Chlorine in PDB 5rax: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010054A

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010054A, PDB code: 5rax 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)	54.88 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.550, 93.730, 93.645, 90.00, 108.10, 90.00
R / Rfree (%)	18.4 / 23.1

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010054A 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 FM010054A (pdb code 5rax). 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 FM010054A, PDB code: 5rax:
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 FM010054A


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 FM010054A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1801 b:28.9 occ:1.00 O A:HOH2266 3.2 57.7 1.0 O A:HOH2171 3.2 28.5 1.0 O A:HOH2143 3.2 24.9 1.0 O A:HOH2185 3.3 62.1 1.0 N A:GLU1513 3.4 27.6 1.0 C A:LEU1511 3.6 23.5 1.0 CA A:LEU1511 3.6 22.2 1.0 CB A:GLU1513 3.7 30.3 1.0 CD A:PRO1512 3.7 29.7 1.0 N A:PRO1512 3.7 27.5 1.0 CG A:GLU1513 3.8 40.1 1.0 O A:LEU1511 4.0 23.5 1.0 CD1 A:LEU1511 4.1 22.9 1.0 CA A:GLU1513 4.1 26.5 1.0 CB A:TRP1402 4.3 28.4 1.0 CG A:PRO1512 4.3 27.4 1.0 CB A:LEU1511 4.3 21.7 1.0 C A:PRO1512 4.4 28.4 1.0 CD2 A:TYR1514 4.5 22.3 1.0 CA A:PRO1512 4.6 27.7 1.0 N A:TYR1514 4.6 21.0 1.0 OE2 A:GLU1513 4.7 54.4 1.0 CD A:GLU1513 4.7 52.0 1.0 O A:HOH2021 4.8 40.1 1.0 CG A:LEU1511 4.8 22.6 1.0 N A:LEU1511 4.8 23.8 1.0 CE2 A:TYR1514 4.9 23.8 1.0 C A:GLU1513 4.9 23.3 1.0

Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010054A


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 FM010054A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:48.0 occ:1.00 O A:HOH1958 3.2 51.8 1.0 NH1 A:ARG1501 3.3 41.2 1.0 C A:MET1498 3.3 44.0 1.0 N A:THR1500 3.4 37.7 1.0 CA A:MET1498 3.4 39.5 1.0 CB A:THR1500 3.5 39.1 1.0 N A:ARG1501 3.6 37.5 1.0 O A:MET1498 3.6 42.8 1.0 CD A:ARG1501 3.6 42.2 1.0 N A:PRO1499 3.7 47.9 1.0 CA A:THR1500 3.8 36.4 1.0 O A:HOH2231 3.8 59.2 1.0 CB A:MET1498 3.9 39.1 1.0 OG1 A:THR1500 3.9 40.4 1.0 CD A:PRO1499 4.2 44.6 1.0 C A:THR1500 4.2 37.5 1.0 C A:PRO1499 4.3 38.8 1.0 CZ A:ARG1501 4.3 41.8 1.0 CB A:ARG1501 4.4 35.6 1.0 NE A:ARG1501 4.5 41.2 1.0 CA A:PRO1499 4.6 40.4 1.0 CG A:ARG1501 4.6 42.1 1.0 CA A:ARG1501 4.6 35.5 1.0 CG A:PRO1499 4.6 42.4 1.0 CG2 A:THR1500 4.7 40.0 1.0 N A:MET1498 4.7 38.0 1.0 O A:MET1497 4.8 34.1 1.0 CG A:MET1498 4.8 42.0 1.0

Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010054A


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 FM010054A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:42.2 occ:1.00 N A:ASN1558 3.1 25.7 1.0 O A:HOH2157 3.3 53.5 1.0 NZ A:LYS1484 3.5 38.2 1.0 O A:HOH2084 3.6 48.4 1.0 OE1 A:GLN1650 3.7 40.0 1.0 CA A:THR1557 3.7 25.0 1.0 CB A:ASN1558 3.8 27.1 1.0 C A:THR1557 3.9 26.2 1.0 CG A:GLN1650 4.0 35.9 1.0 CA A:ASN1558 4.1 26.6 1.0 CG A:ASN1558 4.1 31.3 1.0 ND2 A:ASN1558 4.2 30.4 1.0 CG2 A:THR1557 4.2 26.3 1.0 CD A:GLN1650 4.3 41.9 1.0 O A:HOH2277 4.3 45.0 1.0 O A:THR1556 4.3 27.0 1.0 O A:GLN1650 4.4 33.3 1.0 CB A:THR1557 4.5 28.9 1.0 OD1 A:ASN1558 4.7 26.1 1.0 O A:HOH2073 4.7 45.8 1.0 N A:THR1557 4.8 25.7 1.0 CE A:LYS1484 4.8 40.1 1.0 O A:ASN1558 4.8 21.9 1.0 OG1 A:THR1557 4.9 28.7 1.0 C A:THR1556 5.0 27.6 1.0 C A:ASN1558 5.0 22.0 1.0

Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010054A


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 FM010054A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:60.8 occ:1.00 NE2 A:HIS1712 2.8 27.0 1.0 O A:HOH2235 2.9 35.0 1.0 O A:HOH2118 2.9 20.8 1.0 O A:HOH2014 3.2 42.6 1.0 CD2 A:HIS1712 3.7 30.1 1.0 CD2 A:HIS1709 3.7 29.8 1.0 CE1 A:HIS1712 3.9 28.9 1.0 O A:HOH2190 4.3 55.4 1.0 NE2 A:HIS1709 4.3 28.7 1.0 O A:HOH2178 4.4 21.4 1.0 O A:HOH2270 4.5 65.3 1.0 CG A:HIS1709 4.6 27.7 1.0 O A:HOH2040 4.6 21.4 1.0 CB A:ALA1619 4.7 23.2 1.0 O A:HOH2212 4.8 33.7 1.0 CG A:HIS1712 4.9 29.8 1.0 O A:GLU1708 4.9 26.2 1.0 ND1 A:HIS1712 5.0 26.0 1.0 O A:ALA1685 5.0 20.8 1.0

Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010054A


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 FM010054A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1802 b:44.2 occ:1.00 OG1 B:THR1500 2.8 55.4 1.0 C B:MET1498 3.3 40.9 1.0 N B:THR1500 3.3 36.8 1.0 CA B:MET1498 3.3 40.2 1.0 NH1 B:ARG1501 3.4 41.8 1.0 N B:PRO1499 3.6 45.3 1.0 O B:MET1498 3.6 41.7 1.0 CD B:ARG1501 3.6 42.3 1.0 N B:ARG1501 3.7 43.8 1.0 CB B:THR1500 3.8 44.2 1.0 CD B:PRO1499 3.9 44.8 1.0 CA B:THR1500 3.9 42.6 1.0 CB B:MET1498 3.9 43.7 1.0 CG2 B:THR1500 4.2 47.0 1.0 C B:PRO1499 4.3 41.6 1.0 C B:THR1500 4.3 40.9 1.0 CZ B:ARG1501 4.3 42.0 1.0 NE B:ARG1501 4.4 46.9 1.0 CA B:PRO1499 4.5 44.1 1.0 CG B:PRO1499 4.5 45.7 1.0 CB B:ARG1501 4.5 38.7 1.0 CG B:ARG1501 4.6 41.6 1.0 N B:MET1498 4.6 38.0 1.0 O B:MET1497 4.7 33.6 1.0 CA B:ARG1501 4.8 37.0 1.0 CG B:MET1498 4.8 49.5 1.0 O B:HOH1913 4.8 55.1 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.