Zinc in PDB 5fb0: Crystal Structure of A Phd Finger Bound to Histone H3 T3PH Peptide

The structure of Crystal Structure of A Phd Finger Bound to Histone H3 T3PH Peptide, PDB code: 5fb0 was solved by H.Li, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.14 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.830, 99.160, 53.716, 90.00, 93.17, 90.00
R / Rfree (%)	22.4 / 27.6

The binding sites of Zinc atom in the Crystal Structure of A Phd Finger Bound to Histone H3 T3PH Peptide (pdb code 5fb0). 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 A Phd Finger Bound to Histone H3 T3PH Peptide, PDB code: 5fb0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Phd Finger Bound to Histone H3 T3PH 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 A Phd Finger Bound to Histone H3 T3PH Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:39.1 occ:1.00 ND1 A:HIS725 2.2 44.8 1.0 SG A:CYS708 2.3 48.9 1.0 SG A:CYS728 2.5 36.4 1.0 SG A:CYS705 2.6 33.2 1.0 CB A:CYS705 3.0 30.1 1.0 CG A:HIS725 3.0 37.3 1.0 CE1 A:HIS725 3.1 42.9 1.0 CB A:CYS728 3.1 31.0 1.0 CB A:HIS725 3.4 35.4 1.0 CB A:CYS708 3.7 41.8 1.0 N A:CYS708 4.0 33.0 1.0 N A:HIS725 4.0 45.1 1.0 NE2 A:HIS725 4.1 45.8 1.0 CD2 A:HIS725 4.1 45.9 1.0 CA A:HIS725 4.3 45.5 1.0 CA A:CYS708 4.4 36.2 1.0 CA A:CYS705 4.5 27.4 1.0 CA A:CYS728 4.6 44.8 1.0 CB A:VAL707 4.7 45.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Phd Finger Bound to Histone H3 T3PH 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 A Phd Finger Bound to Histone H3 T3PH Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:38.7 occ:1.00 SG A:CYS720 2.3 42.8 1.0 SG A:CYS742 2.3 34.6 1.0 SG A:CYS717 2.4 40.5 1.0 SG A:CYS745 2.4 41.5 1.0 CB A:CYS720 3.1 41.2 1.0 CB A:CYS717 3.3 40.2 1.0 CB A:CYS742 3.4 33.7 1.0 N A:CYS742 3.6 39.6 1.0 OG1 A:THR719 3.6 42.9 1.0 CB A:CYS745 3.7 44.1 1.0 N A:CYS720 3.8 30.1 1.0 CA A:CYS720 4.0 30.6 1.0 CA A:CYS742 4.0 31.4 1.0 N A:CYS745 4.2 49.4 1.0 C A:THR719 4.4 40.7 1.0 O A:CYS720 4.5 24.3 1.0 C A:CYS720 4.5 27.8 1.0 CA A:CYS745 4.6 47.1 1.0 C A:CYS742 4.6 30.9 1.0 O A:CYS742 4.7 32.9 1.0 C A:SER741 4.7 45.0 1.0 CA A:CYS717 4.8 42.5 1.0 CB A:THR719 4.9 43.1 1.0 N A:THR719 4.9 41.8 1.0 NH1 A:ARG722 4.9 37.9 1.0 CA A:SER741 5.0 43.8 1.0 CA A:THR719 5.0 42.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Phd Finger Bound to Histone H3 T3PH 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 A Phd Finger Bound to Histone H3 T3PH Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:36.8 occ:1.00 ND1 C:HIS725 2.3 48.8 1.0 SG C:CYS708 2.3 50.9 1.0 SG C:CYS705 2.5 33.8 1.0 SG C:CYS728 2.5 38.5 1.0 CB C:CYS705 3.0 28.9 1.0 CB C:CYS728 3.0 39.0 1.0 CE1 C:HIS725 3.1 51.6 1.0 CG C:HIS725 3.2 44.2 1.0 CB C:HIS725 3.5 36.7 1.0 CB C:CYS708 3.7 40.4 1.0 N C:CYS708 3.9 32.5 1.0 NE2 C:HIS725 4.1 54.2 1.0 N C:HIS725 4.1 33.9 1.0 CD2 C:HIS725 4.2 53.0 1.0 CA C:CYS708 4.4 33.8 1.0 CA C:CYS705 4.5 25.2 1.0 CA C:HIS725 4.5 40.1 1.0 CB C:VAL707 4.5 40.6 1.0 CA C:CYS728 4.5 49.1 1.0 N C:VAL707 4.9 35.8 1.0 C C:VAL707 4.9 40.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Phd Finger Bound to Histone H3 T3PH 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 A Phd Finger Bound to Histone H3 T3PH Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn902 b:41.0 occ:1.00 SG C:CYS742 2.3 38.0 1.0 SG C:CYS717 2.4 40.0 1.0 SG C:CYS720 2.4 37.7 1.0 SG C:CYS745 2.5 41.1 1.0 CB C:CYS720 3.2 34.7 1.0 CB C:CYS742 3.3 37.3 1.0 CB C:CYS717 3.4 38.8 1.0 N C:CYS742 3.6 41.8 1.0 OG1 C:THR719 3.6 47.0 1.0 CB C:CYS745 3.7 49.4 1.0 N C:CYS720 3.8 32.8 1.0 CA C:CYS742 4.0 38.8 1.0 CA C:CYS720 4.0 33.1 1.0 N C:CYS745 4.2 50.3 1.0 C C:THR719 4.4 40.8 1.0 O C:CYS720 4.4 29.9 1.0 C C:CYS720 4.5 28.9 1.0 C C:CYS742 4.5 37.2 1.0 O C:CYS742 4.6 36.6 1.0 CA C:CYS745 4.6 52.2 1.0 C C:SER741 4.7 44.7 1.0 N C:THR719 4.8 50.2 1.0 CA C:CYS717 4.8 45.2 1.0 CB C:THR719 4.8 49.0 1.0 CA C:SER741 4.9 45.8 1.0 O C:HOH1009 4.9 51.6 1.0 CA C:THR719 4.9 49.3 1.0 NH1 C:ARG722 5.0 40.5 1.0

X.Zhang, D.Zhao, X.Xiong, Z.He, H.Li. Multifaceted Histone H3 Methylation and Phosphorylation Readout By the Plant Homeodomain Finger of Human Nuclear Antigen SP100C J.Biol.Chem. V. 291 12786 2016.
ISSN: ESSN 1083-351X
PubMed: 27129259
DOI: 10.1074/JBC.M116.721159