Chlorine in PDB 5rap: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM000707A

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM000707A, PDB code: 5rap 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)	54.83 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.490, 93.600, 93.190, 90.00, 107.69, 90.00
R / Rfree (%)	17.8 / 21.6

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM000707A 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 FM000707A (pdb code 5rap). 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 FM000707A, PDB code: 5rap:
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 FM000707A


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 FM000707A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:23.0 occ:1.00 O A:HOH2157 3.2 21.3 1.0 O A:HOH2250 3.2 54.5 1.0 O A:HOH2054 3.3 22.9 1.0 O A:HOH2143 3.3 48.9 1.0 N A:GLU1513 3.4 24.5 1.0 C A:LEU1511 3.5 20.9 1.0 CA A:LEU1511 3.6 19.8 1.0 CB A:GLU1513 3.6 27.4 1.0 N A:PRO1512 3.7 24.8 1.0 CD A:PRO1512 3.7 24.4 1.0 CG A:GLU1513 3.8 32.9 1.0 CD1 A:LEU1511 3.9 20.0 1.0 O A:LEU1511 4.0 20.0 1.0 CA A:GLU1513 4.1 24.0 1.0 CB A:LEU1511 4.3 18.8 1.0 CB A:TRP1402 4.3 22.9 0.5 CD2 A:TYR1514 4.4 19.4 1.0 CG A:PRO1512 4.4 26.7 1.0 C A:PRO1512 4.4 24.4 1.0 OE2 A:GLU1513 4.5 38.1 1.0 N A:TYR1514 4.6 19.3 1.0 CA A:PRO1512 4.6 25.7 1.0 O A:HOH2073 4.6 31.7 1.0 CD A:GLU1513 4.6 41.1 1.0 CG A:LEU1511 4.7 20.0 1.0 CE2 A:TYR1514 4.7 20.1 1.0 N A:LEU1511 4.8 18.7 1.0 C A:GLU1513 4.8 22.7 1.0 CD1 A:TRP1402 4.9 23.9 0.5 CG A:TRP1402 5.0 23.4 0.5

Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM000707A


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 FM000707A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:41.0 occ:1.00 O A:HOH2042 3.2 52.0 1.0 NH1 A:ARG1501 3.3 32.2 1.0 N A:THR1500 3.3 30.1 1.0 C A:MET1498 3.3 37.7 1.0 CA A:MET1498 3.3 33.3 1.0 CD A:ARG1501 3.6 34.4 1.0 CB A:THR1500 3.6 37.1 1.0 N A:ARG1501 3.6 31.9 1.0 O A:MET1498 3.6 35.8 1.0 N A:PRO1499 3.7 39.3 1.0 CB A:MET1498 3.7 37.1 1.0 CA A:THR1500 3.9 32.4 1.0 CD A:PRO1499 3.9 40.3 1.0 OG1 A:THR1500 4.0 36.9 1.0 O A:HOH2222 4.0 48.2 1.0 C A:THR1500 4.2 34.4 1.0 C A:PRO1499 4.3 32.6 1.0 CZ A:ARG1501 4.3 32.3 1.0 NE A:ARG1501 4.4 33.5 1.0 CB A:ARG1501 4.4 30.6 1.0 CA A:PRO1499 4.5 35.1 1.0 CG A:ARG1501 4.6 34.8 1.0 CA A:ARG1501 4.6 30.1 1.0 CG A:PRO1499 4.7 39.5 1.0 N A:MET1498 4.7 31.4 1.0 CG A:MET1498 4.7 38.2 1.0 O A:MET1497 4.7 29.8 1.0 CG2 A:THR1500 4.8 38.0 1.0

Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM000707A


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 FM000707A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:37.0 occ:1.00 N A:ASN1558 3.2 22.1 1.0 O A:HOH2182 3.5 46.5 1.0 OE1 A:GLN1650 3.6 39.9 1.0 NZ A:LYS1484 3.6 37.9 1.0 CA A:THR1557 3.8 23.3 1.0 O A:HOH2085 3.8 51.6 1.0 CB A:ASN1558 3.9 25.4 1.0 C A:THR1557 4.0 23.8 1.0 CG A:GLN1650 4.1 33.1 1.0 CG2 A:THR1557 4.1 25.7 1.0 CA A:ASN1558 4.1 24.8 1.0 CG A:ASN1558 4.2 28.5 1.0 CD A:GLN1650 4.3 35.8 1.0 O A:THR1556 4.3 23.0 1.0 O A:HOH2268 4.4 58.9 1.0 ND2 A:ASN1558 4.4 28.1 1.0 CB A:THR1557 4.4 25.9 1.0 O A:GLN1650 4.5 30.1 1.0 O A:HOH2171 4.7 40.5 1.0 OG1 A:THR1557 4.7 26.8 1.0 N A:THR1557 4.8 23.2 1.0 O A:ASN1558 4.8 20.0 1.0 OD1 A:ASN1558 4.8 24.1 1.0 CE A:LYS1484 4.9 37.1 1.0 C A:ASN1558 5.0 21.4 1.0 C A:THR1556 5.0 25.0 1.0

Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM000707A


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 FM000707A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:50.3 occ:1.00 O A:HOH2232 2.8 34.4 1.0 NE2 A:HIS1712 2.9 22.6 1.0 O A:HOH2058 3.0 18.9 1.0 O A:HOH1942 3.2 45.7 1.0 CD2 A:HIS1709 3.8 25.8 1.0 CD2 A:HIS1712 3.8 25.5 1.0 CE1 A:HIS1712 3.8 25.3 1.0 O A:HOH2183 4.2 58.5 1.0 O A:HOH2174 4.3 20.2 1.0 NE2 A:HIS1709 4.4 25.2 1.0 O A:HOH1985 4.5 19.6 1.0 CG A:HIS1709 4.6 24.1 1.0 CB A:ALA1619 4.7 20.7 1.0 CA A:GLY1412 4.9 24.0 1.0 O A:HOH2209 4.9 36.3 1.0 O A:ALA1685 5.0 17.6 1.0 ND1 A:HIS1712 5.0 23.8 1.0 CG A:HIS1712 5.0 24.7 1.0

Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM000707A


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 FM000707A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1801 b:44.3 occ:1.00 OG1 B:THR1500 2.9 55.5 1.0 C B:MET1498 3.3 40.5 1.0 CA B:MET1498 3.3 40.1 1.0 N B:THR1500 3.3 36.7 1.0 NH1 B:ARG1501 3.4 39.1 1.0 N B:PRO1499 3.5 42.1 1.0 CD B:ARG1501 3.6 41.8 1.0 O B:MET1498 3.7 39.1 1.0 N B:ARG1501 3.7 39.0 1.0 CD B:PRO1499 3.8 44.0 1.0 CB B:THR1500 3.8 43.8 1.0 CB B:MET1498 3.9 42.1 1.0 CA B:THR1500 3.9 40.8 1.0 CG2 B:THR1500 4.2 43.7 1.0 C B:PRO1499 4.2 40.5 1.0 C B:THR1500 4.3 37.6 1.0 CZ B:ARG1501 4.4 40.1 1.0 NE B:ARG1501 4.4 42.8 1.0 CA B:PRO1499 4.4 41.2 1.0 CB B:ARG1501 4.5 37.9 1.0 CG B:PRO1499 4.5 44.8 1.0 CG B:MET1498 4.5 46.6 1.0 O B:MET1497 4.5 36.3 1.0 N B:MET1498 4.6 34.6 1.0 CG B:ARG1501 4.6 40.5 1.0 CA B:ARG1501 4.7 36.5 1.0 OE1 B:GLU1437 4.9 35.4 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.