Chlorine in PDB 5rb3: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039249D

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039249D, PDB code: 5rb3 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)	89.79 / 1.53
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.040, 93.460, 94.340, 90.00, 107.86, 90.00
R / Rfree (%)	18.7 / 20.8

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039249D 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 XS039249D (pdb code 5rb3). 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 XS039249D, PDB code: 5rb3:
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 XS039249D


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 XS039249D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:22.6 occ:1.00 O A:HOH2134 3.2 20.9 1.0 O A:HOH2077 3.3 20.3 1.0 N A:GLU1513 3.4 18.0 1.0 O A:HOH2257 3.5 39.8 1.0 C A:LEU1511 3.5 18.5 1.0 CA A:LEU1511 3.6 16.5 1.0 CB A:GLU1513 3.6 23.2 1.0 O A:HOH2209 3.6 38.6 1.0 N A:PRO1512 3.7 20.1 1.0 CG A:GLU1513 3.8 26.4 1.0 CD A:PRO1512 3.8 20.6 1.0 CD1 A:LEU1511 3.9 19.6 1.0 CA A:GLU1513 4.0 19.3 1.0 O A:LEU1511 4.0 17.1 1.0 CB A:LEU1511 4.2 17.1 1.0 CB A:TRP1402 4.3 18.9 1.0 CD2 A:TYR1514 4.4 15.5 1.0 CG A:PRO1512 4.4 22.9 1.0 C A:PRO1512 4.4 20.0 1.0 N A:TYR1514 4.5 17.4 1.0 CA A:PRO1512 4.6 20.6 1.0 OE2 A:GLU1513 4.6 37.1 1.0 CD A:GLU1513 4.7 40.9 1.0 O A:HOH2039 4.7 30.0 1.0 CG A:LEU1511 4.7 17.9 1.0 CE2 A:TYR1514 4.7 16.6 1.0 N A:LEU1511 4.8 17.4 1.0 C A:GLU1513 4.8 17.7 1.0

Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039249D


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 XS039249D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:38.3 occ:1.00 NH1 A:ARG1501 3.2 30.6 1.0 N A:THR1500 3.4 26.4 1.0 CA A:MET1498 3.4 27.9 1.0 O A:HOH1922 3.4 50.2 1.0 C A:MET1498 3.4 31.9 1.0 CD A:ARG1501 3.5 34.0 1.0 N A:ARG1501 3.6 26.8 1.0 CB A:THR1500 3.6 35.5 1.0 CB A:MET1498 3.7 30.1 1.0 N A:PRO1499 3.8 32.5 1.0 O A:MET1498 3.8 29.8 1.0 CA A:THR1500 3.9 27.9 1.0 CD A:PRO1499 4.1 33.1 1.0 O A:HOH2252 4.1 40.2 1.0 OG1 A:THR1500 4.1 37.3 1.0 C A:THR1500 4.2 26.5 1.0 CZ A:ARG1501 4.3 31.3 1.0 C A:PRO1499 4.3 28.5 1.0 NE A:ARG1501 4.4 32.4 1.0 CB A:ARG1501 4.4 27.6 1.0 CG A:ARG1501 4.5 31.6 1.0 CA A:PRO1499 4.6 29.6 1.0 CA A:ARG1501 4.6 25.6 1.0 CG A:MET1498 4.6 31.1 1.0 O A:MET1497 4.7 30.4 1.0 N A:MET1498 4.7 28.3 1.0 CG A:PRO1499 4.8 33.7 1.0 CG2 A:THR1500 4.8 41.2 1.0 OE1 A:GLU1437 5.0 29.6 1.0 O A:HOH1950 5.0 35.7 1.0

Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039249D


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 XS039249D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:43.4 occ:1.00 N A:ASN1558 3.1 19.5 1.0 O A:HOH2251 3.1 54.0 1.0 O A:HOH1935 3.4 55.8 1.0 OE1 A:GLN1650 3.6 48.7 1.0 CA A:THR1557 3.7 19.9 1.0 NZ A:LYS1484 3.7 30.6 1.0 CB A:ASN1558 3.8 19.8 1.0 C A:THR1557 3.9 20.2 1.0 CG A:GLN1650 4.0 34.9 1.0 CA A:ASN1558 4.0 18.5 1.0 CG A:ASN1558 4.1 23.4 1.0 O A:THR1556 4.2 21.1 1.0 CD A:GLN1650 4.2 39.3 1.0 CG2 A:THR1557 4.2 24.5 1.0 ND2 A:ASN1558 4.3 27.6 1.0 O A:HOH2286 4.5 47.3 1.0 CB A:THR1557 4.5 24.2 1.0 O A:GLN1650 4.5 27.5 1.0 N A:THR1557 4.7 20.0 1.0 OD1 A:ASN1558 4.8 21.9 1.0 O A:ASN1558 4.8 18.1 1.0 O A:HOH2112 4.8 37.2 1.0 OG1 A:THR1557 4.8 24.3 1.0 C A:THR1556 4.9 20.5 1.0 C A:ASN1558 4.9 17.9 1.0

Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039249D


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 XS039249D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:50.2 occ:1.00 NE2 A:HIS1712 2.8 22.6 1.0 O A:HOH2089 3.0 20.0 1.0 O A:HOH2247 3.1 29.2 1.0 O A:HOH1994 3.1 39.3 1.0 CD2 A:HIS1709 3.8 18.1 1.0 CD2 A:HIS1712 3.8 23.3 1.0 CE1 A:HIS1712 3.8 21.2 1.0 O A:HOH2180 4.1 52.1 1.0 NE2 A:HIS1709 4.4 22.1 1.0 O A:HOH2164 4.6 20.3 1.0 CG A:HIS1709 4.6 17.5 1.0 O A:HOH2037 4.6 18.8 1.0 CB A:ALA1619 4.8 17.8 1.0 O A:ALA1685 4.9 16.8 1.0 ND1 A:HIS1712 4.9 23.3 1.0 CG A:HIS1712 5.0 21.0 1.0 O A:GLU1708 5.0 19.8 1.0 O A:HOH2229 5.0 33.2 1.0 CA A:GLY1412 5.0 20.5 1.0

Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039249D


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 XS039249D within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1803 b:41.6 occ:1.00 OG1 B:THR1500 2.8 41.4 1.0 NH1 B:ARG1501 3.3 36.8 1.0 CA B:MET1498 3.3 31.4 1.0 C B:MET1498 3.3 33.9 1.0 N B:THR1500 3.4 32.2 1.0 CD B:ARG1501 3.5 35.7 1.0 N B:PRO1499 3.6 32.6 1.0 N B:ARG1501 3.7 31.6 1.0 CB B:THR1500 3.8 37.6 1.0 O B:MET1498 3.8 30.2 1.0 CD B:PRO1499 3.9 36.4 1.0 CB B:MET1498 3.9 33.0 1.0 CA B:THR1500 4.0 34.5 1.0 CG2 B:THR1500 4.0 38.2 1.0 CZ B:ARG1501 4.3 39.2 1.0 C B:THR1500 4.3 34.6 1.0 C B:PRO1499 4.3 33.4 1.0 NE B:ARG1501 4.3 35.5 1.0 CA B:PRO1499 4.5 36.2 1.0 CB B:ARG1501 4.5 27.1 1.0 CG B:ARG1501 4.5 29.0 1.0 O B:MET1497 4.6 30.7 1.0 N B:MET1498 4.6 31.9 1.0 CG B:PRO1499 4.6 36.6 1.0 CG B:MET1498 4.7 36.6 1.0 CA B:ARG1501 4.7 29.1 1.0 OE1 B:GLU1437 4.9 31.6 1.0 O B:HOH1975 4.9 39.4 1.0 CZ B:PHE1438 5.0 30.5 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.