Zinc in PDB 4x3t: Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452

The structure of Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452, PDB code: 4x3t was solved by C.Ren, J.Jakoncic, M.M.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.61 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.004, 77.309, 66.842, 90.00, 95.55, 90.00
R / Rfree (%)	20.3 / 25.6

The binding sites of Zinc atom in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452 (pdb code 4x3t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452, PDB code: 4x3t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452


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 Chromobox Homolog 7 (CBX7) Chromodomain with MS37452 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:38.3 occ:1.00 NE2 A:HIS47 2.1 25.6 1.0 NE2 B:HIS47 2.2 31.3 1.0 O B:HOH249 2.3 37.9 1.0 CD2 A:HIS47 3.0 27.7 1.0 CD2 B:HIS47 3.1 29.4 1.0 CE1 A:HIS47 3.2 23.7 1.0 CE1 B:HIS47 3.2 27.3 1.0 CG A:HIS47 4.2 27.8 1.0 ND1 A:HIS47 4.2 29.4 1.0 CG B:HIS47 4.2 30.2 1.0 ND1 B:HIS47 4.3 32.4 1.0 O B:HOH219 4.6 50.0 1.0 O A:HOH251 4.6 46.8 1.0 O A:HOH257 4.8 49.3 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452


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 Chromobox Homolog 7 (CBX7) Chromodomain with MS37452 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:49.9 occ:1.00 ND1 A:HIS5 2.0 45.0 1.0 N A:HIS5 2.4 55.8 1.0 CG A:HIS5 2.9 55.0 1.0 CB A:HIS5 3.1 58.3 1.0 CE1 A:HIS5 3.1 45.3 1.0 CA A:HIS5 3.2 54.5 1.0 N A:MET6 3.6 55.2 1.0 C A:HIS5 3.9 55.1 1.0 CD2 A:HIS5 4.0 55.3 1.0 NE2 A:HIS5 4.1 49.0 1.0 O B:GLU45 4.2 34.7 1.0 OE2 B:GLU45 4.4 52.8 1.0 CG B:GLU45 4.6 52.3 1.0 CD B:GLU45 4.7 51.5 1.0 CB B:GLU45 4.8 45.1 1.0 CA A:MET6 4.8 60.9 1.0 O A:MET6 4.8 66.8 1.0 C B:GLU45 4.9 39.0 1.0 O B:ILE48 4.9 35.8 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452


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 Chromobox Homolog 7 (CBX7) Chromodomain with MS37452 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:59.6 occ:1.00 ND1 B:HIS5 2.0 66.2 1.0 O A:HOH252 2.3 55.6 1.0 N B:HIS5 2.5 74.7 1.0 CG B:HIS5 2.9 70.9 1.0 O B:HOH247 3.0 48.6 1.0 CE1 B:HIS5 3.0 68.3 1.0 CB B:HIS5 3.2 67.9 1.0 CA B:HIS5 3.2 72.6 1.0 O B:HOH237 3.3 50.6 1.0 O B:HOH214 3.7 46.1 1.0 N B:MET6 3.8 74.4 1.0 C B:HIS5 4.0 71.2 1.0 CD2 B:HIS5 4.0 70.7 1.0 NE2 B:HIS5 4.1 69.5 1.0 O A:GLU45 4.1 31.2 1.0 O A:HOH202 4.1 37.8 1.0 O B:HOH201 4.3 60.5 1.0 OE2 A:GLU45 4.4 41.3 1.0 O A:ILE48 4.6 37.0 1.0 O B:HOH238 4.6 56.7 1.0 C A:GLU45 4.7 30.0 1.0 CD A:GLU45 4.7 36.4 1.0 CB A:GLU45 4.8 33.8 1.0 CG A:GLU45 4.9 40.8 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452


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 Chromobox Homolog 7 (CBX7) Chromodomain with MS37452 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:45.0 occ:1.00 O C:HOH219 1.8 40.4 1.0 NE2 F:HIS47 1.9 36.6 1.0 NE2 C:HIS47 2.0 38.4 1.0 O F:HOH213 2.1 47.5 1.0 O F:HOH215 2.1 50.0 1.0 O C:HOH224 2.3 41.4 1.0 CD2 F:HIS47 2.9 41.4 1.0 CD2 C:HIS47 2.9 37.8 1.0 CE1 F:HIS47 3.0 41.4 1.0 CE1 C:HIS47 3.1 44.2 1.0 CG F:HIS47 4.0 40.6 1.0 ND1 F:HIS47 4.1 43.2 1.0 CG C:HIS47 4.1 39.5 1.0 ND1 C:HIS47 4.2 45.2 1.0 O C:HOH246 4.5 61.2 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452


