Chlorine in PDB 4jkc: Open and Closed Forms of T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion

The structure of Open and Closed Forms of T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkc 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)	35.29 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.195, 77.932, 93.680, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 16.4

The structure of Open and Closed Forms of T1800E 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 T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion (pdb code 4jkc). 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 T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jkc:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Open and Closed Forms of T1800E 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 T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2001 b:24.9 occ:1.00 O A:HOH2408 3.0 42.7 1.0 O A:HOH2168 3.1 20.5 1.0 N A:GLY1867 3.3 15.4 1.0 O A:HOH2391 3.5 46.9 1.0 CA A:GLY1867 3.7 15.9 1.0 CB A:ARG1865 3.7 16.5 1.0 NZ A:LYS1838 3.8 22.4 1.0 N A:LYS1866 4.1 16.3 1.0 NE A:ARG1865 4.2 16.6 1.0 CD A:ARG1865 4.3 17.6 1.0 C A:ARG1865 4.3 15.2 1.0 CZ A:ARG1865 4.4 17.6 1.0 O A:HOH2147 4.4 31.3 1.0 C A:LYS1866 4.4 14.5 1.0 CA A:ARG1865 4.5 14.7 1.0 CG A:ARG1865 4.6 16.8 1.0 CE A:LYS1838 4.6 22.4 1.0 NH2 A:ARG1865 4.6 22.4 1.0 CA A:LYS1866 4.8 18.1 1.0 C A:GLY1867 4.8 14.5 1.0 NH1 A:ARG1865 4.9 17.0 1.0 O A:ARG1865 4.9 14.6 1.0

Chlorine binding site 2 out of 4 in the Open and Closed Forms of T1800E 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 T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2002 b:18.4 occ:0.55 NZ A:LYS1820 2.0 22.3 0.5 O A:HOH2418 2.2 26.2 0.4 CE A:LYS1820 2.7 20.3 0.5 CD A:LYS1820 2.7 20.1 0.5 O A:HOH2206 3.0 32.8 1.0 O A:HOH2201 3.1 23.2 0.5 O A:HOH2417 3.2 18.6 0.5 O B:HOH2117 3.2 16.8 1.0 C A:GLN1913 3.5 12.8 1.0 N A:MET1914 3.5 11.9 1.0 CB A:MET1914 3.7 14.3 0.5 CB A:MET1914 3.8 13.9 0.5 O A:GLN1913 3.8 13.7 1.0 CA A:GLN1913 3.8 12.0 1.0 CA A:MET1914 4.1 11.9 0.5 N A:GLN1913 4.1 13.6 1.0 CA A:MET1914 4.1 12.3 0.5 CG A:LYS1820 4.2 17.6 0.5 CG A:LYS1820 4.3 14.1 0.5 O A:HOH2335 4.4 41.3 1.0 CE A:LYS1820 4.4 19.5 0.5 CD A:LYS1820 4.5 17.7 0.5 O B:HOH2104 4.5 13.3 1.0 OE1 A:GLU1844 4.5 19.9 1.0 NZ A:LYS1820 4.6 15.0 0.5 O B:HOH2196 4.6 31.8 1.0 O A:HOH2179 4.6 23.9 1.0 O A:HOH2219 4.7 25.6 0.5 C A:PRO1912 4.7 14.8 1.0 CB A:LYS1820 4.8 12.5 0.5 O A:HOH2366 4.9 43.1 1.0 CG A:MET1914 4.9 13.3 0.5 CG A:MET1914 4.9 16.1 0.5 SD A:MET1914 5.0 20.9 0.5 CB A:PRO1912 5.0 18.1 1.0 CB A:LYS1820 5.0 14.1 0.5

Chlorine binding site 3 out of 4 in the Open and Closed Forms of T1800E 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 T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2003 b:36.9 occ:1.00 O B:HOH2110 2.7 15.6 1.0 OE1 B:GLU1855 2.7 27.5 1.0 O A:HOH2316 2.8 42.5 1.0 CD B:GLU1855 3.4 31.2 1.0 CG B:GLU1855 3.6 24.3 1.0 CA A:THR1814 3.6 10.8 1.0 CG2 A:THR1814 3.6 13.7 1.0 CD1 A:LEU1924 3.8 13.9 1.0 CB A:THR1814 3.9 11.9 1.0 NH1 A:ARG1813 3.9 24.8 1.0 O A:ARG1813 4.0 13.7 1.0 O B:HOH2316 4.1 50.6 1.0 O A:HOH2312 4.1 37.9 1.0 CB B:GLU1855 4.1 23.0 1.0 O B:HOH2131 4.2 29.3 1.0 N A:THR1814 4.4 10.2 1.0 C A:ARG1813 4.5 11.0 1.0 OE2 B:GLU1855 4.5 41.6 1.0 O A:THR1814 4.5 11.7 1.0 CZ A:ARG1813 4.6 22.9 1.0 C A:THR1814 4.6 9.8 1.0 O A:HOH2264 4.8 42.8 1.0 CB B:PRO1853 4.9 14.7 1.0 NH2 A:ARG1813 4.9 27.5 1.0 N B:GLU1855 5.0 14.8 1.0 O B:HOH2109 5.0 13.6 1.0

Chlorine binding site 4 out of 4 in the Open and Closed Forms of T1800E 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 T1800E Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2004 b:34.4 occ:1.00 O B:HOH2291 2.3 44.5 1.0 N B:SER1825 3.0 16.9 1.0 O B:HOH2229 3.4 46.0 1.0 O B:HOH2206 3.4 45.5 1.0 CB B:SER1825 3.7 18.7 1.0 CA B:SER1825 3.9 14.9 1.0 CA B:THR1824 3.9 15.4 1.0 C B:THR1824 3.9 14.6 1.0 OG B:SER1825 4.1 21.2 1.0 CG2 B:VAL1826 4.2 17.2 1.0 OG1 B:THR1824 4.2 19.7 1.0 N B:VAL1826 4.2 15.1 1.0 CG1 B:VAL1826 4.4 20.2 1.0 C B:SER1825 4.5 14.3 1.0 CH2 B:TRP1839 4.5 46.7 1.0 O B:HIS1823 4.5 16.5 1.0 CB B:THR1824 4.6 18.0 1.0 CB B:VAL1826 4.8 17.0 1.0 CZ2 B:TRP1839 4.9 41.6 1.0 N B:THR1824 4.9 14.1 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