Chlorine in PDB 4jkh: Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion

The structure of Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkh was solved by M.J.Schellenberg, T.Wu, D.B.Ritchie, K.A.Atta, A.M.Macmillan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.29 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.473, 77.739, 94.234, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21.9

The structure of Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine atom in the Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion (pdb code 4jkh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkh:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2001 b:38.9 occ:1.00 O A:HOH2324 3.0 33.4 1.0 NE A:ARG1941 3.2 17.8 1.0 OE1 A:GLN1890 3.3 34.9 0.5 CG A:GLN1890 3.6 34.9 0.5 CD2 A:HIS1944 3.6 41.5 1.0 CG A:ARG1941 3.6 19.4 1.0 CB A:ARG1941 3.8 20.8 1.0 CD A:ARG1941 4.0 18.3 1.0 CG1 A:VAL1945 4.0 38.8 1.0 NH2 A:ARG1941 4.0 21.6 1.0 CZ A:ARG1941 4.1 19.0 1.0 CA A:ARG1941 4.1 20.8 1.0 CD A:GLN1890 4.2 37.5 0.5 CG A:PRO1892 4.2 31.1 1.0 CB A:GLN1890 4.3 30.1 0.5 O A:ARG1941 4.3 24.0 1.0 CB A:GLN1890 4.3 30.9 0.5 CG A:HIS1944 4.4 37.6 1.0 CG A:GLN1890 4.4 34.5 0.5 CB A:HIS1944 4.5 33.0 1.0 CD A:PRO1892 4.5 30.3 1.0 NE2 A:HIS1944 4.6 42.0 1.0 C A:ARG1941 4.7 21.4 1.0 CD A:GLN1890 4.8 36.1 0.5 NE2 A:GLN1890 4.9 39.5 0.5

Chlorine binding site 2 out of 4 in the Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2002 b:36.3 occ:1.00 O A:HOH2331 3.2 29.7 1.0 N A:GLY1867 3.2 21.9 1.0 CA A:GLY1867 3.7 21.8 1.0 CB A:ARG1865 3.7 25.6 1.0 N A:LYS1866 4.0 20.6 1.0 NZ A:LYS1838 4.0 28.3 1.0 C A:ARG1865 4.1 22.1 1.0 NE A:ARG1865 4.1 25.6 1.0 CD A:ARG1865 4.1 28.1 1.0 CA A:ARG1865 4.2 23.6 1.0 CZ A:ARG1865 4.2 28.3 1.0 O A:HOH2173 4.2 33.8 1.0 NH2 A:ARG1865 4.3 28.6 1.0 C A:LYS1866 4.4 23.5 1.0 CG A:ARG1865 4.6 27.6 1.0 CA A:LYS1866 4.6 25.2 1.0 O A:ARG1865 4.7 22.5 1.0 NH1 A:ARG1865 4.8 27.8 1.0 C A:GLY1867 4.8 21.1 1.0 CE A:LYS1838 4.8 29.9 1.0

Chlorine binding site 3 out of 4 in the Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2003 b:42.2 occ:1.00 O B:HOH2282 2.8 43.3 1.0 O B:HOH2230 2.9 34.5 1.0 N B:LYS1838 3.2 27.6 1.0 NE2 B:GLN1830 3.2 21.7 0.6 CE B:LYS1838 3.3 51.6 1.0 CG B:LYS1838 3.5 42.6 1.0 CA B:ALA1837 3.8 25.0 1.0 OE1 B:GLN1830 3.9 23.2 0.6 C B:ALA1837 3.9 25.6 1.0 CD B:LYS1838 4.0 46.5 1.0 CB B:LYS1838 4.0 37.2 1.0 CD B:GLN1830 4.0 21.8 0.6 OE1 B:GLN1830 4.1 24.6 0.4 CA B:LYS1838 4.1 29.1 1.0 CB B:ALA1837 4.3 25.1 1.0 NH2 B:ARG1865 4.4 28.9 0.4 NH2 B:ARG1865 4.5 29.3 0.6 NZ B:LYS1838 4.6 59.5 1.0 N B:TRP1839 4.8 30.9 1.0 O B:LEU1836 4.9 23.6 1.0 CD1 B:TRP1839 4.9 46.4 1.0 N B:ALA1837 5.0 24.3 1.0

Chlorine binding site 4 out of 4 in the Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Open and Closed Forms of D1781E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2004 b:29.0 occ:1.00 N B:THR1789 3.1 23.9 1.0 O B:HOH2137 3.1 27.4 1.0 O B:HOH2151 3.5 26.2 1.0 CA B:VAL1788 3.7 24.0 1.0 OG1 B:THR1789 3.8 32.0 1.0 CB B:THR1789 3.8 30.0 1.0 CG1 B:VAL1788 3.8 32.1 1.0 C B:VAL1788 3.9 23.9 1.0 CA B:THR1789 4.0 27.6 1.0 CB B:VAL1788 4.3 26.7 1.0 O B:ARG1787 4.6 20.9 1.0 CG2 B:VAL1788 4.7 26.7 1.0 O B:THR1789 4.7 27.1 1.0 O B:HOH2289 4.8 43.3 1.0 N B:VAL1788 4.9 21.9 1.0 C B:THR1789 4.9 28.5 1.0

M.J.Schellenberg, T.Wu, D.B.Ritchie, S.Fica, J.P.Staley, K.A.Atta, P.Lapointe, A.M.Macmillan. A Conformational Switch in PRP8 Mediates Metal Ion Coordination That Promotes Pre-Mrna Exon Ligation. Nat.Struct.Mol.Biol. V. 20 728 2013.
ISSN: ISSN 1545-9993
PubMed: 23686287
DOI: 10.1038/NSMB.2556