Chlorine in PDB 5ram: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D, PDB code: 5ram 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)	88.35 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.030, 93.500, 92.920, 90.00, 108.05, 90.00
R / Rfree (%)	17.5 / 23.6

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D 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 XS038544D (pdb code 5ram). 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 XS038544D, PDB code: 5ram:
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 XS038544D


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 XS038544D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:28.2 occ:1.00 O A:HOH2165 3.1 26.1 1.0 O A:HOH2088 3.2 23.4 1.0 O A:HOH2260 3.2 49.1 1.0 N A:GLU1513 3.4 24.8 1.0 C A:LEU1511 3.5 23.1 1.0 CA A:LEU1511 3.5 20.8 1.0 CB A:GLU1513 3.6 29.8 1.0 N A:PRO1512 3.6 26.3 1.0 CD A:PRO1512 3.7 27.4 1.0 O A:HOH2063 3.8 47.6 1.0 CD1 A:LEU1511 4.0 21.2 1.0 CG A:GLU1513 4.0 36.7 1.0 CA A:GLU1513 4.0 24.6 1.0 O A:LEU1511 4.0 24.7 1.0 CB A:LEU1511 4.2 20.2 1.0 CG A:PRO1512 4.3 28.9 1.0 CD2 A:TYR1514 4.3 20.1 1.0 CB A:TRP1402 4.4 30.6 1.0 C A:PRO1512 4.4 27.5 1.0 OE2 A:GLU1513 4.4 53.9 1.0 N A:TYR1514 4.5 19.9 1.0 CA A:PRO1512 4.6 26.8 1.0 CD A:GLU1513 4.7 57.6 1.0 CG A:LEU1511 4.7 22.3 1.0 N A:LEU1511 4.7 21.6 1.0 O A:HOH2043 4.7 38.4 1.0 C A:GLU1513 4.8 23.0 1.0 CE2 A:TYR1514 4.8 21.4 1.0

Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D


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 XS038544D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:42.1 occ:1.00 O A:HOH1989 3.2 45.6 1.0 C A:MET1498 3.3 41.1 1.0 NH1 A:ARG1501 3.3 33.8 1.0 CA A:MET1498 3.3 38.1 1.0 N A:THR1500 3.4 29.9 1.0 CD A:ARG1501 3.5 39.8 1.0 N A:ARG1501 3.5 31.4 1.0 CB A:THR1500 3.5 39.0 1.0 O A:MET1498 3.7 39.4 1.0 N A:PRO1499 3.7 40.1 1.0 OG1 A:THR1500 3.8 40.9 1.0 CB A:MET1498 3.8 39.1 1.0 CA A:THR1500 3.8 34.7 1.0 O A:HOH2226 3.9 44.4 1.0 CD A:PRO1499 4.1 41.4 1.0 C A:THR1500 4.1 34.0 1.0 CB A:ARG1501 4.3 34.0 1.0 CZ A:ARG1501 4.3 38.3 1.0 C A:PRO1499 4.3 33.9 1.0 NE A:ARG1501 4.4 38.8 1.0 CA A:ARG1501 4.5 33.2 1.0 CG A:ARG1501 4.5 38.6 1.0 CA A:PRO1499 4.6 34.5 1.0 N A:MET1498 4.7 37.0 1.0 CG A:PRO1499 4.7 41.1 1.0 O A:MET1497 4.8 30.2 1.0 CG A:MET1498 4.8 39.7 1.0 CG2 A:THR1500 4.8 41.3 1.0

Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D


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 XS038544D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:56.2 occ:0.50 ND2 A:ASN1558 3.3 26.4 1.0 O A:GLN1650 3.4 29.8 1.0 N A:ASN1558 3.5 25.1 1.0 CB A:ASN1558 3.5 23.9 1.0 CG A:ASN1558 3.6 28.9 1.0 O A:HOH2136 3.6 38.9 1.0 CG A:GLN1650 3.7 35.0 1.0 OE1 A:GLN1650 3.7 37.4 1.0 O A:HOH2274 3.8 51.8 1.0 CA A:ASN1558 4.1 25.1 1.0 O A:HOH2127 4.1 50.6 1.0 CD A:GLN1650 4.1 35.0 1.0 NZ A:LYS1484 4.3 39.9 1.0 OD1 A:ASN1558 4.4 27.3 1.0 C A:THR1557 4.4 22.1 1.0 CA A:THR1557 4.5 24.0 1.0 CB A:GLN1650 4.5 32.0 1.0 C A:GLN1650 4.5 31.9 1.0 CG2 A:THR1557 4.7 25.4 1.0 O A:ASN1558 4.9 22.2 1.0 C A:ASN1558 4.9 22.4 1.0

Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D


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 XS038544D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:49.7 occ:1.00 O A:HOH2227 2.7 39.0 1.0 NE2 A:HIS1712 2.7 24.4 1.0 O A:HOH2107 3.0 22.3 1.0 O A:HOH1975 3.6 41.2 1.0 CD2 A:HIS1712 3.6 27.4 1.0 CE1 A:HIS1712 3.7 25.4 1.0 CD2 A:HIS1709 4.0 25.9 1.0 O A:HOH2268 4.2 71.4 1.0 O A:HOH2157 4.3 21.9 1.0 CB A:ALA1619 4.4 21.6 1.0 O A:HOH2173 4.5 55.2 1.0 O A:HOH2036 4.5 20.1 1.0 O A:HOH2220 4.5 32.2 1.0 NE2 A:HIS1709 4.6 25.5 1.0 CG A:HIS1709 4.7 26.8 1.0 CG A:HIS1712 4.8 26.6 1.0 ND1 A:HIS1712 4.8 23.6 1.0 O A:ALA1685 4.9 19.7 0.6

Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with XS038544D


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 XS038544D within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1802 b:41.1 occ:1.00 OG1 B:THR1500 2.9 64.2 1.0 CA B:MET1498 3.2 42.4 1.0 C B:MET1498 3.2 42.9 1.0 NH1 B:ARG1501 3.3 39.1 1.0 N B:PRO1499 3.5 43.0 1.0 N B:THR1500 3.5 39.6 1.0 N B:ARG1501 3.6 36.9 1.0 O B:MET1498 3.6 42.6 1.0 CD B:PRO1499 3.7 46.2 1.0 CB B:MET1498 3.7 43.5 1.0 CD B:ARG1501 4.0 38.4 1.0 CB B:THR1500 4.1 43.8 1.0 CA B:THR1500 4.1 41.1 1.0 CG B:ARG1501 4.2 39.7 1.0 CB B:ARG1501 4.3 36.6 1.0 C B:THR1500 4.3 38.5 1.0 C B:PRO1499 4.4 39.7 1.0 CZ B:ARG1501 4.4 40.5 1.0 CG B:MET1498 4.4 44.9 1.0 CA B:PRO1499 4.5 43.4 1.0 N B:MET1498 4.5 40.9 1.0 CG B:PRO1499 4.6 46.7 1.0 O B:MET1497 4.6 40.1 1.0 CA B:ARG1501 4.6 34.6 1.0 NE B:ARG1501 4.6 39.6 1.0 CG2 B:THR1500 4.7 46.1 1.0 OE1 B:GLU1437 4.8 31.6 1.0 C B:MET1497 5.0 36.1 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.