Chlorine in PDB 5rab: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001726A

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001726A, PDB code: 5rab 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)	89.00 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.660, 93.640, 93.470, 90.00, 107.80, 90.00
R / Rfree (%)	18.5 / 21

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001726A 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 FM001726A (pdb code 5rab). 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 FM001726A, PDB code: 5rab:
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 FM001726A


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 FM001726A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1801 b:42.3 occ:0.51 CL13 A:S4Y1801 0.0 42.3 0.5 C12 A:S4Y1801 1.8 37.7 0.5 C14 A:S4Y1801 2.7 41.2 0.5 C11 A:S4Y1801 2.8 40.3 0.5 CG1 A:VAL1586 3.6 42.1 0.5 CG2 A:ILE1603 3.7 37.6 0.5 O A:HOH2052 3.8 46.8 0.5 C15 A:S4Y1801 4.1 40.8 0.5 OD1 A:ASP1583 4.1 55.5 0.2 C10 A:S4Y1801 4.1 40.8 0.5 CG A:LEU1587 4.2 62.8 0.5 N A:LEU1587 4.2 49.3 0.5 CD2 A:LEU1587 4.2 62.2 0.5 CB A:VAL1586 4.2 42.5 0.5 O A:ASP1583 4.2 51.3 0.3 CA A:LEU1587 4.4 54.5 0.5 O A:ASP1583 4.4 54.1 0.2 C A:VAL1586 4.5 44.7 0.5 C09 A:S4Y1801 4.6 43.6 0.5 CD1 A:ILE1603 4.6 35.9 0.5 CG A:PRO1610 4.6 24.5 1.0 CD1 A:ILE1590 4.6 55.3 0.5 CG A:ASP1583 4.7 58.4 0.2 CB A:LEU1587 4.8 58.6 0.5 OD2 A:ASP1583 4.9 56.6 0.2 OH A:TYR1695 4.9 32.0 1.0 O A:VAL1586 5.0 43.5 0.5 NE2 A:HIS1606 5.0 42.3 0.5

Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001726A


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 FM001726A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:22.3 occ:1.00 O A:HOH2151 3.2 21.8 1.0 O A:HOH2038 3.3 20.9 1.0 O A:HOH2256 3.4 40.2 1.0 N A:GLU1513 3.4 18.9 1.0 O A:HOH2189 3.4 45.0 1.0 C A:LEU1511 3.5 18.8 1.0 CA A:LEU1511 3.6 17.9 1.0 CB A:GLU1513 3.6 23.8 1.0 N A:PRO1512 3.7 19.3 1.0 CD A:PRO1512 3.7 21.0 1.0 CG A:GLU1513 3.9 27.2 1.0 CD1 A:LEU1511 3.9 19.7 1.0 O A:LEU1511 4.0 17.1 1.0 CA A:GLU1513 4.0 19.7 1.0 CB A:LEU1511 4.2 16.9 1.0 CB A:TRP1402 4.3 18.9 1.0 CD2 A:TYR1514 4.4 16.1 1.0 CG A:PRO1512 4.4 22.5 1.0 C A:PRO1512 4.4 20.5 1.0 N A:TYR1514 4.5 17.7 1.0 OE2 A:GLU1513 4.6 38.8 1.0 CA A:PRO1512 4.6 20.1 1.0 CD A:GLU1513 4.7 39.9 1.0 O A:HOH2018 4.7 28.9 1.0 CG A:LEU1511 4.7 18.2 1.0 N A:LEU1511 4.7 17.1 1.0 C A:GLU1513 4.8 18.6 1.0 CE2 A:TYR1514 4.8 18.6 1.0 CG A:TRP1402 5.0 20.6 1.0

Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001726A


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 FM001726A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:36.2 occ:1.00 O A:HOH2118 3.0 41.0 1.0 NH1 A:ARG1501 3.3 32.1 1.0 CA A:MET1498 3.3 27.4 1.0 C A:MET1498 3.4 32.3 1.0 N A:THR1500 3.4 26.3 1.0 N A:ARG1501 3.6 27.8 1.0 CD A:ARG1501 3.6 37.3 1.0 CB A:THR1500 3.6 36.8 1.0 N A:PRO1499 3.7 29.2 1.0 O A:MET1498 3.8 27.7 1.0 CB A:MET1498 3.8 28.2 1.0 CA A:THR1500 3.9 27.9 1.0 O A:HOH2232 3.9 46.3 1.0 CD A:PRO1499 4.0 33.7 1.0 OG1 A:THR1500 4.1 35.4 1.0 C A:THR1500 4.2 29.3 1.0 CZ A:ARG1501 4.3 32.9 1.0 C A:PRO1499 4.3 28.0 1.0 CB A:ARG1501 4.4 28.4 1.0 NE A:ARG1501 4.4 32.4 1.0 CG A:ARG1501 4.5 34.4 1.0 CA A:PRO1499 4.5 28.5 1.0 CA A:ARG1501 4.6 27.1 1.0 N A:MET1498 4.7 25.7 1.0 CG A:PRO1499 4.7 32.8 1.0 CG A:MET1498 4.7 27.6 1.0 O A:MET1497 4.7 27.6 1.0 CG2 A:THR1500 4.8 35.5 1.0 OE1 A:GLU1437 5.0 28.8 1.0

Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001726A


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 FM001726A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:30.5 occ:1.00 N A:ASN1558 3.3 18.4 1.0 OE1 A:GLN1650 3.4 33.2 1.0 NZ A:LYS1484 3.6 28.1 1.0 O A:HOH2205 3.6 32.4 1.0 CA A:THR1557 3.8 19.4 1.0 CG A:GLN1650 4.0 25.6 1.0 CB A:ASN1558 4.0 19.5 1.0 C A:THR1557 4.0 19.0 1.0 CG2 A:THR1557 4.1 23.0 1.0 CD A:GLN1650 4.1 25.5 1.0 O A:HOH2083 4.1 48.7 1.0 CA A:ASN1558 4.2 18.2 1.0 CG A:ASN1558 4.4 21.8 1.0 O A:THR1556 4.4 20.6 1.0 CB A:THR1557 4.4 22.6 1.0 O A:GLN1650 4.5 24.3 1.0 O A:HOH2270 4.5 48.1 1.0 ND2 A:ASN1558 4.5 24.8 1.0 O A:HOH2165 4.7 35.7 1.0 OG1 A:THR1557 4.8 22.1 1.0 O A:ASN1558 4.8 17.8 1.0 N A:THR1557 4.8 18.4 1.0 CE A:LYS1484 4.8 33.8 1.0 OD1 A:ASN1558 5.0 21.4 1.0

Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001726A


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 FM001726A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:45.4 occ:1.00 NE2 A:HIS1712 2.9 23.2 1.0 O A:HOH2240 2.9 30.3 1.0 O A:HOH2082 3.1 20.5 1.0 O A:HOH2002 3.2 35.7 1.0 CE1 A:HIS1712 3.8 21.1 1.0 CD2 A:HIS1709 3.8 20.2 1.0 CD2 A:HIS1712 3.9 23.8 1.0 O A:HOH2201 4.0 54.8 1.0 NE2 A:HIS1709 4.4 22.8 1.0 O A:HOH2178 4.5 19.8 1.0 O A:HOH2040 4.6 17.6 1.0 CG A:HIS1709 4.7 18.2 1.0 CB A:ALA1619 4.8 19.4 1.0 O A:HOH2223 4.9 31.3 1.0 O A:HOH2096 4.9 44.6 1.0 ND1 A:HIS1712 5.0 24.0 1.0 CA A:GLY1412 5.0 22.0 1.0

Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001726A


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 FM001726A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1801 b:40.7 occ:1.00 OG1 B:THR1500 2.8 46.3 1.0 NH1 B:ARG1501 3.3 36.7 1.0 CA B:MET1498 3.3 34.0 1.0 C B:MET1498 3.3 34.9 1.0 N B:THR1500 3.4 34.6 1.0 CD B:ARG1501 3.4 35.9 1.0 N B:PRO1499 3.6 33.7 1.0 N B:ARG1501 3.7 33.8 1.0 O B:MET1498 3.8 32.9 1.0 CB B:THR1500 3.8 40.5 1.0 CB B:MET1498 3.9 31.9 1.0 CD B:PRO1499 3.9 37.3 1.0 CA B:THR1500 4.0 37.3 1.0 CG2 B:THR1500 4.2 39.0 1.0 CZ B:ARG1501 4.3 34.3 1.0 C B:THR1500 4.3 34.7 1.0 NE B:ARG1501 4.3 36.2 1.0 C B:PRO1499 4.3 34.8 1.0 CB B:ARG1501 4.5 31.0 1.0 CG B:ARG1501 4.5 33.4 1.0 CA B:PRO1499 4.5 36.4 1.0 CG B:PRO1499 4.5 39.2 1.0 N B:MET1498 4.6 30.8 1.0 CG B:MET1498 4.6 36.2 1.0 O B:MET1497 4.6 34.8 1.0 CA B:ARG1501 4.7 33.9 1.0 OE1 B:GLU1437 4.8 32.5 1.0 CZ B:PHE1438 5.0 32.6 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.