Chlorine in PDB 5ran: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D, PDB code: 5ran 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)	88.93 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.520, 93.750, 93.605, 90.00, 108.18, 90.00
R / Rfree (%)	18.3 / 22.5

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D 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 XS039080D (pdb code 5ran). 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 XS039080D, PDB code: 5ran:
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 XS039080D


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 XS039080D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:30.2 occ:1.00 O A:HOH2158 3.2 28.9 1.0 O A:HOH2244 3.2 50.2 1.0 O A:HOH2144 3.2 23.1 1.0 N A:GLU1513 3.4 26.3 1.0 CB A:GLU1513 3.5 32.9 1.0 C A:LEU1511 3.5 24.1 1.0 CA A:LEU1511 3.6 22.4 1.0 O A:HOH2124 3.6 47.0 1.0 N A:PRO1512 3.7 26.9 1.0 CG A:GLU1513 3.8 42.4 1.0 CD A:PRO1512 3.8 30.0 1.0 CD1 A:LEU1511 3.9 24.9 1.0 O A:LEU1511 4.0 22.5 1.0 CA A:GLU1513 4.0 27.3 1.0 CB A:LEU1511 4.2 21.3 1.0 CD2 A:TYR1514 4.3 20.9 1.0 CB A:TRP1402 4.3 28.3 1.0 C A:PRO1512 4.4 27.8 1.0 N A:TYR1514 4.4 22.8 1.0 CG A:PRO1512 4.4 29.0 1.0 CA A:PRO1512 4.6 26.7 1.0 CG A:LEU1511 4.7 24.2 1.0 OE2 A:GLU1513 4.7 58.4 1.0 C A:GLU1513 4.7 25.2 1.0 CE2 A:TYR1514 4.7 21.5 1.0 CD A:GLU1513 4.8 59.1 1.0 N A:LEU1511 4.8 21.9 1.0 O A:HOH2004 4.8 36.4 1.0

Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D


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 XS039080D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:45.3 occ:1.00 O A:HOH1947 3.3 49.6 1.0 C A:MET1498 3.3 45.3 1.0 NH1 A:ARG1501 3.3 41.8 1.0 CA A:MET1498 3.3 41.6 1.0 N A:THR1500 3.3 36.7 1.0 CD A:ARG1501 3.6 40.9 1.0 N A:ARG1501 3.6 36.2 1.0 O A:MET1498 3.6 47.6 1.0 CB A:THR1500 3.6 42.3 1.0 N A:PRO1499 3.7 44.1 1.0 O A:HOH2209 3.7 48.4 1.0 CB A:MET1498 3.8 42.8 1.0 CA A:THR1500 3.9 38.6 1.0 OG1 A:THR1500 4.1 46.6 1.0 CD A:PRO1499 4.1 46.0 1.0 C A:THR1500 4.2 39.6 1.0 C A:PRO1499 4.3 40.6 1.0 CZ A:ARG1501 4.3 42.9 1.0 CB A:ARG1501 4.4 37.9 1.0 NE A:ARG1501 4.4 41.1 1.0 CA A:PRO1499 4.6 42.7 1.0 CA A:ARG1501 4.6 38.1 1.0 CG A:ARG1501 4.6 40.4 1.0 N A:MET1498 4.7 39.2 1.0 CG A:MET1498 4.7 44.3 1.0 CG A:PRO1499 4.7 44.7 1.0 O A:MET1497 4.7 34.7 1.0 CG2 A:THR1500 4.8 43.3 1.0

Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D


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 XS039080D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:58.1 occ:0.50 N A:ASN1558 3.3 26.3 1.0 OE1 A:GLN1650 3.4 41.3 1.0 O A:HOH2186 3.5 45.4 1.0 CB A:ASN1558 3.8 26.4 1.0 CG A:GLN1650 3.9 33.9 1.0 NZ A:LYS1484 3.9 43.7 1.0 CD A:GLN1650 4.0 39.1 1.0 CA A:THR1557 4.1 26.2 1.0 CG A:ASN1558 4.1 28.7 1.0 O A:GLN1650 4.2 31.6 1.0 CA A:ASN1558 4.2 27.0 1.0 ND2 A:ASN1558 4.2 27.8 1.0 C A:THR1557 4.2 26.1 1.0 CG2 A:THR1557 4.3 28.7 1.0 O A:THR1556 4.7 26.0 1.0 CB A:THR1557 4.7 28.8 1.0 O A:ASN1558 4.9 21.2 1.0 OD1 A:ASN1558 4.9 25.9 1.0 CB A:GLN1650 4.9 30.2 1.0 C A:ASN1558 5.0 24.9 1.0

Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D


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 XS039080D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:54.5 occ:1.00 NE2 A:HIS1712 2.8 27.3 1.0 O A:HOH2079 2.9 21.3 1.0 O A:HOH2228 3.0 32.9 1.0 O A:HOH1957 3.4 44.2 1.0 CD2 A:HIS1712 3.6 27.5 1.0 CD2 A:HIS1709 3.7 23.8 1.0 CE1 A:HIS1712 3.8 25.4 1.0 NE2 A:HIS1709 4.4 24.7 1.0 O A:HOH2156 4.5 23.8 1.0 CG A:HIS1709 4.5 24.4 1.0 O A:HOH2148 4.5 54.8 1.0 O A:HOH2038 4.5 19.7 1.0 CB A:ALA1619 4.6 24.2 1.0 O A:HOH2212 4.8 72.4 1.0 O A:ALA1685 4.8 20.7 1.0 CG A:HIS1712 4.9 26.0 1.0 O A:GLU1708 4.9 24.8 1.0 ND1 A:HIS1712 4.9 25.6 1.0 CB A:HIS1709 4.9 23.4 1.0 CA A:HIS1709 5.0 25.0 1.0

Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS039080D


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 XS039080D within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1802 b:46.3 occ:1.00 OG1 B:THR1500 2.9 62.0 1.0 CA B:MET1498 3.2 41.1 1.0 NH1 B:ARG1501 3.2 40.3 1.0 C B:MET1498 3.3 44.7 1.0 N B:THR1500 3.5 41.2 1.0 N B:PRO1499 3.6 46.1 1.0 N B:ARG1501 3.6 43.3 1.0 CB B:MET1498 3.7 42.4 1.0 O B:MET1498 3.7 44.0 1.0 CD B:PRO1499 3.9 47.4 1.0 CG B:ARG1501 4.0 42.8 1.0 CB B:THR1500 4.0 49.5 1.0 CD B:ARG1501 4.1 42.3 1.0 CA B:THR1500 4.1 47.1 1.0 CB B:ARG1501 4.2 40.4 1.0 C B:THR1500 4.3 43.9 1.0 CZ B:ARG1501 4.3 42.8 1.0 C B:PRO1499 4.4 40.9 1.0 CG B:MET1498 4.5 46.2 1.0 CA B:PRO1499 4.5 44.9 1.0 CG2 B:THR1500 4.5 52.1 1.0 N B:MET1498 4.5 41.4 1.0 CA B:ARG1501 4.6 41.1 1.0 O B:MET1497 4.6 40.9 1.0 NE B:ARG1501 4.6 44.3 1.0 CG B:PRO1499 4.7 48.4 1.0 O B:HOH1937 4.8 51.7 1.0 OE1 B:GLU1437 4.8 37.3 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.