Chlorine in PDB 5raf: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A, PDB code: 5raf was solved by M.Snee, R.Nowak, C.Johansson, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.52 / 1.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.800, 93.700, 93.250, 90.00, 107.84, 90.00
R / Rfree (%)	18.4 / 21.2

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A (pdb code 5raf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A, PDB code: 5raf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:23.6 occ:1.00 O A:HOH2177 3.2 49.3 1.0 O A:HOH2142 3.3 24.0 1.0 O A:HOH2256 3.3 40.2 1.0 O A:HOH2009 3.3 21.8 1.0 N A:GLU1513 3.4 19.6 1.0 C A:LEU1511 3.5 19.6 1.0 CA A:LEU1511 3.6 18.1 1.0 CB A:GLU1513 3.6 23.2 1.0 N A:PRO1512 3.7 20.0 1.0 CD A:PRO1512 3.7 21.3 1.0 CG A:GLU1513 3.8 27.7 1.0 CD1 A:LEU1511 4.0 19.2 1.0 O A:LEU1511 4.0 16.4 1.0 CA A:GLU1513 4.1 20.2 1.0 CB A:TRP1402 4.3 20.7 1.0 CB A:LEU1511 4.3 17.6 1.0 CD2 A:TYR1514 4.3 16.0 1.0 CG A:PRO1512 4.4 21.9 1.0 C A:PRO1512 4.4 21.8 1.0 OE2 A:GLU1513 4.5 34.3 1.0 N A:TYR1514 4.5 17.8 1.0 CA A:PRO1512 4.6 21.3 1.0 CD A:GLU1513 4.6 37.7 1.0 O A:HOH2004 4.7 28.2 1.0 N A:LEU1511 4.7 17.6 1.0 CG A:LEU1511 4.7 18.3 1.0 CE2 A:TYR1514 4.8 18.8 1.0 C A:GLU1513 4.8 18.4 1.0

Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:39.6 occ:1.00 O A:HOH2071 3.2 45.4 1.0 NH1 A:ARG1501 3.2 34.0 1.0 CA A:MET1498 3.3 32.6 1.0 C A:MET1498 3.4 35.3 1.0 N A:THR1500 3.4 31.1 1.0 CD A:ARG1501 3.5 37.6 1.0 N A:ARG1501 3.6 30.1 1.0 CB A:THR1500 3.6 40.2 1.0 CB A:MET1498 3.7 33.6 1.0 O A:MET1498 3.7 31.9 1.0 N A:PRO1499 3.7 36.5 1.0 CA A:THR1500 3.9 31.2 1.0 O A:HOH2216 4.0 46.0 1.0 OG1 A:THR1500 4.0 38.8 1.0 CD A:PRO1499 4.1 38.3 1.0 C A:THR1500 4.2 32.3 1.0 CZ A:ARG1501 4.3 36.7 1.0 C A:PRO1499 4.4 30.5 1.0 NE A:ARG1501 4.4 37.1 1.0 CB A:ARG1501 4.4 30.1 1.0 CG A:ARG1501 4.5 35.5 1.0 CA A:ARG1501 4.6 29.2 1.0 CA A:PRO1499 4.6 32.8 1.0 N A:MET1498 4.7 29.9 1.0 CG A:MET1498 4.7 35.1 1.0 O A:MET1497 4.7 28.7 1.0 CG A:PRO1499 4.8 34.6 1.0 CG2 A:THR1500 4.8 40.0 1.0

Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:37.8 occ:1.00 N A:ASN1558 3.2 19.8 1.0 O A:HOH1915 3.2 60.2 1.0 OE1 A:GLN1650 3.5 39.1 1.0 O A:HOH2213 3.6 43.3 1.0 NZ A:LYS1484 3.7 32.5 1.0 CA A:THR1557 3.8 20.5 1.0 CB A:ASN1558 3.9 21.8 1.0 C A:THR1557 4.0 21.1 1.0 CG A:GLN1650 4.0 31.1 1.0 CA A:ASN1558 4.1 19.7 1.0 CG2 A:THR1557 4.2 25.2 1.0 CD A:GLN1650 4.2 33.4 1.0 CG A:ASN1558 4.3 23.7 1.0 O A:THR1556 4.3 22.3 1.0 O A:HOH2269 4.4 51.3 1.0 O A:GLN1650 4.5 25.6 1.0 CB A:THR1557 4.5 25.7 1.0 ND2 A:ASN1558 4.5 24.4 1.0 O A:ASN1558 4.8 19.9 1.0 O A:HOH2135 4.8 43.0 1.0 N A:THR1557 4.8 20.3 1.0 OG1 A:THR1557 4.8 24.7 1.0 OD1 A:ASN1558 4.9 22.7 1.0 C A:ASN1558 4.9 17.7 1.0 CE A:LYS1484 5.0 33.6 1.0 C A:THR1556 5.0 22.3 1.0

Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:46.3 occ:1.00 NE2 A:HIS1712 2.8 23.3 1.0 O A:HOH2234 3.0 29.8 1.0 O A:HOH2093 3.0 20.7 1.0 O A:HOH2078 3.2 35.6 1.0 CE1 A:HIS1712 3.7 20.1 1.0 CD2 A:HIS1712 3.8 23.9 1.0 CD2 A:HIS1709 3.9 21.6 1.0 O A:HOH2184 4.2 55.2 1.0 NE2 A:HIS1709 4.4 23.1 1.0 O A:HOH2168 4.4 20.8 1.0 O A:HOH2030 4.6 18.6 1.0 CG A:HIS1709 4.7 18.1 1.0 CB A:ALA1619 4.7 20.1 1.0 O A:HOH2069 4.8 45.0 1.0 ND1 A:HIS1712 4.9 23.6 1.0 O A:HOH2215 4.9 31.1 1.0 CA A:GLY1412 4.9 20.5 1.0 O A:ALA1685 4.9 16.1 1.0 CG A:HIS1712 5.0 23.3 1.0

Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001559A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1801 b:41.7 occ:1.00 OG1 B:THR1500 2.7 45.9 1.0 NH1 B:ARG1501 3.3 37.5 1.0 CA B:MET1498 3.3 34.4 1.0 C B:MET1498 3.4 35.6 1.0 N B:THR1500 3.4 32.2 1.0 CD B:ARG1501 3.4 39.2 1.0 N B:PRO1499 3.6 34.6 1.0 N B:ARG1501 3.7 34.5 1.0 O B:MET1498 3.8 33.3 1.0 CB B:THR1500 3.8 39.3 1.0 CB B:MET1498 3.9 35.5 1.0 CD B:PRO1499 3.9 36.6 1.0 CA B:THR1500 4.0 35.9 1.0 CZ B:ARG1501 4.3 37.0 1.0 CG2 B:THR1500 4.3 37.8 1.0 C B:THR1500 4.3 32.7 1.0 C B:PRO1499 4.3 35.1 1.0 NE B:ARG1501 4.3 38.6 1.0 CB B:ARG1501 4.4 31.5 1.0 CG B:ARG1501 4.5 35.2 1.0 CG B:PRO1499 4.5 38.0 1.0 CA B:PRO1499 4.5 35.1 1.0 CG B:MET1498 4.6 40.2 1.0 N B:MET1498 4.6 33.5 1.0 O B:MET1497 4.7 35.8 1.0 CA B:ARG1501 4.7 33.3 1.0 OE1 B:GLU1437 4.8 34.1 1.0

M.Snee, R.Nowak, C.Johansson, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann. Pandda Analysis Group Deposition of Human JMJD1B Screened Against the Dspl Fragment Library To Be Published.