Iron in PDB 4x3s: Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide

The structure of Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide, PDB code: 4x3s was solved by C.Ren, A.N.Plotnikov, M.M.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.26 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.027, 46.040, 80.797, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 22.2

The binding sites of Iron atom in the Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide (pdb code 4x3s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide, PDB code: 4x3s:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:20.5 occ:0.76 FE A:FE101 0.0 20.5 0.8 O7 A:CIT102 1.9 22.9 1.0 O4 A:CIT102 2.0 31.2 1.0 O4 B:CIT102 2.1 24.9 1.0 O7 B:CIT102 2.1 22.7 1.0 O5 A:CIT102 2.1 22.2 1.0 O6 B:CIT102 2.1 27.5 1.0 FE A:FE101 2.4 28.4 0.2 C6 A:CIT102 2.7 23.0 1.0 C3 A:CIT102 2.8 25.2 1.0 C3 B:CIT102 2.8 24.8 1.0 C6 B:CIT102 2.8 28.7 1.0 C5 A:CIT102 3.0 26.6 1.0 C5 B:CIT102 3.0 32.9 1.0 C4 A:CIT102 3.4 24.6 1.0 C4 B:CIT102 3.4 26.4 1.0 O1 B:CIT102 3.9 29.5 1.0 O A:HOH217 4.0 34.3 1.0 O6 A:CIT102 4.0 25.6 1.0 O5 B:CIT102 4.0 22.3 1.0 C2 A:CIT102 4.1 24.1 1.0 C2 B:CIT102 4.2 23.1 1.0 O3 B:CIT102 4.2 33.2 1.0 O3 A:CIT102 4.2 32.8 1.0 NH1 A:ARG22 4.3 23.9 0.6 O1 A:CIT102 4.3 24.9 1.0 N B:LYS23 4.3 24.1 1.0 NH1 A:ARG20 4.3 18.7 1.0 C1 A:CIT102 4.5 30.3 1.0 NH2 A:ARG22 4.5 22.4 0.6 C1 B:CIT102 4.5 26.9 1.0 CZ A:ARG22 4.9 20.9 0.6