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 Chromobox Homolog 7 (CBX7) Chromodomain with MS37452 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn103 b:60.5 occ:1.00 ND1 C:HIS5 1.9 58.1 1.0 O C:HOH225 2.0 50.3 1.0 O F:HOH212 2.4 57.8 1.0 N C:HIS5 2.6 69.5 1.0 CG C:HIS5 2.7 66.7 1.0 CB C:HIS5 2.9 66.0 1.0 CE1 C:HIS5 3.1 65.4 1.0 CA C:HIS5 3.2 63.6 1.0 O C:HOH217 3.3 50.4 1.0 O F:HOH217 3.6 53.9 1.0 N C:MET6 3.9 61.6 1.0 CD2 C:HIS5 3.9 61.8 1.0 C C:HIS5 4.1 59.0 1.0 NE2 C:HIS5 4.1 57.1 1.0 O F:GLU45 4.3 62.9 1.0 O F:ILE48 4.4 56.1 1.0 CG F:GLU45 4.9 60.5 1.0 C F:GLU45 4.9 57.8 1.0 CB F:GLU45 4.9 64.1 1.0 CD F:GLU45 5.0 67.8 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452


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 Chromobox Homolog 7 (CBX7) Chromodomain with MS37452 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:35.8 occ:1.00 NE2 D:HIS47 2.2 28.2 1.0 NE2 E:HIS47 2.2 29.0 1.0 O D:HOH221 2.3 26.4 1.0 O E:HOH227 2.3 27.0 1.0 CE1 D:HIS47 3.1 27.6 1.0 CE1 E:HIS47 3.1 29.5 1.0 CD2 D:HIS47 3.2 29.0 1.0 CD2 E:HIS47 3.2 30.9 1.0 O17 E:45E101 3.6 32.3 1.0 O17 D:45E101 3.7 29.2 1.0 ND1 D:HIS47 4.2 32.8 1.0 ND1 E:HIS47 4.3 34.1 1.0 CG D:HIS47 4.3 32.5 1.0 CG E:HIS47 4.3 32.5 1.0 O E:HOH236 4.4 48.9 1.0 C21 D:45E101 4.5 56.1 1.0 OE1 D:GLU43 4.5 31.8 1.0 C16 E:45E101 4.6 32.5 1.0 OE1 E:GLU43 4.6 31.2 1.0 O19 D:45E101 4.6 37.0 1.0 O19 E:45E101 4.7 38.2 1.0 C16 D:45E101 4.7 33.0 1.0 O E:HOH248 4.9 42.0 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn103 b:82.2 occ:1.00 ND1 D:HIS5 2.0 38.4 1.0 O D:HOH243 2.2 68.4 1.0 N D:HIS5 2.2 56.8 1.0 O D:HOH229 2.8 59.9 1.0 CG D:HIS5 2.9 42.5 1.0 CE1 D:HIS5 3.0 46.0 1.0 CA D:HIS5 3.2 59.2 1.0 CB D:HIS5 3.2 52.6 1.0 N D:MET6 3.8 48.6 1.0 C D:HIS5 4.0 52.6 1.0 NE2 D:HIS5 4.1 48.8 1.0 CD2 D:HIS5 4.1 42.7 1.0 CG D:MET6 4.7 55.9 1.0 O D:HOH227 4.8 55.2 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn102 b:69.6 occ:1.00 N E:HIS5 2.1 63.5 1.0 CD2 E:HIS5 2.4 43.6 1.0 CG E:HIS5 3.0 50.8 1.0 CA E:HIS5 3.0 67.1 1.0 O E:HOH201 3.1 65.5 1.0 CB E:HIS5 3.2 61.2 1.0 NE2 E:HIS5 3.6 36.9 1.0 N E:MET6 3.7 60.5 1.0 O E:HOH251 3.7 47.1 1.0 C E:HIS5 3.9 70.2 1.0 ND1 E:HIS5 4.3 48.5 1.0 CE1 E:HIS5 4.5 44.6 1.0 CG E:MET6 4.7 56.0 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with MS37452 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn102 b:40.2 occ:1.00 ND1 F:HIS5 1.9 32.3 1.0 O F:HOH201 1.9 39.3 1.0 N F:HIS5 2.3 35.7 1.0 O C:HOH223 2.4 47.9 1.0 CE1 F:HIS5 2.9 41.1 1.0 CG F:HIS5 2.9 36.9 1.0 O F:HOH204 3.0 38.5 1.0 O F:HOH218 3.1 34.5 1.0 CA F:HIS5 3.2 35.8 1.0 CB F:HIS5 3.2 37.8 1.0 O C:HOH210 3.5 40.4 1.0 N F:MET6 3.8 35.3 1.0 O F:HOH206 3.9 36.7 1.0 C F:HIS5 4.0 32.6 1.0 NE2 F:HIS5 4.0 43.1 1.0 CD2 F:HIS5 4.0 38.5 1.0 OE1 C:GLU45 4.2 31.1 1.0 O C:GLU45 4.2 31.9 1.0 O C:ILE48 4.6 35.8 1.0 CB C:GLU45 4.8 33.3 1.0 CD C:GLU45 4.8 34.0 1.0 C C:GLU45 4.9 33.6 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