Sodium in PDB 1wte: Crystal Structure of Type II Restrcition Endonuclease, ECOO109I Complexed with Cognate Dna

All present enzymatic activity of Crystal Structure of Type II Restrcition Endonuclease, ECOO109I Complexed with Cognate Dna:
3.1.21.4;

The structure of Crystal Structure of Type II Restrcition Endonuclease, ECOO109I Complexed with Cognate Dna, PDB code: 1wte was solved by H.Hashimoto, T.Shimizu, T.Imasaki, M.Kato, N.Shichijo, K.Kita, M.Sato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.64 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.103, 71.879, 203.240, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 22.3

The binding sites of Sodium atom in the Crystal Structure of Type II Restrcition Endonuclease, ECOO109I Complexed with Cognate Dna (pdb code 1wte). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Type II Restrcition Endonuclease, ECOO109I Complexed with Cognate Dna, PDB code: 1wte:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Type II Restrcition Endonuclease, ECOO109I Complexed with Cognate Dna


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 Type II Restrcition Endonuclease, ECOO109I Complexed with Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:10.4 occ:1.00 OP1 X:DG6 2.2 16.4 0.5 OD2 A:ASP110 2.3 15.5 1.0 O A:LEU125 2.3 13.3 1.0 O A:HOH1022 2.3 20.4 1.0 O X:HOH27 2.4 22.6 1.0 O A:HOH1018 2.4 14.8 1.0 CG A:ASP110 3.1 17.0 1.0 OD1 A:ASP110 3.2 21.1 1.0 P X:DG6 3.4 20.7 0.5 C A:LEU125 3.4 14.0 1.0 N A:LEU125 3.6 13.5 1.0 CA A:LEU125 3.9 14.8 1.0 O5' X:DG6 3.9 16.2 0.5 OP2 X:DG6 4.0 18.4 0.5 CB A:LEU125 4.2 15.2 1.0 C5' X:DG6 4.3 14.7 0.5 OD1 A:ASP77 4.3 23.3 1.0 O X:HOH32 4.3 25.8 1.0 O A:HOH1069 4.4 31.2 1.0 CB A:ASP110 4.5 14.6 1.0 NZ A:LYS126 4.5 19.9 1.0 O A:HOH1062 4.5 30.9 1.0 CE A:LYS126 4.6 20.6 1.0 O X:HOH30 4.6 15.3 1.0 N A:LYS126 4.6 13.1 1.0 O3' X:DG5 4.6 17.4 0.5 C A:SER124 4.6 14.8 1.0 OP2 X:DC7 4.6 12.1 0.5 CD A:LYS126 4.7 17.8 1.0 OG A:SER124 4.8 16.1 1.0 CG A:ASP77 5.0 18.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Type II Restrcition Endonuclease, ECOO109I Complexed with Cognate Dna


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 Type II Restrcition Endonuclease, ECOO109I Complexed with Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1002 b:12.0 occ:1.00 O B:HOH1066 2.2 18.3 1.0 OP1 Y:DG6 2.2 18.3 0.5 O B:LEU125 2.3 13.1 1.0 OD2 B:ASP110 2.4 16.0 1.0 O B:HOH1004 2.4 14.6 1.0 O Y:HOH29 2.5 24.5 1.0 CG B:ASP110 3.1 19.5 1.0 OD1 B:ASP110 3.2 19.4 1.0 C B:LEU125 3.4 13.9 1.0 P Y:DG6 3.4 20.5 0.5 N B:LEU125 3.5 14.2 1.0 OP2 Y:DG6 3.9 18.6 0.5 CA B:LEU125 3.9 14.6 1.0 CB B:LEU125 4.1 15.2 1.0 OD1 B:ASP77 4.2 23.7 1.0 NZ B:LYS126 4.2 19.8 1.0 O B:HOH1111 4.2 27.3 1.0 C5' Y:DG6 4.2 14.0 0.5 O5' Y:DG6 4.3 14.7 0.5 O B:HOH1050 4.5 23.1 1.0 CB B:ASP110 4.5 18.4 1.0 N B:LYS126 4.6 13.3 1.0 O B:HOH1043 4.6 26.2 1.0 CD B:LYS126 4.6 16.1 1.0 C B:SER124 4.6 15.6 1.0 O3' Y:DG5 4.6 18.2 0.5 O Y:HOH27 4.6 13.2 1.0 CE B:LYS126 4.7 18.3 1.0 OG B:SER124 4.7 15.0 1.0 OP2 Y:DG7 4.8 12.5 0.5 CG B:ASP77 5.0 19.4 1.0

H.Hashimoto, T.Shimizu, T.Imasaki, M.Kato, N.Shichijo, K.Kita, M.Sato. Crystal Structures of Type II Restriction Endonuclease ECOO109I and Its Complex with Cognate Dna J.Biol.Chem. V. 280 5605 2005.
ISSN: ISSN 0021-9258
PubMed: 15590682
DOI: 10.1074/JBC.M411684200