Sodium in PDB 3oqg: Restriction Endonuclease HPY188I in Complex with Substrate Dna

The structure of Restriction Endonuclease HPY188I in Complex with Substrate Dna, PDB code: 3oqg was solved by M.Sokolowska, H.Czapinska, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 1.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.236, 65.236, 220.630, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.2

The structure of Restriction Endonuclease HPY188I in Complex with Substrate Dna also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Restriction Endonuclease HPY188I in Complex with Substrate Dna (pdb code 3oqg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Restriction Endonuclease HPY188I in Complex with Substrate Dna, PDB code: 3oqg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Restriction Endonuclease HPY188I in Complex with Substrate Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Restriction Endonuclease HPY188I in Complex with Substrate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na171 b:30.2 occ:1.00 OP1 C:DG1 2.3 21.1 0.5 OE2 A:GLU149 2.3 28.6 1.0 O A:HOH238 2.4 27.1 1.0 O B:HOH203 2.4 26.9 1.0 OP1 D:DG1 2.4 11.8 0.5 O3' D:DA0 2.5 16.8 0.5 O3' C:DT0 2.5 21.5 0.5 O A:HOH276 2.6 31.7 1.0 P C:DG1 3.0 21.5 0.5 P D:DG1 3.0 15.5 0.5 CD A:GLU149 3.1 29.3 1.0 OE1 A:GLU149 3.3 34.1 1.0 C3' C:DT0 3.6 20.0 0.5 C3' D:DA0 3.7 17.3 0.5 ND1 B:HIS76 3.7 19.9 1.0 O5' C:DG1 3.9 19.4 0.5 C4' C:DT0 3.9 19.8 0.5 C5' C:DG1 3.9 20.5 0.5 C4' D:DA0 4.0 18.5 0.5 OP2 D:DG1 4.1 16.1 0.5 CA B:GLY75 4.1 18.2 1.0 O A:HOH203 4.1 34.4 1.0 O5' D:DG1 4.1 14.8 0.5 OP2 C:DG1 4.2 21.3 0.5 C5' D:DG1 4.2 14.8 0.5 CE1 B:HIS76 4.2 23.6 1.0 N B:HIS76 4.3 18.8 1.0 C5' D:DA0 4.4 19.0 0.5 CG A:GLU149 4.4 26.7 1.0 O A:HOH286 4.5 35.2 1.0 O B:ILE74 4.5 19.0 1.0 C B:GLY75 4.6 18.8 1.0 C5' C:DT0 4.6 18.2 0.5 O C:HOH401 4.6 46.6 1.0 O B:HOH172 4.7 49.4 1.0 C2' D:DA0 4.9 17.4 0.5 C2' C:DT0 4.9 19.1 0.5 CG B:HIS76 4.9 20.4 1.0 O A:HOH232 5.0 35.6 1.0

Sodium binding site 2 out of 2 in the Restriction Endonuclease HPY188I in Complex with Substrate Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Restriction Endonuclease HPY188I in Complex with Substrate Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na171 b:28.9 occ:1.00 OE2 B:GLU149 2.3 30.1 1.0 O B:HOH232 2.4 29.1 1.0 O B:HOH216 2.4 26.9 1.0 OP1 C:DG1 2.4 17.7 0.5 O A:HOH218 2.4 24.1 1.0 O3' C:DT0 2.4 18.6 0.5 OP1 D:DG1 2.5 15.8 0.5 O3' D:DA0 2.5 18.6 0.5 P C:DG1 3.0 18.5 0.5 P D:DG1 3.1 18.7 0.5 CD B:GLU149 3.1 30.3 1.0 OE1 B:GLU149 3.3 33.9 1.0 C3' C:DT0 3.6 18.4 0.5 C3' D:DA0 3.7 18.8 0.5 ND1 A:HIS76 3.8 20.7 1.0 C4' C:DT0 3.9 18.5 0.5 C4' D:DA0 4.0 19.6 0.5 C5' C:DG1 4.0 17.5 0.5 O5' C:DG1 4.0 16.2 0.5 OP2 D:DG1 4.1 18.2 0.5 CA A:GLY75 4.1 19.1 1.0 OP2 C:DG1 4.2 17.1 0.5 O5' D:DG1 4.2 17.1 0.5 O B:HOH276 4.3 38.3 1.0 C5' D:DG1 4.3 17.3 0.5 N A:HIS76 4.3 18.6 1.0 CE1 A:HIS76 4.4 25.5 1.0 CG B:GLU149 4.4 27.5 1.0 C5' D:DA0 4.5 19.2 0.5 O B:HOH230 4.5 34.9 1.0 C5' C:DT0 4.5 16.5 0.5 O A:ILE74 4.5 20.9 1.0 C A:GLY75 4.6 18.9 1.0 O A:HOH173 4.8 37.5 1.0 C2' C:DT0 4.9 18.0 0.5 C2' D:DA0 4.9 18.2 0.5

M.Sokolowska, H.Czapinska, M.Bochtler. HPY188I-Dna Pre- and Post-Cleavage Complexes--Snapshots of the Giy-Yig Nuclease Mediated Catalysis. Nucleic Acids Res. V. 39 1554 2011.
ISSN: ISSN 0305-1048
PubMed: 20935048
DOI: 10.1093/NAR/GKQ821