Chlorine in PDB 5oab: A Novel Crystal Form of Human RNASE6 at Atomic Resolution

The structure of A Novel Crystal Form of Human RNASE6 at Atomic Resolution, PDB code: 5oab was solved by G.Prats-Ejarque, M.Moussaoui, E.Boix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.70 / 1.11
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	95.405, 95.405, 95.405, 90.00, 90.00, 90.00
R / Rfree (%)	11.7 / 14.1

The structure of A Novel Crystal Form of Human RNASE6 at Atomic Resolution also contains other interesting chemical elements:

Potassium	(K)	1 atom
Sodium	(Na)	3 atoms

The binding sites of Chlorine atom in the A Novel Crystal Form of Human RNASE6 at Atomic Resolution (pdb code 5oab). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the A Novel Crystal Form of Human RNASE6 at Atomic Resolution, PDB code: 5oab:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the A Novel Crystal Form of Human RNASE6 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of A Novel Crystal Form of Human RNASE6 at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl210 b:45.9 occ:1.00 O A:HOH500 2.8 25.4 1.0 NA A:NA207 2.9 38.3 1.0 O A:HOH439 3.1 13.8 1.0 HD22 A:ASN64 3.2 11.6 1.0 HZ1 A:LYS7 3.2 12.4 1.0 NE2 A:HIS122 3.4 10.3 0.8 HZ2 A:LYS7 3.6 12.4 1.0 NZ A:LYS7 3.8 10.4 1.0 ND2 A:ASN64 3.9 9.6 1.0 HD21 A:ASN64 3.9 11.6 1.0 HE1 A:HIS122 4.0 12.7 0.8 CE1 A:HIS122 4.0 10.6 0.8 O A:HOH484 4.1 12.5 0.7 CD2 A:HIS122 4.3 9.2 0.8 O A:HOH510 4.4 12.1 0.5 HZ3 A:LYS7 4.4 12.4 1.0 HE3 A:LYS7 4.5 10.8 1.0 HD2 A:HIS122 4.6 11.0 0.8 HZ3 A:TRP1 4.7 13.8 0.5 CE A:LYS7 4.8 9.0 1.0 HH11 A:ARG66 5.0 13.8 1.0 HD3 A:ARG66 5.0 12.2 1.0

Chlorine binding site 2 out of 3 in the A Novel Crystal Form of Human RNASE6 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of A Novel Crystal Form of Human RNASE6 at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl211 b:15.3 occ:0.60 HE21 A:GLN14 2.2 14.1 1.0 HA A:PHE11 2.4 7.4 1.0 O2 A:PO4202 2.9 11.0 0.7 HD2 A:HIS15 2.9 10.9 1.0 NE2 A:GLN14 3.0 11.8 1.0 NA A:NA209 3.0 14.4 1.0 HE22 A:GLN14 3.2 14.1 1.0 CA A:PHE11 3.3 6.2 1.0 HD2 A:PHE11 3.3 9.1 1.0 HB2 A:PHE11 3.3 8.2 1.0 CD2 A:HIS15 3.5 9.1 1.0 HB2 A:GLN14 3.6 9.0 1.0 O A:HOH349 3.6 20.9 0.9 O3 A:PO4202 3.6 13.6 0.7 HD1 A:TRP10 3.7 10.6 1.0 NE2 A:HIS15 3.7 9.7 1.0 HA A:HIS122 3.7 10.8 0.2 HA A:HIS122 3.7 8.6 0.8 P A:PO4202 3.7 11.5 0.7 N A:PHE11 3.7 6.4 1.0 CB A:PHE11 3.7 6.8 1.0 O A:VAL121 3.9 8.4 1.0 CD2 A:PHE11 4.0 7.6 1.0 O A:TRP10 4.1 6.6 1.0 CD1 A:TRP10 4.1 8.8 1.0 HG3 A:GLN14 4.1 10.3 1.0 C A:TRP10 4.1 6.0 1.0 H A:PHE11 4.1 7.7 1.0 CD A:GLN14 4.1 9.8 1.0 H A:LEU123 4.3 9.7 0.2 HD1 A:HIS122 4.3 14.8 0.2 CG A:PHE11 4.3 7.0 1.0 H A:LEU123 4.3 9.7 0.8 O4 A:PO4202 4.3 17.5 0.7 HD1 A:HIS122 4.3 11.2 0.8 CB A:GLN14 4.3 7.5 1.0 CG A:GLN14 4.4 8.6 1.0 C A:PHE11 4.5 6.1 1.0 HB3 A:TRP10 4.5 8.3 1.0 HB3 A:PHE11 4.6 8.2 1.0 O A:PHE11 4.6 6.5 1.0 HB3 A:GLN14 4.6 9.0 1.0 CA A:HIS122 4.6 9.0 0.2 CA A:HIS122 4.7 7.1 0.8 NE1 A:TRP10 4.7 9.4 1.0 CG A:TRP10 4.7 7.5 1.0 C A:VAL121 4.7 7.6 1.0 HE1 A:TRP10 4.7 11.3 1.0 O A:HOH521 4.8 14.6 0.5 CG A:HIS15 4.8 7.8 1.0 O A:LYS7 4.9 6.7 1.0 CE1 A:HIS15 4.9 8.7 1.0 ND1 A:HIS122 4.9 9.3 0.8 O A:HOH345 5.0 17.0 0.8

