Chlorine in PDB 5rb2: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001784A

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001784A, PDB code: 5rb2 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)	47.47 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.770, 93.660, 93.430, 90.00, 107.83, 90.00
R / Rfree (%)	18.4 / 20.8

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001784A 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 FM001784A (pdb code 5rb2). 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 FM001784A, PDB code: 5rb2:
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 FM001784A


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 FM001784A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:21.3 occ:1.00 O A:HOH2145 3.2 22.8 1.0 O A:HOH1998 3.3 20.1 1.0 O A:HOH2263 3.3 38.6 1.0 N A:GLU1513 3.4 18.4 1.0 O A:HOH2186 3.4 44.0 1.0 C A:LEU1511 3.5 18.1 1.0 CA A:LEU1511 3.6 16.5 1.0 CB A:GLU1513 3.7 22.3 1.0 N A:PRO1512 3.7 18.6 1.0 CD A:PRO1512 3.8 20.3 1.0 CG A:GLU1513 3.9 25.8 1.0 CD1 A:LEU1511 3.9 18.0 1.0 O A:LEU1511 4.0 15.9 1.0 CA A:GLU1513 4.1 18.9 1.0 CB A:LEU1511 4.2 16.8 1.0 CB A:TRP1402 4.2 19.2 1.0 CD2 A:TYR1514 4.4 15.9 1.0 CG A:PRO1512 4.4 22.2 1.0 C A:PRO1512 4.4 18.9 1.0 OE2 A:GLU1513 4.5 36.0 1.0 N A:TYR1514 4.6 17.0 1.0 CA A:PRO1512 4.6 18.9 1.0 CD A:GLU1513 4.7 37.5 1.0 O A:HOH1983 4.7 29.9 1.0 CG A:LEU1511 4.7 16.8 1.0 N A:LEU1511 4.8 16.0 1.0 CE2 A:TYR1514 4.8 17.6 1.0 C A:GLU1513 4.8 17.6 1.0 CG A:TRP1402 5.0 18.6 1.0

Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001784A


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 FM001784A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:35.9 occ:1.00 O A:HOH2101 3.2 40.4 1.0 NH1 A:ARG1501 3.3 31.0 1.0 CA A:MET1498 3.3 28.5 1.0 C A:MET1498 3.4 32.1 1.0 N A:THR1500 3.4 26.0 1.0 CD A:ARG1501 3.5 35.1 1.0 N A:ARG1501 3.5 26.4 1.0 CB A:THR1500 3.6 36.2 1.0 N A:PRO1499 3.7 29.3 1.0 CB A:MET1498 3.8 29.1 1.0 O A:MET1498 3.8 28.1 1.0 O A:HOH2226 3.8 43.2 1.0 CA A:THR1500 3.9 29.4 1.0 CD A:PRO1499 4.0 30.8 1.0 OG1 A:THR1500 4.1 35.4 1.0 C A:THR1500 4.2 27.8 1.0 CZ A:ARG1501 4.3 31.4 1.0 C A:PRO1499 4.3 28.1 1.0 CB A:ARG1501 4.4 26.2 1.0 NE A:ARG1501 4.4 31.8 1.0 CG A:ARG1501 4.5 32.1 1.0 CA A:PRO1499 4.6 28.7 1.0 CA A:ARG1501 4.6 25.7 1.0 N A:MET1498 4.7 26.5 1.0 CG A:MET1498 4.7 28.6 1.0 CG A:PRO1499 4.7 31.9 1.0 O A:MET1497 4.7 27.1 1.0 CG2 A:THR1500 4.8 38.9 1.0 OE1 A:GLU1437 5.0 28.9 1.0

Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001784A


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 FM001784A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:39.7 occ:1.00 N A:ASN1558 3.1 18.2 1.0 O A:HOH2231 3.2 48.6 1.0 O A:HOH1930 3.3 60.6 1.0 NZ A:LYS1484 3.6 31.4 1.0 OE1 A:GLN1650 3.7 41.2 1.0 CA A:THR1557 3.7 19.4 1.0 C A:THR1557 3.9 18.9 1.0 CB A:ASN1558 3.9 19.2 1.0 CG A:GLN1650 4.0 30.8 1.0 CA A:ASN1558 4.1 17.9 1.0 O A:THR1556 4.2 20.4 1.0 CG2 A:THR1557 4.2 23.7 1.0 CG A:ASN1558 4.2 21.2 1.0 CD A:GLN1650 4.3 35.2 1.0 ND2 A:ASN1558 4.3 25.1 1.0 O A:HOH2274 4.4 45.1 1.0 CB A:THR1557 4.4 22.8 1.0 O A:GLN1650 4.5 24.6 1.0 N A:THR1557 4.7 17.8 1.0 O A:HOH2093 4.7 36.7 1.0 OD1 A:ASN1558 4.8 21.2 1.0 O A:ASN1558 4.8 18.1 1.0 OG1 A:THR1557 4.8 22.8 1.0 C A:THR1556 4.9 19.5 1.0 CE A:LYS1484 4.9 32.8 1.0 C A:ASN1558 4.9 16.6 1.0

Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001784A


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 FM001784A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:46.5 occ:1.00 NE2 A:HIS1712 2.9 23.0 1.0 O A:HOH2236 3.0 29.9 1.0 O A:HOH2080 3.0 19.3 1.0 O A:HOH2012 3.2 37.4 1.0 CD2 A:HIS1709 3.8 18.3 1.0 CD2 A:HIS1712 3.8 24.4 1.0 CE1 A:HIS1712 3.8 21.7 1.0 NE2 A:HIS1709 4.3 21.6 1.0 O A:HOH2188 4.4 54.5 1.0 O A:HOH2172 4.5 19.6 1.0 O A:HOH2044 4.6 17.2 1.0 CG A:HIS1709 4.6 17.4 1.0 CB A:ALA1619 4.7 18.9 1.0 O A:HOH2003 4.8 43.7 1.0 CA A:GLY1412 4.9 21.2 1.0 O A:ALA1685 5.0 17.1 1.0 ND1 A:HIS1712 5.0 22.8 1.0 O A:HOH2222 5.0 33.1 1.0

Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001784A


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 FM001784A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1802 b:40.7 occ:1.00 OG1 B:THR1500 2.8 46.0 1.0 CA B:MET1498 3.3 32.1 1.0 C B:MET1498 3.3 32.7 1.0 NH1 B:ARG1501 3.3 36.3 1.0 N B:THR1500 3.4 31.3 1.0 CD B:ARG1501 3.4 35.5 1.0 N B:PRO1499 3.6 28.5 1.0 N B:ARG1501 3.7 32.0 1.0 O B:MET1498 3.7 31.1 1.0 CD B:PRO1499 3.8 33.4 1.0 CB B:MET1498 3.8 31.7 1.0 CB B:THR1500 3.9 36.4 1.0 CA B:THR1500 4.0 32.5 1.0 CG2 B:THR1500 4.3 35.5 1.0 CZ B:ARG1501 4.3 35.3 1.0 C B:PRO1499 4.3 31.1 1.0 C B:THR1500 4.3 30.5 1.0 NE B:ARG1501 4.3 35.3 1.0 CG B:PRO1499 4.4 34.8 1.0 CB B:ARG1501 4.5 30.6 1.0 CA B:PRO1499 4.5 33.0 1.0 CG B:ARG1501 4.5 34.1 1.0 CG B:MET1498 4.5 35.4 1.0 N B:MET1498 4.6 30.9 1.0 O B:MET1497 4.6 31.5 1.0 CA B:ARG1501 4.7 30.8 1.0 OE1 B:GLU1437 4.9 32.0 1.0 CZ B:PHE1438 5.0 29.7 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.