Calcium 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:

Sodium

(Na)

1 atom

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the I-Scei in Complex with A Bottom Nicked Dna Substrate, PDB code: 3c0w:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the I-Scei in Complex with A Bottom Nicked Dna Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca301 b:27.4 occ:1.00 OP1 B:DA14 2.2 33.9 1.0 OD2 A:ASP44 2.2 29.3 1.0 O A:HOH477 2.3 32.9 1.0 OP2 D:DC17 2.4 44.6 1.0 O A:ASP144 2.4 30.6 1.0 OP1 D:DC17 2.6 44.1 1.0 P D:DC17 2.9 46.1 1.0 CG A:ASP44 3.1 29.7 1.0 OD1 A:ASP44 3.2 33.3 1.0 C A:ASP144 3.4 33.5 1.0 P B:DA14 3.7 32.3 1.0 NA A:NA303 3.8 32.2 1.0 CA A:ASP144 3.9 31.9 1.0 OP3 D:DC17 3.9 45.8 1.0 NZ A:LYS223 4.2 40.6 1.0 O3' B:DA13 4.2 33.9 1.0 O5' D:DC17 4.2 44.0 1.0 O A:MET143 4.3 28.2 1.0 NE1 A:TRP62 4.3 29.4 1.0 CD1 A:TRP62 4.4 29.9 1.0 CB A:ASP44 4.4 30.2 1.0 C5' B:DA14 4.5 32.2 1.0 N A:ASP145 4.5 33.5 1.0 OP2 B:DA14 4.6 36.4 1.0 C4' B:DA14 4.6 32.9 1.0 O5' B:DA14 4.6 35.4 1.0 OD1 A:ASP145 4.7 38.5 1.0 CB A:ASP144 4.8 34.4 1.0 CA A:ASP145 4.9 32.5 1.0 N A:ASP144 5.0 30.1 1.0

Calcium binding site 2 out of 3 in the I-Scei in Complex with A Bottom Nicked Dna Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of I-Scei in Complex with A Bottom Nicked Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:31.0 occ:1.00 O A:HOH437 2.2 33.5 1.0 O A:GLY43 2.3 30.3 1.0 O B:HOH460 2.4 34.0 1.0 OP2 B:DC15 2.4 30.9 1.0 OD2 A:ASP145 2.4 36.2 1.0 O C:HOH418 2.5 36.5 1.0 CG A:ASP145 3.2 36.0 1.0 OD1 A:ASP145 3.2 38.5 1.0 C A:GLY43 3.4 31.0 1.0 P B:DC15 3.6 29.7 1.0 O A:HOH459 3.7 43.5 1.0 O A:LEU42 3.8 31.3 1.0 NA A:NA303 3.9 32.2 1.0 CA A:GLY43 4.1 31.0 1.0 O5' B:DC15 4.1 31.9 1.0 OP2 C:DT16 4.1 39.6 1.0 O A:HOH402 4.3 28.5 1.0 C5' B:DC15 4.3 29.6 1.0 OP1 B:DC15 4.4 27.0 1.0 N A:ASP44 4.4 31.1 1.0 OD1 A:ASP44 4.4 33.3 1.0 O A:ASN163 4.4 32.7 1.0 C A:LEU42 4.6 31.4 1.0 CB A:ASP145 4.6 33.0 1.0 CA A:ASP44 4.6 29.2 1.0 OG A:SER166 4.7 43.9 1.0 N A:GLY43 4.7 30.1 1.0 O3' B:DA14 4.8 32.4 1.0

Calcium binding site 3 out of 3 in the I-Scei in Complex with A Bottom Nicked Dna Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of I-Scei in Complex with A Bottom Nicked Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:32.2 occ:1.00 OP1 B:DC15 2.2 27.0 1.0 O C:HOH436 2.3 39.3 1.0 OP1 C:DT16 2.3 41.3 1.0 O C:HOH417 2.3 41.2 1.0 O B:HOH410 2.4 37.9 1.0 O C:HOH420 2.6 32.7 1.0 P C:DT16 3.7 43.0 1.0 P B:DC15 3.7 29.7 1.0 O4' B:DC15 3.8 31.8 1.0 O4' C:DA15 3.9 38.2 1.0 C5' C:DT16 3.9 52.2 1.0 C4' B:DC15 4.1 31.0 1.0 O3' B:DA14 4.3 32.4 1.0 OP2 C:DT16 4.3 39.6 1.0 O5' C:DT16 4.3 46.3 1.0 C4' C:DA15 4.4 39.2 1.0 O B:HOH433 4.4 39.9 1.0 OP2 B:DC15 4.5 30.9 1.0 O B:HOH460 4.5 34.0 1.0 C1' C:DA15 4.6 39.7 1.0 N3 B:DA14 4.6 33.0 1.0 O B:HOH411 4.6 41.6 1.0 C4' C:DT16 4.7 54.5 1.0 N3 C:DA15 4.7 40.9 1.0 O2 C:DT14 4.7 36.2 1.0 O5' B:DC15 4.7 31.9 1.0 C1' B:DC15 4.8 32.4 1.0 O3' C:DA15 4.9 40.6 1.0 C2' B:DA14 4.9 31.2 1.0 C1' B:DA14 5.0 32.4 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