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Chlorine in PDB 4jk7: Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion

Protein crystallography data

The structure of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jk7 was solved by M.J.Schellenberg, T.Wu, D.B.Ritchie, K.Atta, A.M.Macmillan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.02 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.029, 78.024, 93.805, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 17.7

Other elements in 4jk7:

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

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion (pdb code 4jk7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion, PDB code: 4jk7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4jk7

Go back to Chlorine Binding Sites List in 4jk7
Chlorine binding site 1 out of 5 in the Open and Closed Forms of Wild-Type 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 Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2003

b:24.0
occ:1.00
 O A:HOH2388 3.2 44.0 1.0
N A:TYR1930 3.3 11.7 1.0
O A:HOH2158 3.4 33.3 1.0
N A:SER1929 3.8 11.9 1.0
CB A:TYR1930 3.8 13.9 1.0
CB A:SER1928 3.9 14.5 1.0
CB A:SER1929 3.9 12.7 1.0
CB A:PHE1772 3.9 28.9 0.5
CD2 A:PHE1772 3.9 22.9 0.5
CG A:PHE1772 4.0 24.3 0.5
CB A:PHE1772 4.1 31.2 0.5
CA A:SER1929 4.1 11.5 1.0
CG A:PHE1772 4.1 24.4 0.5
CA A:TYR1930 4.1 11.7 1.0
OG A:SER1928 4.2 15.1 1.0
C A:SER1929 4.2 12.0 1.0
CD2 A:PHE1772 4.3 21.9 0.5
C A:SER1928 4.5 11.7 1.0
O A:HOH2352 4.6 33.2 1.0
CE2 A:PHE1772 4.7 22.5 0.5
OG A:SER1929 4.7 15.2 1.0
CA A:SER1928 4.7 13.4 1.0
CD1 A:PHE1772 4.8 20.4 0.5
CD1 A:PHE1772 4.8 22.5 0.5
CE2 A:PHE1772 5.0 20.4 0.5

Chlorine binding site 2 out of 5 in 4jk7

Go back to Chlorine Binding Sites List in 4jk7
Chlorine binding site 2 out of 5 in the Open and Closed Forms of Wild-Type 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 Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2004

b:27.9
occ:1.00
 O A:HOH2263 2.9 32.2 1.0
O A:HOH2276 3.0 26.4 1.0
NE A:ARG1941 3.2 12.8 1.0
CG A:ARG1941 3.6 12.6 1.0
CB A:ARG1941 3.7 13.4 1.0
CD2 A:HIS1944 3.9 19.6 1.0
CD A:ARG1941 4.0 12.4 1.0
NH2 A:ARG1941 4.0 15.7 1.0
CA A:ARG1941 4.1 12.7 1.0
CZ A:ARG1941 4.1 14.1 1.0
CG A:PRO1892 4.1 13.5 1.0
CB A:GLN1890 4.3 16.5 1.0
CG1 A:VAL1945 4.3 22.4 0.5
O A:ARG1941 4.4 14.9 1.0
CG2 A:VAL1945 4.5 21.4 0.5
CD A:PRO1892 4.5 13.7 1.0
CG A:HIS1944 4.7 17.3 1.0
C A:ARG1941 4.7 13.6 1.0
OE1 A:GLN1890 4.7 26.7 1.0
CB A:HIS1944 4.8 16.0 1.0
CG A:GLN1890 4.8 19.8 1.0
CB A:PRO1892 4.8 13.5 1.0
NE2 A:HIS1944 4.9 26.2 1.0

