Chlorine in PDB 5rag: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001767A

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001767A, PDB code: 5rag 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)	64.66 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.660, 93.750, 93.500, 90.00, 107.69, 90.00
R / Rfree (%)	18.2 / 20.2

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001767A also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Manganese	(Mn)	2 atoms

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001767A (pdb code 5rag). 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 FM001767A, PDB code: 5rag:
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 FM001767A


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 FM001767A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:20.0 occ:1.00 O A:HOH2129 3.2 19.4 1.0 O A:HOH2261 3.3 35.8 1.0 O A:HOH2001 3.4 18.5 1.0 N A:GLU1513 3.4 16.8 1.0 C A:LEU1511 3.6 16.9 1.0 O A:HOH2187 3.6 37.5 1.0 CA A:LEU1511 3.6 16.3 1.0 CB A:GLU1513 3.7 21.1 1.0 N A:PRO1512 3.7 17.0 1.0 CD A:PRO1512 3.8 17.3 1.0 CG A:GLU1513 3.9 24.9 1.0 CD1 A:LEU1511 3.9 16.4 1.0 O A:LEU1511 4.1 15.0 1.0 CA A:GLU1513 4.1 17.4 1.0 CB A:LEU1511 4.3 15.2 1.0 CB A:TRP1402 4.3 15.2 1.0 CD2 A:TYR1514 4.4 13.7 1.0 C A:PRO1512 4.4 16.5 1.0 CG A:PRO1512 4.4 20.0 1.0 OE2 A:GLU1513 4.5 33.7 1.0 N A:TYR1514 4.6 16.7 1.0 O A:HOH2012 4.6 27.1 1.0 CA A:PRO1512 4.6 17.5 1.0 CD A:GLU1513 4.7 37.0 1.0 CG A:LEU1511 4.7 16.4 1.0 N A:LEU1511 4.8 15.3 1.0 CE2 A:TYR1514 4.8 17.1 1.0 C A:GLU1513 4.8 16.6 1.0 CG A:TRP1402 5.0 15.9 1.0 CD1 A:TRP1402 5.0 17.5 1.0

Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001767A


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 FM001767A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:31.6 occ:1.00 O A:HOH2122 3.1 40.2 1.0 NH1 A:ARG1501 3.3 29.1 1.0 N A:THR1500 3.4 22.6 1.0 CA A:MET1498 3.4 24.3 1.0 C A:MET1498 3.4 27.1 1.0 CD A:ARG1501 3.6 31.7 1.0 N A:ARG1501 3.6 22.6 1.0 N A:PRO1499 3.7 25.1 1.0 CB A:THR1500 3.7 31.9 1.0 O A:MET1498 3.8 24.5 1.0 CB A:MET1498 3.8 25.5 1.0 O A:HOH2237 3.9 41.4 1.0 CA A:THR1500 3.9 24.6 1.0 CD A:PRO1499 4.0 26.8 1.0 OG1 A:THR1500 4.1 31.4 1.0 C A:THR1500 4.2 24.1 1.0 C A:PRO1499 4.3 23.6 1.0 CZ A:ARG1501 4.3 30.4 1.0 CB A:ARG1501 4.4 22.2 1.0 NE A:ARG1501 4.4 27.5 1.0 CG A:ARG1501 4.5 28.1 1.0 CA A:PRO1499 4.5 24.5 1.0 CA A:ARG1501 4.6 21.8 1.0 N A:MET1498 4.7 22.2 1.0 CG A:MET1498 4.7 25.9 1.0 CG A:PRO1499 4.7 27.3 1.0 O A:MET1497 4.8 24.1 1.0 CG2 A:THR1500 4.9 35.9 1.0

Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001767A


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 FM001767A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:33.7 occ:1.00 N A:ASN1558 3.2 17.5 1.0 O A:HOH2231 3.3 50.9 1.0 O A:HOH1919 3.4 56.0 1.0 OE1 A:GLN1650 3.5 38.1 1.0 NZ A:LYS1484 3.5 25.8 1.0 CA A:THR1557 3.7 17.1 1.0 C A:THR1557 4.0 17.9 1.0 CG A:GLN1650 4.0 27.6 1.0 CB A:ASN1558 4.0 18.4 1.0 CD A:GLN1650 4.1 28.9 1.0 CG2 A:THR1557 4.1 20.6 1.0 CA A:ASN1558 4.2 17.0 1.0 O A:THR1556 4.3 19.3 1.0 CG A:ASN1558 4.3 20.4 1.0 CB A:THR1557 4.4 20.6 1.0 O A:GLN1650 4.5 23.9 1.0 ND2 A:ASN1558 4.5 25.0 1.0 O A:HOH2283 4.6 48.1 1.0 O A:HOH2146 4.6 34.7 1.0 OG1 A:THR1557 4.8 21.1 1.0 N A:THR1557 4.8 16.3 1.0 CE A:LYS1484 4.8 30.2 1.0 O A:ASN1558 4.8 16.6 1.0 OD1 A:ASN1558 4.9 19.9 1.0 C A:THR1556 5.0 18.4 1.0

Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001767A


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 FM001767A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:48.5 occ:1.00 NE2 A:HIS1712 2.8 22.1 1.0 O A:HOH2236 3.0 29.6 1.0 O A:HOH2081 3.1 17.7 1.0 O A:HOH1965 3.1 34.5 1.0 CD2 A:HIS1712 3.7 21.9 1.0 CE1 A:HIS1712 3.8 19.6 1.0 CD2 A:HIS1709 3.9 18.0 1.0 O A:HOH2184 4.0 52.1 1.0 O A:HOH2160 4.5 18.1 1.0 CG A:HIS1709 4.6 16.5 1.0 NE2 A:HIS1709 4.7 20.0 1.0 O A:HOH2049 4.7 15.7 1.0 CB A:ALA1619 4.7 17.3 1.0 CG A:HIS1712 4.9 19.8 1.0 ND1 A:HIS1712 4.9 22.6 1.0 O A:GLU1708 4.9 17.1 1.0 O A:HOH2221 4.9 31.1 1.0 O A:ALA1685 5.0 14.8 1.0 CB A:HIS1709 5.0 16.8 1.0

Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001767A


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 FM001767A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1801 b:40.4 occ:1.00 OG1 B:THR1500 2.8 42.6 1.0 NH1 B:ARG1501 3.3 34.4 1.0 CA B:MET1498 3.3 32.5 1.0 C B:MET1498 3.3 31.0 1.0 N B:THR1500 3.4 29.1 1.0 CD B:ARG1501 3.4 32.8 1.0 N B:PRO1499 3.6 31.2 1.0 N B:ARG1501 3.7 30.3 1.0 CD B:PRO1499 3.7 32.3 1.0 O B:MET1498 3.8 28.9 1.0 CB B:THR1500 3.8 34.4 1.0 CB B:MET1498 3.9 31.9 1.0 CA B:THR1500 4.0 30.0 1.0 CG2 B:THR1500 4.2 35.4 1.0 CZ B:ARG1501 4.3 32.6 1.0 C B:THR1500 4.3 31.0 1.0 C B:PRO1499 4.3 31.0 1.0 NE B:ARG1501 4.3 33.6 1.0 CG B:PRO1499 4.5 34.5 1.0 CA B:PRO1499 4.5 32.6 1.0 CB B:ARG1501 4.5 27.1 1.0 CG B:ARG1501 4.5 30.4 1.0 CG B:MET1498 4.6 37.8 1.0 O B:MET1497 4.6 32.7 1.0 N B:MET1498 4.6 29.3 1.0 CA B:ARG1501 4.7 28.0 1.0 OE1 B:GLU1437 4.9 29.6 1.0 CZ B:PHE1438 5.0 28.3 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.