Atomistry » Chlorine » PDB 4jk9-4jtg » 4jkh
Atomistry »
  Chlorine »
    PDB 4jk9-4jtg »
      4jkh »

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

Protein crystallography data

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

Other elements in 4jkh:

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

Chlorine Binding Sites:

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 4jkh

Go back to Chlorine Binding Sites List in 4jkh
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 4jkh

Go back to Chlorine Binding Sites List in 4jkh
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 4jkh

Go back to Chlorine Binding Sites List in 4jkh
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 4jkh

Go back to Chlorine Binding Sites List in 4jkh
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

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: Sat Dec 12 10:48:25 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy