Sodium in PDB 3gox: Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta

The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta, PDB code: 3gox 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)	19.60 / 1.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	90.682, 90.682, 334.933, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 18.6

The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta (pdb code 3gox). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta, PDB code: 3gox:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:18.6 occ:1.00 OP1 D:DA3 2.2 23.5 0.5 OP1 C:DT3 2.3 28.1 0.5 OD1 A:ASP148 2.3 15.2 1.0 OD1 A:ASN165 2.3 15.7 1.0 O A:HOH271 2.3 17.6 1.0 O C:HOH201 2.5 21.5 1.0 O3' D:DG2 2.8 16.7 0.5 O3' C:DG2 2.9 18.4 0.5 P D:DA3 3.1 22.5 0.5 P C:DT3 3.1 24.6 0.5 CG A:ASN165 3.3 14.9 1.0 CG A:ASP148 3.4 15.6 1.0 C3' D:DG2 3.6 14.3 0.5 C3' C:DG2 3.6 15.4 0.5 ND2 A:ASN165 3.7 15.6 1.0 O5' C:DT3 3.7 25.3 0.5 O5' D:DA3 3.9 22.6 0.5 C4' D:DG2 3.9 12.5 0.5 C4' C:DG2 3.9 13.5 0.5 NH2 A:ARG157 4.0 18.2 1.0 CB A:ASP148 4.1 17.2 1.0 CA A:ASP148 4.1 16.7 1.0 O A:HIS149 4.1 18.0 1.0 N A:HIS149 4.2 16.1 1.0 OP2 D:DA3 4.3 23.4 0.5 OD2 A:ASP173 4.4 22.7 1.0 OD2 A:ASP148 4.4 17.5 1.0 OP2 C:DT3 4.4 25.9 0.5 O A:HOH230 4.5 31.1 1.0 O A:ASN165 4.6 14.4 1.0 CB A:ASN165 4.6 13.2 1.0 C A:ASP148 4.7 16.7 1.0 C5' C:DG2 4.8 13.7 0.5 C5' D:DG2 4.8 12.8 0.5 CD1 A:LEU168 4.8 20.5 1.0 OD1 A:ASP173 4.9 23.6 1.0 CA A:ASN165 5.0 14.0 1.0 O4' D:DG2 5.0 12.0 0.5 O4' C:DG2 5.0 12.9 0.5 C2' D:DG2 5.0 12.5 0.5

Sodium binding site 2 out of 3 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:18.7 occ:1.00 OP1 C:DT3 2.2 26.9 0.5 OP1 D:DA3 2.2 23.1 0.5 OD1 B:ASP148 2.3 14.9 1.0 OD1 B:ASN165 2.3 15.0 1.0 O B:HOH239 2.3 18.3 1.0 O C:HOH328 2.5 20.5 1.0 O3' D:DG2 2.8 16.5 0.5 O3' C:DG2 2.9 17.8 0.5 P D:DA3 3.1 23.9 0.5 P C:DT3 3.1 25.7 0.5 CG B:ASN165 3.3 14.9 1.0 CG B:ASP148 3.4 16.9 1.0 C3' D:DG2 3.6 14.7 0.5 C3' C:DG2 3.6 15.5 0.5 O5' C:DT3 3.7 25.9 0.5 ND2 B:ASN165 3.7 15.3 1.0 O5' D:DA3 3.9 23.3 0.5 C4' C:DG2 3.9 13.6 0.5 C4' D:DG2 3.9 13.0 0.5 NH2 B:ARG157 4.0 17.1 1.0 CB B:ASP148 4.1 16.8 1.0 CA B:ASP148 4.1 17.1 1.0 N B:HIS149 4.2 16.5 1.0 O B:HIS149 4.2 16.4 1.0 OD2 B:ASP148 4.3 16.4 1.0 OP2 D:DA3 4.3 23.6 0.5 O B:HOH247 4.4 30.7 1.0 OP2 C:DT3 4.4 25.0 0.5 OD2 B:ASP173 4.4 23.9 1.0 O B:ASN165 4.6 14.1 1.0 CB B:ASN165 4.6 14.0 1.0 C B:ASP148 4.7 16.6 1.0 C5' C:DG2 4.8 13.0 0.5 CD1 B:LEU168 4.8 20.5 1.0 C5' D:DG2 4.8 12.4 0.5 OD1 B:ASP173 4.8 22.7 1.0 CA B:ASN165 4.9 13.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta within 5.0Å range: probe atom residue distance (Å) B Occ B:Na307 b:23.5 occ:1.00 O B:TYR57 2.3 16.3 1.0 O B:HOH455 2.4 36.6 1.0 O B:HOH361 2.5 27.9 1.0 O B:HOH213 2.5 21.1 1.0 OH B:TYR63 2.5 12.2 1.0 C B:TYR57 3.5 14.4 1.0 CZ B:TYR63 3.5 10.6 1.0 CE2 B:TYR63 3.7 10.7 1.0 CB B:TYR57 4.2 14.8 1.0 CA B:TYR57 4.3 14.7 1.0 N B:ARG58 4.4 12.9 1.0 CA B:ARG58 4.6 12.4 1.0 CE1 B:TYR63 4.7 8.8 1.0 CG B:ARG58 4.9 12.8 1.0 O B:HOH360 4.9 19.3 1.0 CD2 B:TYR63 5.0 10.4 1.0

M.Sokolowska, H.Czapinska, M.Bochtler. Crystal Structure of the Beta Beta Alpha-Me Type II Restriction Endonuclease HPY99I with Target Dna. Nucleic Acids Res. V. 37 3799 2009.
ISSN: ISSN 0305-1048
PubMed: 19380375
DOI: 10.1093/NAR/GKP228