Chlorine in PDB 5rb4: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001677A

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001677A, PDB code: 5rb4 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)	64.66 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.870, 93.660, 93.692, 90.00, 107.88, 90.00
R / Rfree (%)	18.5 / 20.9

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001677A 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 FM001677A (pdb code 5rb4). 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 FM001677A, PDB code: 5rb4:
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 FM001677A


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 FM001677A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1801 b:54.9 occ:0.45 CL1 A:A6Z1801 0.0 54.9 0.5 C5 A:A6Z1801 1.7 50.5 0.5 C4 A:A6Z1801 2.6 50.0 0.5 C6 A:A6Z1801 2.7 48.9 0.5 O A:ILE1603 3.3 39.7 0.5 CD A:PRO1610 3.6 28.0 1.0 O A:HOH2193 3.6 36.1 0.5 CG A:PRO1610 3.7 28.8 1.0 O A:HOH1918 3.7 38.9 0.5 O A:HOH1971 3.9 47.2 0.5 CG2 A:ILE1603 3.9 36.0 0.5 C3 A:A6Z1801 4.0 50.3 0.5 C1 A:A6Z1801 4.0 47.6 0.5 CD1 A:ILE1603 4.2 35.3 0.5 C A:ILE1603 4.2 39.4 0.5 CA A:ILE1603 4.2 36.9 0.5 ND1 A:HIS1606 4.2 44.1 0.5 O A:GLU1608 4.3 28.4 0.5 C2 A:A6Z1801 4.5 49.5 0.5 CB A:ILE1603 4.5 34.9 0.5 CE1 A:HIS1606 4.7 43.5 0.5 CB A:PRO1610 4.7 25.8 1.0 CA A:HIS1606 4.9 42.0 0.5 N A:PRO1610 5.0 26.3 1.0 CG1 A:ILE1603 5.0 34.6 0.5

Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001677A


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 FM001677A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:23.0 occ:1.00 O A:HOH2139 3.2 23.3 1.0 O A:HOH2264 3.3 41.3 1.0 O A:HOH2022 3.3 22.1 1.0 N A:GLU1513 3.4 19.6 1.0 O A:HOH2195 3.4 47.6 1.0 C A:LEU1511 3.5 18.9 1.0 CA A:LEU1511 3.6 18.1 1.0 CB A:GLU1513 3.6 24.3 1.0 N A:PRO1512 3.7 20.4 1.0 CD A:PRO1512 3.8 22.7 1.0 CG A:GLU1513 3.8 27.9 1.0 CD1 A:LEU1511 3.9 19.5 1.0 O A:LEU1511 4.0 17.5 1.0 CA A:GLU1513 4.1 20.5 1.0 CB A:LEU1511 4.2 17.5 1.0 CB A:TRP1402 4.3 21.1 1.0 CD2 A:TYR1514 4.3 16.5 1.0 CG A:PRO1512 4.4 24.5 1.0 C A:PRO1512 4.4 21.9 1.0 N A:TYR1514 4.6 18.4 1.0 OE2 A:GLU1513 4.6 37.7 1.0 CA A:PRO1512 4.6 21.1 1.0 CD A:GLU1513 4.7 39.5 1.0 CG A:LEU1511 4.7 17.9 1.0 O A:HOH1968 4.7 30.5 1.0 N A:LEU1511 4.8 18.1 1.0 CE2 A:TYR1514 4.8 18.4 1.0 C A:GLU1513 4.8 19.5 1.0 CG A:TRP1402 5.0 20.9 1.0

Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001677A


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 FM001677A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:38.2 occ:1.00 O A:HOH2105 3.2 43.9 1.0 NH1 A:ARG1501 3.3 32.6 1.0 CA A:MET1498 3.3 31.7 1.0 C A:MET1498 3.4 34.3 1.0 N A:THR1500 3.4 28.7 1.0 CD A:ARG1501 3.5 35.0 1.0 N A:ARG1501 3.6 27.4 1.0 CB A:THR1500 3.6 39.3 1.0 N A:PRO1499 3.7 32.2 1.0 CB A:MET1498 3.7 30.4 1.0 O A:MET1498 3.7 30.9 1.0 CA A:THR1500 3.9 29.3 1.0 O A:HOH2224 4.0 44.2 1.0 CD A:PRO1499 4.0 35.2 1.0 OG1 A:THR1500 4.1 37.6 1.0 C A:THR1500 4.2 30.2 1.0 CZ A:ARG1501 4.3 32.5 1.0 C A:PRO1499 4.4 30.6 1.0 NE A:ARG1501 4.4 32.9 1.0 CB A:ARG1501 4.4 27.8 1.0 CG A:ARG1501 4.5 32.6 1.0 CA A:ARG1501 4.6 27.5 1.0 CA A:PRO1499 4.6 31.2 1.0 N A:MET1498 4.6 27.6 1.0 CG A:MET1498 4.7 32.2 1.0 O A:MET1497 4.7 30.1 1.0 CG2 A:THR1500 4.8 39.9 1.0 CG A:PRO1499 4.8 35.0 1.0 OE1 A:GLU1437 5.0 30.4 1.0

Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001677A


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 FM001677A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:41.3 occ:1.00 N A:ASN1558 3.1 20.1 1.0 O A:HOH2229 3.3 52.6 1.0 O A:HOH1916 3.3 60.7 1.0 NZ A:LYS1484 3.6 30.1 1.0 OE1 A:GLN1650 3.6 45.3 1.0 CA A:THR1557 3.7 19.6 1.0 C A:THR1557 3.9 19.9 1.0 CB A:ASN1558 3.9 20.3 1.0 CG A:GLN1650 4.0 33.8 1.0 CA A:ASN1558 4.1 19.4 1.0 CG2 A:THR1557 4.1 24.8 1.0 O A:THR1556 4.2 22.3 1.0 CG A:ASN1558 4.2 22.8 1.0 CD A:GLN1650 4.3 37.1 1.0 CB A:THR1557 4.4 24.5 1.0 O A:HOH2276 4.4 48.1 1.0 ND2 A:ASN1558 4.4 27.0 1.0 O A:GLN1650 4.5 26.2 1.0 O A:HOH2120 4.7 38.0 1.0 N A:THR1557 4.7 19.4 1.0 O A:ASN1558 4.8 18.5 1.0 OG1 A:THR1557 4.8 24.0 1.0 OD1 A:ASN1558 4.8 22.7 1.0 C A:THR1556 4.9 22.6 1.0 C A:ASN1558 4.9 17.5 1.0 CE A:LYS1484 4.9 33.2 1.0

Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001677A


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 FM001677A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:48.8 occ:1.00 NE2 A:HIS1712 2.8 24.1 1.0 O A:HOH2237 3.0 30.7 1.0 O A:HOH2099 3.0 21.5 1.0 O A:HOH1996 3.2 36.8 1.0 CE1 A:HIS1712 3.8 21.0 1.0 CD2 A:HIS1712 3.8 25.4 1.0 CD2 A:HIS1709 3.8 19.9 1.0 O A:HOH2174 4.1 54.1 1.0 NE2 A:HIS1709 4.4 22.4 1.0 O A:HOH2164 4.5 20.5 1.0 CG A:HIS1709 4.6 18.5 1.0 O A:HOH2054 4.6 19.0 1.0 CB A:ALA1619 4.8 19.8 1.0 O A:HOH2045 4.8 42.1 1.0 ND1 A:HIS1712 4.9 23.9 1.0 CA A:GLY1412 5.0 22.7 1.0 CG A:HIS1712 5.0 22.0 1.0 O A:ALA1685 5.0 17.9 1.0 O A:GLU1708 5.0 21.4 1.0

Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM001677A


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 FM001677A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1801 b:42.4 occ:1.00 OG1 B:THR1500 2.7 40.6 1.0 C B:MET1498 3.3 33.0 1.0 CA B:MET1498 3.3 32.9 1.0 N B:THR1500 3.3 30.9 1.0 NH1 B:ARG1501 3.4 36.8 1.0 CD B:ARG1501 3.5 35.4 1.0 N B:PRO1499 3.6 32.6 1.0 N B:ARG1501 3.7 32.8 1.0 O B:MET1498 3.7 31.6 1.0 CB B:THR1500 3.7 36.0 1.0 CD B:PRO1499 3.8 37.6 1.0 CB B:MET1498 3.9 31.8 1.0 CA B:THR1500 3.9 35.0 1.0 CG2 B:THR1500 4.1 37.7 1.0 C B:PRO1499 4.3 33.1 1.0 C B:THR1500 4.3 31.9 1.0 CZ B:ARG1501 4.3 35.7 1.0 NE B:ARG1501 4.4 36.5 1.0 CA B:PRO1499 4.5 34.6 1.0 CB B:ARG1501 4.5 29.5 1.0 CG B:PRO1499 4.5 38.7 1.0 CG B:ARG1501 4.5 32.2 1.0 N B:MET1498 4.6 30.6 1.0 O B:MET1497 4.6 31.2 1.0 CG B:MET1498 4.6 36.8 1.0 CA B:ARG1501 4.7 32.1 1.0 OE1 B:GLU1437 4.8 32.0 1.0 CZ B:PHE1438 5.0 31.4 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.