Sodium in PDB 3fc3: Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I

The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I, PDB code: 3fc3 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)	19.71 / 1.75
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	90.089, 90.089, 334.254, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 20.5

The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I 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 (pdb code 3fc3). 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, PDB code: 3fc3:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:26.8 occ:1.00 OD1 A:ASP148 2.2 22.4 1.0 OD1 A:ASN165 2.3 21.4 1.0 O A:HOH439 2.4 23.1 1.0 OP1 C:DT3 2.4 27.9 0.5 O3' D:DG2 2.5 20.5 0.5 O A:HOH516 2.6 31.6 1.0 OP1 D:DA3 2.7 21.5 0.5 O3' C:DG2 2.8 27.3 0.5 P C:DT3 3.1 28.7 0.5 P D:DA3 3.1 22.9 0.5 CG A:ASP148 3.3 23.6 1.0 CG A:ASN165 3.3 20.0 1.0 C3' C:DG2 3.5 26.1 0.5 C3' D:DG2 3.6 21.0 0.5 O5' C:DT3 3.7 29.8 0.5 ND2 A:ASN165 3.8 20.6 1.0 C4' C:DG2 3.9 24.7 0.5 O5' D:DA3 3.9 23.4 0.5 C4' D:DG2 3.9 21.1 0.5 NH2 A:ARG157 3.9 24.8 1.0 CB A:ASP148 4.0 24.3 1.0 N A:HIS149 4.1 23.8 1.0 CA A:ASP148 4.1 24.1 1.0 O A:HIS149 4.1 23.5 1.0 OD2 A:ASP148 4.3 21.5 1.0 OD2 A:ASP173 4.4 32.4 1.0 OP2 C:DT3 4.4 28.7 0.5 OP2 D:DA3 4.4 19.9 0.5 O A:HOH515 4.6 36.3 1.0 C A:ASP148 4.6 23.8 1.0 O A:ASN165 4.6 20.3 1.0 CB A:ASN165 4.6 17.9 1.0 CD1 A:LEU168 4.7 25.9 1.0 C5' C:DG2 4.7 24.1 0.5 C5' D:DG2 4.8 21.7 0.5 OD1 A:ASP173 4.9 32.7 1.0 C2' D:DG2 4.9 19.4 0.5 O4' D:DG2 4.9 20.0 0.5 CA A:ASN165 4.9 18.9 1.0 O4' C:DG2 4.9 24.9 0.5 C2' C:DG2 5.0 25.7 0.5

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:26.3 occ:1.00 OD1 B:ASP148 2.3 22.1 1.0 OD1 B:ASN165 2.3 21.7 1.0 O B:HOH208 2.3 24.9 1.0 OP1 C:DT3 2.4 27.9 0.5 O3' D:DG2 2.4 20.5 0.5 O B:HOH466 2.5 27.3 1.0 OP1 D:DA3 2.6 21.5 0.5 O3' C:DG2 2.7 27.3 0.5 P C:DT3 3.0 28.7 0.5 P D:DA3 3.1 22.9 0.5 CG B:ASN165 3.3 18.8 1.0 CG B:ASP148 3.4 24.1 1.0 C3' C:DG2 3.5 26.1 0.5 C3' D:DG2 3.6 21.0 0.5 O5' C:DT3 3.7 29.8 0.5 ND2 B:ASN165 3.7 18.9 1.0 O5' D:DA3 3.8 23.4 0.5 C4' C:DG2 3.8 24.7 0.5 C4' D:DG2 3.9 21.1 0.5 NH2 B:ARG157 4.0 23.9 1.0 CA B:ASP148 4.1 23.8 1.0 CB B:ASP148 4.1 23.5 1.0 N B:HIS149 4.1 23.4 1.0 O B:HIS149 4.1 22.5 1.0 OD2 B:ASP148 4.3 22.1 1.0 OP2 C:DT3 4.4 28.7 0.5 OP2 D:DA3 4.4 19.9 0.5 OD2 B:ASP173 4.4 30.9 1.0 O C:HOH212 4.5 41.2 1.0 O B:ASN165 4.6 20.2 1.0 CB B:ASN165 4.6 19.6 1.0 C B:ASP148 4.6 23.4 1.0 C5' C:DG2 4.7 24.1 0.5 OD1 B:ASP173 4.8 28.9 1.0 C5' D:DG2 4.8 21.7 0.5 CD1 B:LEU168 4.9 26.2 1.0 C2' D:DG2 4.9 19.4 0.5 C2' C:DG2 4.9 25.7 0.5 O4' D:DG2 4.9 20.0 0.5 CA B:ASN165 4.9 19.0 1.0 O4' C:DG2 5.0 24.9 0.5

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na307 b:30.5 occ:1.00 O B:TYR57 2.3 22.0 1.0 O B:HOH198 2.4 32.6 1.0 OH B:TYR63 2.4 17.2 1.0 CZ B:TYR63 3.4 17.2 1.0 C B:TYR57 3.5 20.9 1.0 CE2 B:TYR63 3.6 17.6 1.0 CB B:TYR57 4.1 21.5 1.0 CA B:TYR57 4.3 21.1 1.0 N B:ARG58 4.4 19.4 1.0 CA B:ARG58 4.6 19.5 1.0 CE1 B:TYR63 4.6 16.2 1.0 CG B:ARG58 4.9 20.2 1.0 O B:HOH482 4.9 23.5 1.0 CD2 B:TYR63 5.0 17.6 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