Chlorine in PDB 4jka: Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion

The structure of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion, PDB code: 4jka 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)	36.13 / 1.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.249, 78.223, 94.373, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 16.6

The structure of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion also contains other interesting chemical elements:

Cobalt

(Co)

8 atoms

The binding sites of Chlorine atom in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion (pdb code 4jka). 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion, PDB code: 4jka:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2004 b:27.9 occ:1.00 O A:HOH2313 3.2 48.6 1.0 N A:TYR1930 3.3 12.6 1.0 O A:HOH2177 3.4 31.6 1.0 N A:SER1929 3.8 12.6 1.0 CB A:TYR1930 3.8 15.3 1.0 CB A:SER1928 3.8 15.1 1.0 CB A:SER1929 3.9 14.3 1.0 CB A:PHE1772 4.0 34.1 1.0 CA A:SER1929 4.1 12.9 1.0 OG A:SER1928 4.1 15.7 1.0 CA A:TYR1930 4.1 12.8 1.0 CG A:PHE1772 4.1 26.4 1.0 C A:SER1929 4.2 11.8 1.0 O A:HOH2125 4.2 21.3 0.5 CD2 A:PHE1772 4.5 26.5 1.0 C A:SER1928 4.5 12.1 1.0 CD1 A:PHE1772 4.7 27.0 1.0 CA A:SER1928 4.7 13.7 1.0 OG A:SER1929 4.7 17.1 1.0

Chlorine binding site 2 out of 4 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2004 b:20.2 occ:1.00 OG1 B:THR1824 3.1 17.9 1.0 O B:HOH2158 3.1 24.7 1.0 N B:ALA1837 3.3 18.1 1.0 CG B:GLN1830 3.7 16.2 1.0 CD B:GLN1830 3.7 17.0 1.0 CA B:TRP1827 3.8 15.3 1.0 CB B:ALA1837 3.8 20.5 1.0 NE2 B:GLN1830 3.8 19.9 1.0 CB B:THR1824 3.8 16.0 1.0 CD1 B:LEU1836 3.8 21.3 1.0 CG2 B:THR1824 3.9 16.6 1.0 N B:TRP1827 3.9 14.4 1.0 CA B:LEU1836 4.0 16.9 1.0 CA B:ALA1837 4.1 19.1 1.0 C B:LEU1836 4.1 17.0 1.0 CG2 B:VAL1826 4.1 17.8 1.0 CB B:TRP1827 4.2 16.8 1.0 CE B:LYS1840 4.2 28.6 1.0 CD B:LYS1840 4.2 27.3 1.0 C B:VAL1826 4.2 14.6 1.0 OE1 B:GLN1830 4.3 19.1 1.0 CG B:LEU1836 4.4 19.4 1.0 O B:VAL1826 4.4 16.2 1.0 O B:GLN1835 4.6 23.4 1.0 CB B:LEU1836 4.8 17.9 1.0

Chlorine binding site 3 out of 4 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2005 b:27.9 occ:1.00 NZ B:LYS1840 3.1 30.8 1.0 N B:SER1825 3.1 14.8 1.0 O B:HOH2322 3.2 44.1 1.0 CB B:SER1825 3.7 17.5 1.0 CE B:LYS1840 3.8 28.6 1.0 CA B:SER1825 3.9 15.7 1.0 CA B:THR1824 4.0 14.7 1.0 C B:THR1824 4.1 15.2 1.0 CG2 B:VAL1826 4.1 17.8 1.0 O B:HOH2166 4.2 37.4 1.0 OG B:SER1825 4.2 20.7 1.0 N B:VAL1826 4.2 15.0 1.0 CG1 B:VAL1826 4.2 19.9 1.0 OG1 B:THR1824 4.3 17.9 1.0 C B:SER1825 4.4 15.4 1.0 O B:HIS1823 4.6 17.1 1.0 O B:HOH2293 4.7 41.8 1.0 CB B:VAL1826 4.7 17.7 1.0 CB B:THR1824 4.7 16.0 1.0

Chlorine binding site 4 out of 4 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co 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 R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2006 b:30.3 occ:1.00 O B:HOH2428 3.0 41.1 1.0 ND1 B:HIS1944 3.1 25.8 1.0 NZ B:LYS1898 3.3 29.9 1.0 CA B:ALA1895 3.6 18.1 1.0 CA B:HIS1944 3.7 18.4 1.0 CE B:LYS1898 3.7 27.3 1.0 CG B:GLN1894 3.8 21.7 1.0 N B:ALA1895 3.8 18.4 1.0 CB B:ALA1895 3.8 19.0 1.0 CG B:HIS1944 3.9 22.7 1.0 CB B:HIS1944 4.0 18.6 1.0 CD B:LYS1898 4.0 24.7 1.0 CE1 B:HIS1944 4.1 29.2 1.0 C B:GLN1894 4.2 19.9 1.0 O B:GLN1894 4.3 22.9 1.0 O B:HIS1944 4.4 25.5 1.0 N B:HIS1944 4.5 18.2 1.0 C B:HIS1944 4.6 21.0 1.0 CD B:GLN1894 4.7 23.2 1.0 O B:LEU1943 4.7 19.4 1.0 CB B:GLN1894 4.8 22.4 1.0 O B:HOH2348 4.8 42.0 1.0 O B:HOH2187 4.8 42.3 1.0 NE2 B:GLN1894 4.9 26.1 1.0 CG B:LYS1898 4.9 24.3 1.0 C B:ALA1895 5.0 18.6 1.0 C B:LEU1943 5.0 16.5 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