Chlorine in PDB 5rb6: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A, PDB code: 5rb6 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)	89.05 / 1.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.840, 93.730, 93.530, 90.00, 107.81, 90.00
R / Rfree (%)	18.2 / 20.8

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A 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 FM001569A (pdb code 5rb6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A, PDB code: 5rb6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A


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 FM001569A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1801 b:22.1 occ:0.48 CL A:S9V1801 0.0 22.1 0.5 C8 A:S9V1801 1.7 21.2 0.5 C9 A:S9V1801 2.7 21.1 0.5 C7 A:S9V1801 2.7 21.1 0.5 CB A:ASN1400 3.1 26.3 1.0 O A:ASN1400 3.2 20.6 1.0 C A:ASN1400 3.2 21.3 1.0 OD1 A:ASN1398 3.4 26.1 1.0 CA A:ASN1400 3.7 22.5 1.0 N A:ASN1401 3.8 19.9 1.0 CD1 A:ILE1404 3.8 28.8 1.0 C10 A:S9V1801 4.0 21.5 0.5 C6 A:S9V1801 4.0 21.9 0.5 CG A:ASN1398 4.1 27.1 1.0 CA A:ASN1401 4.3 20.6 1.0 N A:ASN1400 4.3 21.2 1.0 O A:HOH1911 4.4 34.8 1.0 CG A:ASN1400 4.4 32.6 1.0 OD1 A:ASN1401 4.4 19.5 1.0 C5 A:S9V1801 4.5 22.1 0.5 CG1 A:ILE1404 4.5 27.6 1.0 ND2 A:ASN1400 4.7 36.8 1.0 CB A:ASN1398 4.8 24.6 1.0 ND2 A:ASN1398 4.9 25.6 1.0 CB A:SER1381 5.0 22.6 0.5

Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A


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 FM001569A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:21.3 occ:1.00 O A:HOH2142 3.2 21.2 1.0 O A:HOH2251 3.3 38.1 1.0 O A:HOH1975 3.3 19.6 1.0 N A:GLU1513 3.4 19.3 1.0 O A:HOH2194 3.5 45.6 1.0 C A:LEU1511 3.5 17.5 1.0 CA A:LEU1511 3.6 17.1 1.0 CB A:GLU1513 3.6 23.0 1.0 N A:PRO1512 3.7 18.2 1.0 CD A:PRO1512 3.8 18.9 1.0 CG A:GLU1513 3.9 27.1 1.0 CD1 A:LEU1511 3.9 18.1 1.0 O A:LEU1511 4.0 15.8 1.0 CA A:GLU1513 4.1 20.1 1.0 CB A:LEU1511 4.2 17.1 1.0 CB A:TRP1402 4.3 17.7 1.0 CD2 A:TYR1514 4.4 14.7 1.0 CG A:PRO1512 4.4 21.3 1.0 C A:PRO1512 4.4 19.6 1.0 OE2 A:GLU1513 4.5 34.6 1.0 N A:TYR1514 4.6 16.8 1.0 CA A:PRO1512 4.6 19.3 1.0 O A:HOH2047 4.6 29.8 1.0 CD A:GLU1513 4.7 39.4 1.0 CG A:LEU1511 4.7 17.4 1.0 N A:LEU1511 4.7 15.9 1.0 C A:GLU1513 4.8 17.1 1.0 CE2 A:TYR1514 4.8 17.2 1.0 CG A:TRP1402 5.0 18.8 1.0

Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A


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 FM001569A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:35.9 occ:1.00 O A:HOH2090 3.2 41.6 1.0 NH1 A:ARG1501 3.2 30.6 1.0 CA A:MET1498 3.3 30.0 1.0 C A:MET1498 3.4 32.5 1.0 N A:THR1500 3.4 26.6 1.0 CD A:ARG1501 3.6 32.8 1.0 N A:ARG1501 3.6 27.8 1.0 CB A:THR1500 3.6 37.0 1.0 N A:PRO1499 3.7 31.0 1.0 CB A:MET1498 3.7 27.5 1.0 O A:MET1498 3.8 29.6 1.0 CA A:THR1500 3.9 28.6 1.0 O A:HOH2231 4.0 44.6 1.0 CD A:PRO1499 4.0 32.9 1.0 OG1 A:THR1500 4.1 34.6 1.0 C A:THR1500 4.2 29.9 1.0 CZ A:ARG1501 4.2 31.9 1.0 C A:PRO1499 4.3 27.8 1.0 NE A:ARG1501 4.4 32.1 1.0 CB A:ARG1501 4.4 26.6 1.0 CG A:ARG1501 4.6 32.4 1.0 CA A:PRO1499 4.6 29.6 1.0 CA A:ARG1501 4.6 24.6 1.0 N A:MET1498 4.6 25.2 1.0 CG A:MET1498 4.7 31.4 1.0 O A:MET1497 4.7 28.6 1.0 CG A:PRO1499 4.8 31.1 1.0 CG2 A:THR1500 4.8 38.4 1.0

Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A


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 FM001569A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:39.5 occ:1.00 N A:ASN1558 3.1 18.8 1.0 O A:HOH2225 3.2 46.4 1.0 O A:HOH1910 3.3 56.2 1.0 NZ A:LYS1484 3.5 30.4 1.0 OE1 A:GLN1650 3.6 46.9 1.0 CA A:THR1557 3.7 19.2 1.0 C A:THR1557 3.9 19.2 1.0 CB A:ASN1558 3.9 20.5 1.0 CG A:GLN1650 4.0 34.1 1.0 CA A:ASN1558 4.1 19.1 1.0 CG2 A:THR1557 4.2 24.5 1.0 CG A:ASN1558 4.2 24.2 1.0 CD A:GLN1650 4.2 39.8 1.0 O A:THR1556 4.3 21.1 1.0 ND2 A:ASN1558 4.4 26.1 1.0 O A:HOH2274 4.4 48.6 1.0 CB A:THR1557 4.4 23.0 1.0 O A:GLN1650 4.5 25.2 1.0 N A:THR1557 4.7 19.2 1.0 O A:HOH2160 4.7 36.8 1.0 O A:ASN1558 4.8 17.2 1.0 OD1 A:ASN1558 4.8 22.1 1.0 OG1 A:THR1557 4.8 24.1 1.0 CE A:LYS1484 4.9 32.9 1.0 C A:THR1556 4.9 21.9 1.0 C A:ASN1558 4.9 17.2 1.0

Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A


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 FM001569A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:49.4 occ:1.00 NE2 A:HIS1712 2.9 21.9 1.0 O A:HOH2097 3.0 19.6 1.0 O A:HOH2236 3.0 30.5 1.0 O A:HOH1952 3.2 39.7 1.0 CD2 A:HIS1712 3.8 23.4 1.0 CE1 A:HIS1712 3.8 20.6 1.0 CD2 A:HIS1709 3.8 19.7 1.0 O A:HOH2164 4.3 58.8 1.0 NE2 A:HIS1709 4.5 21.6 1.0 O A:HOH2171 4.6 19.3 1.0 CG A:HIS1709 4.6 17.4 1.0 O A:HOH2030 4.7 18.8 1.0 CB A:ALA1619 4.7 20.4 1.0 O A:ALA1685 4.9 16.4 1.0 ND1 A:HIS1712 5.0 22.9 1.0 O A:GLU1708 5.0 19.1 1.0 CG A:HIS1712 5.0 21.0 1.0 CA A:GLY1412 5.0 21.1 1.0 O A:HOH2223 5.0 30.1 1.0

Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001569A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1801 b:40.1 occ:1.00 OG1 B:THR1500 2.7 42.4 1.0 CA B:MET1498 3.3 34.1 1.0 C B:MET1498 3.3 33.9 1.0 NH1 B:ARG1501 3.3 35.1 1.0 N B:THR1500 3.4 32.2 1.0 CD B:ARG1501 3.5 37.8 1.0 N B:PRO1499 3.6 31.7 1.0 N B:ARG1501 3.7 34.3 1.0 O B:MET1498 3.8 31.0 1.0 CB B:THR1500 3.8 37.0 1.0 CB B:MET1498 3.9 32.1 1.0 CD B:PRO1499 3.9 36.9 1.0 CA B:THR1500 4.0 34.0 1.0 CG2 B:THR1500 4.1 36.3 1.0 CZ B:ARG1501 4.3 34.0 1.0 C B:PRO1499 4.3 33.9 1.0 C B:THR1500 4.3 33.8 1.0 NE B:ARG1501 4.4 36.2 1.0 CB B:ARG1501 4.5 30.2 1.0 CA B:PRO1499 4.5 34.5 1.0 CG B:ARG1501 4.5 34.6 1.0 CG B:PRO1499 4.6 37.6 1.0 N B:MET1498 4.6 30.3 1.0 O B:MET1497 4.6 31.6 1.0 CG B:MET1498 4.6 36.8 1.0 CA B:ARG1501 4.7 32.3 1.0 OE1 B:GLU1437 4.9 31.1 1.0 CZ B:PHE1438 5.0 29.5 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.