Chlorine binding site 3 out of 3 in the A Novel Crystal Form of Human RNASE6 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of A Novel Crystal Form of Human RNASE6 at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl212 b:13.8 occ:0.46 OE1 A:GLN110 0.5 9.8 0.3 CD A:GLN110 1.7 9.7 0.3 H A:LYS7 2.1 7.8 1.0 NE2 A:GLN110 2.7 9.4 0.3 K A:K213 2.7 19.2 0.4 O A:HOH346 2.7 7.9 1.0 HG3 A:GLN110 2.7 11.2 0.3 HB2 A:LYS7 2.8 8.5 1.0 HE22 A:GLN110 2.8 11.3 0.3 CG A:GLN110 2.8 9.3 0.3 HB A:THR6 2.9 8.1 1.0 HG3 A:LYS7 2.9 9.7 1.0 N A:LYS7 3.0 6.5 1.0 HG3 A:GLN110 3.3 12.0 0.7 HG2 A:GLN110 3.4 11.2 0.3 CB A:LYS7 3.4 7.1 1.0 HB2 A:GLN110 3.4 11.5 0.7 HE21 A:GLN110 3.5 11.3 0.3 HA A:THR6 3.5 8.2 1.0 CG A:LYS7 3.5 8.1 1.0 HD3 A:LYS7 3.5 9.7 1.0 H A:ALA8 3.7 7.5 1.0 CB A:THR6 3.7 6.8 1.0 CA A:LYS7 3.7 7.1 1.0 HB2 A:GLN110 3.8 10.4 0.3 CA A:THR6 3.9 6.9 1.0 C A:THR6 3.9 6.4 1.0 CB A:GLN110 3.9 8.7 0.3 CG A:GLN110 4.0 10.0 0.7 CD A:LYS7 4.0 8.1 1.0 CB A:GLN110 4.1 9.6 0.7 HG2 A:GLN110 4.1 12.0 0.7 O A:HOH401 4.1 9.3 1.0 HG22 A:THR6 4.3 9.7 1.0 HB3 A:LYS7 4.3 8.5 1.0 HD2 A:LYS7 4.3 9.7 1.0 HB3 A:GLN110 4.3 10.4 0.3 HG2 A:LYS7 4.4 9.7 1.0 N A:ALA8 4.4 6.3 1.0 O A:HOH456 4.4 14.2 0.4 HA A:LYS7 4.5 8.5 1.0 HB3 A:GLN110 4.5 11.5 0.7 CG2 A:THR6 4.5 8.1 1.0 C A:LYS7 4.6 6.8 1.0 OG1 A:THR6 4.7 6.9 1.0 HZ2 A:TRP1 4.8 10.9 0.5 HG11 A:VAL121 4.8 9.9 1.0 HG21 A:THR6 4.8 9.7 1.0 HG12 A:VAL121 4.8 9.9 1.0 H A:GLN110 4.8 10.4 0.3 OD2 A:ASP113 4.9 8.1 1.0 HG1 A:THR6 4.9 8.3 1.0 O A:HOH456 4.9 14.2 0.6 H A:GLN110 4.9 10.7 0.7 CZ2 A:TRP1 5.0 9.1 0.5

G.Prats-Ejarque, J.A.Blanco, V.A.Salazar, V.M.Nogues, M.Moussaoui, E.Boix. Characterization of An Rnase with Two Catalytic Centers. Human RNASE6 Catalytic and Phosphate-Binding Site Arrangement Favors the Endonuclease Cleavage of Polymeric Substrates. Biochim Biophys Acta Gen V.1863 105 2019SUBJ.
ISSN: ISSN 1872-8006
PubMed: 30287244
DOI: 10.1016/J.BBAGEN.2018.09.021