Chlorine binding site 3 out of 5 in 4jk7

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Chlorine binding site 3 out of 5 in the Open and Closed Forms of Wild-Type 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 Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2005

b:23.2
occ:1.00
 O A:HOH2337 3.2 19.6 1.0
N A:GLY1867 3.3 14.3 1.0
CA A:GLY1867 3.7 14.8 1.0
CB A:ARG1865 3.7 15.4 1.0
NZ A:LYS1838 3.9 21.2 1.0
O A:HOH2487 3.9 48.9 1.0
N A:LYS1866 4.1 14.7 1.0
NE A:ARG1865 4.2 16.9 1.0
CD A:ARG1865 4.3 17.1 1.0
C A:ARG1865 4.3 14.3 1.0
CZ A:ARG1865 4.4 17.9 1.0
O A:HOH2177 4.4 29.8 1.0
C A:LYS1866 4.5 15.0 1.0
CA A:ARG1865 4.5 13.5 1.0
CG A:ARG1865 4.6 16.2 1.0
CE A:LYS1838 4.6 21.1 1.0
NH2 A:ARG1865 4.6 21.3 1.0
CA A:LYS1866 4.8 17.1 1.0
C A:GLY1867 4.8 14.2 1.0
NH1 A:ARG1865 4.9 17.9 1.0
O A:ARG1865 4.9 14.3 1.0

Chlorine binding site 4 out of 5 in 4jk7

Go back to Chlorine Binding Sites List in 4jk7
Chlorine binding site 4 out of 5 in the Open and Closed Forms of Wild-Type 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 Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2003

b:21.7
occ:1.00
 OG1 B:THR1824 3.0 17.9 1.0
O B:HOH2221 3.1 24.7 1.0
N B:ALA1837 3.2 18.9 1.0
CA B:LEU1836 3.6 19.7 1.0
CG B:GLN1830 3.7 15.7 1.0
CB B:THR1824 3.7 16.3 1.0
CD B:GLN1830 3.8 15.4 1.0
CE B:LYS1840 3.8 27.9 1.0
CD B:LYS1840 3.9 30.6 1.0
CA B:TRP1827 3.9 13.1 1.0
NE2 B:GLN1830 3.9 17.5 1.0
CG2 B:THR1824 3.9 16.2 1.0
C B:LEU1836 3.9 20.8 1.0
CB B:ALA1837 4.0 21.4 1.0
N B:TRP1827 4.0 12.7 1.0
CD2 B:LEU1836 4.1 16.2 1.0
CG2 B:VAL1826 4.1 15.9 1.0
CA B:ALA1837 4.1 19.5 1.0
O B:GLN1835 4.2 28.8 1.0
C B:VAL1826 4.3 12.8 1.0
CB B:TRP1827 4.3 13.9 1.0
CB B:LEU1836 4.3 19.6 1.0
OE1 B:GLN1830 4.3 17.2 1.0
O B:VAL1826 4.5 13.6 1.0
N B:LEU1836 4.7 20.4 1.0
C B:GLN1835 4.9 20.5 1.0
CG B:LEU1836 4.9 18.8 1.0

Chlorine binding site 5 out of 5 in 4jk7

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Chlorine binding site 5 out of 5 in the Open and Closed Forms of Wild-Type 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 5 of Open and Closed Forms of Wild-Type Human PRP8 Rnase H-Like Domain with Bound Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2004

b:23.1
occ:1.00
 N B:THR1789 3.2 15.5 1.0
O B:HOH2137 3.2 23.7 1.0
O B:HOH2150 3.6 26.3 1.0
CA B:VAL1788 3.7 16.3 0.3
CA B:VAL1788 3.7 16.3 0.7
C B:VAL1788 3.9 16.4 1.0
CB B:THR1789 3.9 19.6 1.0
OG1 B:THR1789 4.0 24.7 1.0
CG1 B:VAL1788 4.0 19.8 0.7
CA B:THR1789 4.2 17.2 1.0
CB B:VAL1788 4.2 19.6 0.3
CB B:VAL1788 4.3 19.8 0.7
CG2 B:VAL1788 4.6 20.8 0.7
CG1 B:VAL1788 4.6 21.6 0.3
O B:ARG1787 4.6 16.4 1.0
N B:VAL1788 4.8 15.3 1.0
O B:THR1789 4.8 17.6 1.0
O B:HOH2383 4.9 41.4 1.0
O B:HOH2357 5.0 44.9 1.0

Reference:

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
Page generated: Sun Jul 21 17:29:49 2024

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