Sodium in PDB 3c0w: I-Scei in Complex with A Bottom Nicked Dna Substrate

The structure of I-Scei in Complex with A Bottom Nicked Dna Substrate, PDB code: 3c0w was solved by C.M.Moure, F.S.Gimble, F.A.Quiocho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.00 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.610, 80.610, 127.090, 90.00, 90.00, 90.00
R / Rfree (%)	26.8 / 28.7

The structure of I-Scei in Complex with A Bottom Nicked Dna Substrate also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the I-Scei in Complex with A Bottom Nicked Dna Substrate (pdb code 3c0w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the I-Scei in Complex with A Bottom Nicked Dna Substrate, PDB code: 3c0w:

Sodium binding site 1 out of 1 in the I-Scei in Complex with A Bottom Nicked Dna Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of I-Scei in Complex with A Bottom Nicked Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:32.2 occ:1.00 OP2 D:DC17 2.0 44.6 1.0 OD1 A:ASP44 2.1 33.3 1.0 O C:HOH490 2.2 32.1 1.0 OD1 A:ASP145 2.3 38.5 1.0 OP2 B:DC15 2.4 30.9 1.0 O3' B:DA14 2.8 32.4 1.0 P B:DC15 3.2 29.7 1.0 CG A:ASP44 3.3 29.7 1.0 O3' C:DT16 3.4 58.1 1.0 P D:DC17 3.4 46.1 1.0 CG A:ASP145 3.5 36.0 1.0 C3' B:DA14 3.7 33.1 1.0 OP3 D:DC17 3.8 45.8 1.0 CA A:CA301 3.8 27.4 1.0 OD2 A:ASP44 3.9 29.3 1.0 CA A:CA304 3.9 31.0 1.0 O5' D:DC17 4.0 44.0 1.0 C4' B:DA14 4.0 32.9 1.0 O A:ASP144 4.1 30.6 1.0 OD2 A:ASP145 4.2 36.2 1.0 O5' B:DC15 4.2 31.9 1.0 C4' C:DT16 4.3 54.5 1.0 C3' C:DT16 4.3 56.6 1.0 OP1 B:DC15 4.3 27.0 1.0 CB A:ASP44 4.5 30.2 1.0 O A:GLY43 4.5 30.3 1.0 CA A:ASP145 4.5 32.5 1.0 CB A:ASP145 4.6 33.0 1.0 OP1 D:DC17 4.6 44.1 1.0 CA A:ASP44 4.6 29.2 1.0 C A:ASP144 4.6 33.5 1.0 O C:HOH418 4.7 36.5 1.0 OP1 B:DA14 4.7 33.9 1.0 C A:GLY43 4.8 31.0 1.0 N A:ASP145 4.9 33.5 1.0 N A:ASP44 4.9 31.1 1.0 O4' C:DT16 5.0 56.2 1.0 C5' B:DA14 5.0 32.2 1.0

C.M.Moure, F.S.Gimble, F.A.Quiocho. Crystal Structures of I-Scei Complexed to Nicked Dna Substrates: Snapshots of Intermediates Along the Dna Cleavage Reaction Pathway. Nucleic Acids Res. V. 36 3287 2008.
ISSN: ISSN 0305-1048
PubMed: 18424798
DOI: 10.1093/NAR/GKN178