HIS169 4.1 49.8 1.0 CG A:HIS173 4.4 71.9 1.0

Nickel binding site 2 out of 3 in the Structure of the Yeast CTR9/PAF1 Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the Yeast CTR9/PAF1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni802 b:42.5 occ:0.50 NI A:NI803 2.6 37.2 1.0 OE2 A:GLU119 2.8 42.6 1.0 NE2 A:HIS118 3.0 35.9 1.0 OE1 A:GLU119 3.0 29.6 1.0 CD2 A:HIS118 3.2 24.3 1.0 CD A:GLU119 3.3 29.3 1.0 O A:HOH978 4.1 28.2 1.0 CE1 A:HIS118 4.2 20.3 1.0 CG A:GLN122 4.2 18.8 1.0 CG A:HIS118 4.5 28.0 1.0 NE2 A:HIS102 4.6 23.4 1.0 CD2 A:HIS102 4.8 22.6 1.0 CG A:GLU119 4.8 26.3 1.0 ND1 A:HIS118 5.0 26.4 1.0

Nickel binding site 3 out of 3 in the Structure of the Yeast CTR9/PAF1 Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of the Yeast CTR9/PAF1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni803 b:37.2 occ:1.00 NE2 A:HIS102 2.2 23.4 1.0 O A:HOH978 2.5 28.2 1.0 NI A:NI802 2.6 42.5 0.5 CD2 A:HIS102 3.0 22.6 1.0 OE1 A:GLU119 3.2 29.6 1.0 CE1 A:HIS102 3.4 20.6 1.0 CG A:GLN122 3.9 18.8 1.0 CG A:HIS102 4.2 20.4 1.0 CD A:GLU119 4.2 29.3 1.0 CB A:GLN122 4.3 19.3 1.0 ND1 A:HIS102 4.4 16.4 1.0 OE2 A:GLU119 4.5 42.6 1.0 CD1 A:LEU105 4.6 24.2 1.0 CD A:GLN122 4.9 30.8 1.0

Y.Xie, M.Zheng, X.Chu, Y.Chen, H.Xu, J.Wang, H.Zhou, J.Long. PAF1 and CTR9 Subcomplex Formation Is Essential For PAF1 Complex Assembly and Functional Regulation. Nat Commun V. 9 3795 2018.
ISSN: ESSN 2041-1723
PubMed: 30228257
DOI: 10.1038/S41467-018-06237-7