Chlorine in PDB 5rai: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C, PDB code: 5rai 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)	89.01 / 1.54
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.520, 93.540, 93.681, 90.00, 108.17, 90.00
R / Rfree (%)	19.1 / 21.8

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C 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 XS040404C (pdb code 5rai). 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 XS040404C, PDB code: 5rai:
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 XS040404C


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 XS040404C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:24.5 occ:1.00 O A:HOH2146 3.2 23.4 1.0 O A:HOH2064 3.3 22.4 1.0 N A:GLU1513 3.4 19.0 1.0 C A:LEU1511 3.5 18.6 1.0 CA A:LEU1511 3.6 17.7 1.0 CB A:GLU1513 3.6 22.6 1.0 N A:PRO1512 3.7 19.1 1.0 CD A:PRO1512 3.8 20.9 1.0 CD1 A:LEU1511 3.9 18.7 1.0 CG A:GLU1513 3.9 29.3 1.0 O A:LEU1511 4.0 17.0 1.0 CA A:GLU1513 4.0 19.5 1.0 CB A:LEU1511 4.2 17.2 1.0 CB A:TRP1402 4.3 19.4 1.0 CD2 A:TYR1514 4.4 17.5 1.0 C A:PRO1512 4.4 20.3 1.0 CG A:PRO1512 4.5 22.8 1.0 N A:TYR1514 4.5 18.8 1.0 OE2 A:GLU1513 4.6 38.9 1.0 CA A:PRO1512 4.6 20.4 1.0 O A:HOH2074 4.7 29.8 1.0 CG A:LEU1511 4.7 18.8 1.0 CD A:GLU1513 4.7 41.1 1.0 C A:GLU1513 4.8 18.1 1.0 N A:LEU1511 4.8 17.7 1.0 CE2 A:TYR1514 4.8 17.4 1.0

Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C


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 XS040404C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:34.0 occ:1.00 O A:HOH2043 3.2 40.2 1.0 NH1 A:ARG1501 3.3 31.3 1.0 CA A:MET1498 3.4 24.9 1.0 N A:THR1500 3.4 26.4 1.0 C A:MET1498 3.4 32.0 1.0 N A:ARG1501 3.5 25.8 1.0 CB A:THR1500 3.7 32.9 1.0 N A:PRO1499 3.7 30.3 1.0 O A:HOH2219 3.7 43.1 1.0 O A:MET1498 3.8 27.4 1.0 CB A:MET1498 3.8 28.0 1.0 CA A:THR1500 3.9 29.6 1.0 CD A:ARG1501 3.9 32.9 1.0 CD A:PRO1499 4.1 32.2 1.0 CG A:ARG1501 4.1 29.8 1.0 C A:THR1500 4.2 28.3 1.0 OG1 A:THR1500 4.2 37.5 1.0 CB A:ARG1501 4.2 25.2 1.0 CZ A:ARG1501 4.3 31.6 1.0 C A:PRO1499 4.3 28.7 1.0 CA A:ARG1501 4.5 25.6 1.0 NE A:ARG1501 4.5 32.9 1.0 CA A:PRO1499 4.6 28.2 1.0 CG A:MET1498 4.6 28.8 1.0 N A:MET1498 4.7 26.0 1.0 O A:MET1497 4.7 29.3 1.0 CG A:PRO1499 4.8 34.4 1.0 OE1 A:GLU1437 4.9 26.9 1.0 CG2 A:THR1500 4.9 38.0 1.0

Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C


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 XS040404C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:34.4 occ:1.00 N A:ASN1558 3.2 20.5 1.0 OE1 A:GLN1650 3.4 39.4 1.0 O A:HOH2195 3.6 41.6 1.0 O A:HOH2077 3.6 54.0 1.0 NZ A:LYS1484 3.7 26.7 1.0 CA A:THR1557 3.8 19.7 1.0 CB A:ASN1558 3.9 23.9 1.0 C A:THR1557 4.0 20.8 1.0 CG A:GLN1650 4.0 29.4 1.0 O A:HOH2260 4.1 48.4 1.0 CG2 A:THR1557 4.1 20.0 1.0 CD A:GLN1650 4.1 32.7 1.0 CA A:ASN1558 4.2 20.7 1.0 CG A:ASN1558 4.3 26.3 1.0 O A:THR1556 4.4 23.7 1.0 O A:GLN1650 4.4 29.2 1.0 CB A:THR1557 4.4 19.6 1.0 ND2 A:ASN1558 4.5 30.0 1.0 O A:ASN1558 4.8 19.8 1.0 N A:THR1557 4.8 19.9 1.0 OG1 A:THR1557 4.9 21.4 1.0 OD1 A:ASN1558 4.9 23.9 1.0 C A:ASN1558 5.0 19.2 1.0 O A:HOH1929 5.0 31.9 1.0

Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C


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 XS040404C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:52.1 occ:1.00 NE2 A:HIS1712 2.8 27.5 1.0 O A:HOH2233 2.9 29.9 1.0 O A:HOH2134 3.0 20.9 1.0 O A:HOH1992 3.1 36.3 1.0 CD2 A:HIS1712 3.7 28.5 1.0 CD2 A:HIS1709 3.7 22.4 1.0 CE1 A:HIS1712 3.8 26.7 1.0 O A:HOH2170 4.1 47.8 1.0 NE2 A:HIS1709 4.4 23.0 1.0 O A:HOH2159 4.5 20.5 1.0 CG A:HIS1709 4.5 19.2 1.0 O A:HOH2053 4.7 18.2 1.0 O A:HOH2031 4.7 50.6 1.0 O A:GLU1708 4.8 20.1 1.0 O A:HOH2269 4.9 58.9 1.0 CB A:ALA1619 4.9 18.3 1.0 CG A:HIS1712 4.9 25.0 1.0 ND1 A:HIS1712 4.9 29.9 1.0 CB A:HIS1709 5.0 19.8 1.0

Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS040404C


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 XS040404C within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1801 b:36.2 occ:1.00 OG1 B:THR1500 2.7 51.1 1.0 NH1 B:ARG1501 3.2 34.5 1.0 CA B:MET1498 3.3 32.8 1.0 C B:MET1498 3.4 33.7 1.0 N B:THR1500 3.4 30.2 1.0 N B:ARG1501 3.5 31.4 1.0 N B:PRO1499 3.7 34.2 1.0 CB B:MET1498 3.7 31.4 1.0 CB B:THR1500 3.7 40.1 1.0 O B:MET1498 3.8 32.6 1.0 CG B:ARG1501 3.9 31.1 1.0 CA B:THR1500 3.9 33.7 1.0 CD B:PRO1499 4.0 34.0 1.0 CD B:ARG1501 4.1 33.1 1.0 CG2 B:THR1500 4.1 37.3 1.0 CB B:ARG1501 4.2 28.9 1.0 C B:THR1500 4.2 31.1 1.0 CZ B:ARG1501 4.3 34.4 1.0 C B:PRO1499 4.4 31.2 1.0 CA B:ARG1501 4.5 30.9 1.0 CG B:MET1498 4.5 35.3 1.0 NE B:ARG1501 4.6 35.3 1.0 CA B:PRO1499 4.6 32.9 1.0 N B:MET1498 4.7 33.1 1.0 O B:MET1497 4.7 32.4 1.0 CG B:PRO1499 4.9 35.0 1.0 OE1 B:GLU1437 4.9 31.5 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.