Iron binding site 2 out of 4 in the Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:28.4 occ:0.24 FE A:FE101 0.0 28.4 0.2 O7 A:CIT102 1.9 22.9 1.0 O7 B:CIT102 2.1 22.7 1.0 O1 A:CIT102 2.3 24.9 1.0 FE A:FE101 2.4 20.5 0.8 O5 A:CIT102 2.4 22.2 1.0 C1 A:CIT102 2.6 30.3 1.0 C3 A:CIT102 2.6 25.2 1.0 O1 B:CIT102 2.7 29.5 1.0 C6 A:CIT102 2.8 23.0 1.0 C2 A:CIT102 3.1 24.1 1.0 O2 A:CIT102 3.3 43.6 1.0 C3 B:CIT102 3.5 24.8 1.0 O6 B:CIT102 3.6 27.5 1.0 O A:HOH217 3.7 34.3 1.0 C1 B:CIT102 3.7 26.9 1.0 O6 A:CIT102 3.9 25.6 1.0 C6 B:CIT102 4.0 28.7 1.0 C4 A:CIT102 4.0 24.6 1.0 O4 A:CIT102 4.0 31.2 1.0 O4 B:CIT102 4.1 24.9 1.0 C2 B:CIT102 4.1 23.1 1.0 NE1 A:TRP42 4.5 19.6 1.0 C5 A:CIT102 4.5 26.6 1.0 CD1 A:TRP42 4.5 20.2 1.0 C4 B:CIT102 4.6 26.4 1.0 C5 B:CIT102 4.7 32.9 1.0 O2 B:CIT102 4.9 28.2 1.0 NH1 A:ARG20 4.9 18.7 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:20.4 occ:0.75 FE B:FE101 0.0 20.4 0.8 O7 B:CIT103 1.9 24.5 1.0 O7 A:CIT103 2.0 23.1 1.0 O3 B:CIT103 2.0 27.5 1.0 O3 A:CIT103 2.0 27.8 1.0 O5 A:CIT103 2.1 25.7 1.0 O5 B:CIT103 2.1 21.4 1.0 FE B:FE101 2.5 29.3 0.2 C3 B:CIT103 2.8 23.6 1.0 C6 B:CIT103 2.8 21.4 1.0 C6 A:CIT103 2.8 25.9 1.0 C3 A:CIT103 2.8 22.9 1.0 C5 B:CIT103 3.0 28.9 1.0 C5 A:CIT103 3.0 26.8 1.0 C4 B:CIT103 3.3 24.4 1.0 C4 A:CIT103 3.4 25.9 1.0 O1 A:CIT103 3.9 28.8 1.0 O B:HOH220 3.9 33.3 1.0 O A:HOH224 3.9 30.9 1.0 O6 A:CIT103 4.0 22.1 1.0 O6 B:CIT103 4.0 24.4 1.0 C2 B:CIT103 4.0 26.0 1.0 O4 A:CIT103 4.2 33.2 1.0 O4 B:CIT103 4.2 37.2 1.0 C2 A:CIT103 4.2 23.0 1.0 N A:LYS23 4.3 24.5 1.0 O2 B:CIT103 4.3 27.5 1.0 NH1 B:ARG22 4.3 23.8 0.6 NH1 B:ARG20 4.4 19.5 1.0 C1 A:CIT103 4.5 27.0 1.0 NH2 B:ARG22 4.6 25.8 0.6 C1 B:CIT103 4.7 32.2 1.0 CA A:LYS23 5.0 24.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Chromobox Homology 7 (CBX7) with SETDB1-1170ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:29.3 occ:0.25 FE B:FE101 0.0 29.3 0.2 O7 B:CIT103 1.9 24.5 1.0 O7 A:CIT103 2.0 23.1 1.0 O A:HOH224 2.3 30.9 1.0 O2 B:CIT103 2.3 27.5 1.0 FE B:FE101 2.5 20.4 0.8 O5 B:CIT103 2.5 21.4 1.0 O1 A:CIT103 2.6 28.8 1.0 C3 B:CIT103 2.7 23.6 1.0 C6 B:CIT103 2.8 21.4 1.0 C1 B:CIT103 3.1 32.2 1.0 C2 B:CIT103 3.1 26.0 1.0 C3 A:CIT103 3.4 22.9 1.0 O5 A:CIT103 3.6 25.7 1.0 C1 A:CIT103 3.7 27.0 1.0 O B:HOH220 3.7 33.3 1.0 C6 A:CIT103 3.9 25.9 1.0 O6 B:CIT103 4.0 24.4 1.0 C2 A:CIT103 4.1 23.0 1.0 O3 A:CIT103 4.1 27.8 1.0 C4 B:CIT103 4.1 24.4 1.0 O3 B:CIT103 4.1 27.5 1.0 O1 B:CIT103 4.2 45.2 1.0 NE1 B:TRP42 4.5 18.9 1.0 C4 A:CIT103 4.5 25.9 1.0 CD1 B:TRP42 4.6 18.8 1.0 C5 B:CIT103 4.6 28.9 1.0 C5 A:CIT103 4.7 26.8 1.0 O2 A:CIT103 4.8 30.8 1.0 NH1 B:ARG20 4.9 19.5 1.0

C.Ren, K.Morohashi, A.N.Plotnikov, J.Jakoncic, S.G.Smith, J.Li, L.Zeng, Y.Rodriguez, V.Stojanoff, M.Walsh, M.M.Zhou. Small-Molecule Modulators of Methyl-Lysine Binding For the CBX7 Chromodomain. Chem.Biol. V. 22 161 2015.
ISSN: ISSN 1074-5521
PubMed: 25660273
DOI: 10.1016/J.CHEMBIOL.2014.11.021