Chlorine in PDB 5raa: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM009990A

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM009990A, PDB code: 5raa 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)	89.00 / 1.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.290, 93.610, 93.420, 90.00, 107.69, 90.00
R / Rfree (%)	18.3 / 21

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM009990A 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 FM009990A (pdb code 5raa). 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 FM009990A, PDB code: 5raa:
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 FM009990A


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 FM009990A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1801 b:42.4 occ:0.64 CL10 A:S3Y1801 0.0 42.4 0.6 C09 A:S3Y1801 1.8 39.1 0.6 C11 A:S3Y1801 2.7 35.1 0.6 C08 A:S3Y1801 2.7 36.8 0.6 OD1 A:ASN1398 3.4 25.0 1.0 CG A:ASN1398 3.5 26.5 1.0 OD1 A:ASN1401 3.7 19.3 1.0 CB A:SER1381 3.9 20.4 0.6 CB A:ASN1398 3.9 22.9 1.0 CB A:ASN1400 3.9 22.9 1.0 C12 A:S3Y1801 4.0 41.5 0.6 CD1 A:ILE1404 4.0 22.9 1.0 C07 A:S3Y1801 4.0 39.3 0.6 ND2 A:ASN1398 4.0 23.9 1.0 C A:ASN1400 4.2 20.1 1.0 N A:ASN1401 4.3 19.0 1.0 O A:HOH2023 4.3 13.2 0.6 O A:ASN1400 4.5 21.1 1.0 C06 A:S3Y1801 4.5 41.3 0.6 CA A:ASN1400 4.6 21.4 1.0 CA A:SER1381 4.6 19.6 0.6 CA A:ASN1401 4.6 19.9 1.0 CG A:ASN1401 4.7 21.6 1.0 N A:ASN1400 5.0 21.2 1.0 OG A:SER1381 5.0 19.5 0.6 ND2 A:ASN1400 5.0 29.2 1.0 CG A:ASN1400 5.0 26.2 1.0

Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM009990A


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 FM009990A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1802 b:23.8 occ:1.00 O A:HOH2132 3.2 21.9 1.0 O A:HOH2250 3.2 39.2 1.0 O A:HOH2014 3.3 22.4 1.0 N A:GLU1513 3.4 20.9 1.0 O A:HOH2189 3.5 43.8 1.0 CB A:GLU1513 3.6 24.3 1.0 CA A:LEU1511 3.6 17.0 1.0 C A:LEU1511 3.6 19.1 1.0 CD A:PRO1512 3.7 21.3 1.0 N A:PRO1512 3.7 20.9 1.0 CG A:GLU1513 3.9 28.8 1.0 CD1 A:LEU1511 3.9 17.9 1.0 CA A:GLU1513 4.1 21.4 1.0 O A:LEU1511 4.1 17.6 1.0 CB A:LEU1511 4.3 16.6 1.0 CB A:TRP1402 4.3 18.8 1.0 CG A:PRO1512 4.4 25.2 1.0 CD2 A:TYR1514 4.4 16.8 1.0 C A:PRO1512 4.5 21.2 1.0 OE2 A:GLU1513 4.5 39.2 1.0 O A:HOH2032 4.6 28.3 1.0 N A:TYR1514 4.6 19.0 1.0 CA A:PRO1512 4.6 21.2 1.0 CD A:GLU1513 4.7 40.1 1.0 CG A:LEU1511 4.8 18.9 1.0 CE2 A:TYR1514 4.8 18.4 1.0 N A:LEU1511 4.8 16.1 1.0 C A:GLU1513 4.8 20.1 1.0 CD1 A:TRP1402 5.0 20.6 1.0 CG A:TRP1402 5.0 19.8 1.0

Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM009990A


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 FM009990A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1803 b:34.6 occ:1.00 O A:HOH2104 3.2 38.3 1.0 NH1 A:ARG1501 3.3 33.0 1.0 CA A:MET1498 3.3 27.6 1.0 N A:THR1500 3.4 25.2 1.0 C A:MET1498 3.4 29.8 1.0 N A:ARG1501 3.6 25.5 1.0 N A:PRO1499 3.7 30.8 1.0 CB A:THR1500 3.7 35.7 1.0 CB A:MET1498 3.7 28.3 1.0 O A:MET1498 3.8 28.2 1.0 CD A:ARG1501 3.8 32.1 1.0 O A:HOH2222 3.8 41.4 1.0 CA A:THR1500 3.9 27.2 1.0 CD A:PRO1499 4.0 31.4 1.0 OG1 A:THR1500 4.1 35.8 1.0 CG A:ARG1501 4.2 29.8 1.0 C A:THR1500 4.2 27.0 1.0 CZ A:ARG1501 4.3 34.3 1.0 CB A:ARG1501 4.3 23.9 1.0 C A:PRO1499 4.3 26.1 1.0 NE A:ARG1501 4.5 30.4 1.0 CA A:PRO1499 4.5 27.6 1.0 CA A:ARG1501 4.6 25.5 1.0 CG A:MET1498 4.7 29.4 1.0 N A:MET1498 4.7 24.9 1.0 O A:MET1497 4.7 28.9 1.0 CG A:PRO1499 4.8 32.0 1.0

Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM009990A


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 FM009990A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1804 b:30.6 occ:1.00 N A:ASN1558 3.3 19.4 1.0 OE1 A:GLN1650 3.4 34.5 1.0 NZ A:LYS1484 3.7 29.6 1.0 O A:HOH2198 3.7 30.3 1.0 CA A:THR1557 3.8 19.4 1.0 CG A:GLN1650 4.0 27.8 1.0 CB A:ASN1558 4.0 19.7 1.0 C A:THR1557 4.0 20.9 1.0 CD A:GLN1650 4.1 29.7 1.0 O A:HOH2057 4.1 48.2 1.0 CG2 A:THR1557 4.1 22.6 1.0 CA A:ASN1558 4.2 18.9 1.0 O A:THR1556 4.3 20.1 1.0 CG A:ASN1558 4.4 22.1 1.0 CB A:THR1557 4.4 22.4 1.0 O A:GLN1650 4.5 25.4 1.0 ND2 A:ASN1558 4.5 23.3 1.0 O A:HOH2261 4.7 42.3 1.0 OG1 A:THR1557 4.8 22.4 1.0 O A:HOH2167 4.8 34.5 1.0 O A:ASN1558 4.9 18.8 1.0 N A:THR1557 4.9 19.7 1.0 CE A:LYS1484 4.9 33.6 1.0 OD1 A:ASN1558 4.9 21.2 1.0

Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM009990A


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 FM009990A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1805 b:53.2 occ:1.00 NE2 A:HIS1712 2.8 24.7 1.0 O A:HOH2225 3.0 30.1 1.0 O A:HOH2058 3.1 19.2 1.0 O A:HOH1952 3.2 36.9 1.0 CD2 A:HIS1712 3.7 26.1 1.0 O A:HOH2188 3.8 57.4 1.0 CE1 A:HIS1712 3.8 25.4 1.0 CD2 A:HIS1709 3.9 20.7 1.0 O A:HOH2169 4.5 18.2 1.0 NE2 A:HIS1709 4.6 22.5 1.0 CG A:HIS1709 4.6 18.6 1.0 O A:HOH2016 4.7 17.1 1.0 CB A:ALA1619 4.8 18.3 1.0 O A:HOH2212 4.8 34.6 1.0 O A:GLU1708 4.9 20.8 1.0 CG A:HIS1712 4.9 22.5 1.0 ND1 A:HIS1712 4.9 27.0 1.0 CB A:HIS1709 4.9 20.3 1.0 O A:ALA1685 5.0 17.1 1.0

Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM009990A


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 FM009990A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1801 b:41.5 occ:1.00 OG1 B:THR1500 2.8 52.8 1.0 NH1 B:ARG1501 3.2 39.3 1.0 C B:MET1498 3.3 36.5 1.0 CA B:MET1498 3.4 35.0 1.0 N B:THR1500 3.4 33.7 1.0 CD B:ARG1501 3.5 39.8 1.0 N B:PRO1499 3.6 35.5 1.0 N B:ARG1501 3.6 35.7 1.0 O B:MET1498 3.7 31.7 1.0 CB B:THR1500 3.8 42.3 1.0 CD B:PRO1499 3.9 41.3 1.0 CB B:MET1498 3.9 36.8 1.0 CA B:THR1500 3.9 36.3 1.0 CZ B:ARG1501 4.2 35.7 1.0 CG2 B:THR1500 4.2 39.8 1.0 C B:THR1500 4.3 35.5 1.0 C B:PRO1499 4.3 35.4 1.0 NE B:ARG1501 4.3 41.7 1.0 CA B:PRO1499 4.5 37.2 1.0 CB B:ARG1501 4.5 33.1 1.0 CG B:ARG1501 4.5 37.9 1.0 CG B:MET1498 4.5 39.7 1.0 CG B:PRO1499 4.6 45.1 1.0 CA B:ARG1501 4.7 32.6 1.0 N B:MET1498 4.7 35.1 1.0 O B:MET1497 4.7 36.6 1.0 OE1 B:GLU1437 5.0 32.5 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.