Calcium in PDB 3c0x: I-Scei in Complex with A Top Nicked Dna Substrate

The structure of I-Scei in Complex with A Top Nicked Dna Substrate, PDB code: 3c0x 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)	36.08 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.680, 80.680, 128.320, 90.00, 90.00, 90.00
R / Rfree (%)	25.5 / 28.8

The binding sites of Calcium atom in the I-Scei in Complex with A Top Nicked Dna Substrate (pdb code 3c0x). 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 Top Nicked Dna Substrate, PDB code: 3c0x:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the I-Scei in Complex with A Top 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 Top Nicked Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:48.6 occ:1.00 O D:HOH432 2.0 39.6 1.0 O C:HOH433 2.2 48.3 1.0 OP3 C:DC15 2.3 47.6 1.0 OP1 D:DT16 2.5 42.9 1.0 O D:HOH412 2.7 29.7 1.0 P C:DC15 3.4 36.9 1.0 O4' D:DA15 3.5 41.0 1.0 P D:DT16 3.7 43.5 1.0 C4' D:DA15 3.9 41.1 1.0 OP1 C:DC15 3.9 40.4 1.0 OP2 D:DT16 3.9 44.2 1.0 OP2 C:DC15 4.0 42.1 1.0 O4' C:DC15 4.1 36.6 1.0 O3' B:DA14 4.2 34.8 1.0 O C:HOH409 4.4 43.9 1.0 C1' D:DA15 4.5 40.1 1.0 C4' C:DC15 4.5 38.5 1.0 N3 D:DA15 4.6 41.6 1.0 O2 D:DT14 4.6 45.5 1.0 O4' D:DT16 4.7 39.8 1.0 N3 B:DA14 4.7 37.9 1.0 O5' D:DT16 4.7 45.1 1.0 O5' C:DC15 4.7 40.9 1.0 O3' D:DA15 4.8 42.4 1.0 C5' D:DA15 4.9 40.5 1.0 C3' D:DA15 4.9 40.6 1.0 C2' B:DA14 4.9 35.0 1.0 C4' D:DT16 4.9 40.0 1.0

Calcium binding site 2 out of 3 in the I-Scei in Complex with A Top 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 Top Nicked Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:34.3 occ:1.00 O D:HOH435 2.1 26.0 1.0 OP1 B:DA14 2.2 35.8 1.0 O A:ASP144 2.3 33.4 1.0 O A:HOH428 2.4 37.1 1.0 OD2 A:ASP44 2.4 34.1 1.0 OP1 D:DC17 2.5 36.2 1.0 C A:ASP144 3.4 34.4 1.0 CG A:ASP44 3.4 34.4 1.0 P B:DA14 3.7 33.5 1.0 P D:DC17 3.7 36.0 1.0 OD1 A:ASP44 3.7 33.6 1.0 CA A:ASP144 3.9 33.1 1.0 OP2 D:DC17 4.1 40.0 1.0 O A:MET143 4.3 32.0 1.0 O3' B:DA13 4.3 35.1 1.0 C5' B:DA14 4.3 35.6 1.0 NE1 A:TRP62 4.4 31.4 1.0 C5' D:DC17 4.4 42.1 1.0 O5' D:DC17 4.5 40.3 1.0 CD1 A:TRP62 4.5 31.5 1.0 N A:ASP145 4.5 34.1 1.0 O5' B:DA14 4.5 36.2 1.0 C4' B:DA14 4.6 35.7 1.0 OD1 A:ASP145 4.6 42.3 1.0 OP2 B:DA14 4.7 36.9 1.0 CB A:ASP44 4.7 32.7 1.0 CB A:ASP144 4.7 33.8 1.0 CA A:ASP145 4.9 32.8 1.0 N A:ASP144 4.9 33.4 1.0 O3' D:DT16 5.0 37.1 1.0 NZ A:LYS223 5.0 45.5 1.0

Calcium binding site 3 out of 3 in the I-Scei in Complex with A Top 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 Top Nicked Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:41.6 occ:1.00 OP2 C:DC15 1.9 42.1 1.0 OD1 A:ASP145 2.1 42.3 1.0 OP2 D:DC17 2.2 40.0 1.0 OD1 A:ASP44 2.4 33.6 1.0 O A:HOH425 2.9 40.8 1.0 CG A:ASP145 3.0 40.8 1.0 O A:HOH442 3.0 46.0 1.0 P C:DC15 3.2 36.9 1.0 OD2 A:ASP145 3.3 44.2 1.0 O5' C:DC15 3.4 40.9 1.0 O A:GLY43 3.4 36.0 1.0 O3' B:DA14 3.6 34.8 1.0 CG A:ASP44 3.6 34.4 1.0 P D:DC17 3.6 36.0 1.0 C A:GLY43 3.9 33.8 1.0 OP1 C:DC15 4.0 40.4 1.0 CB A:ASP145 4.2 34.4 1.0 OP3 C:DC15 4.2 47.6 1.0 O3' D:DT16 4.3 37.1 1.0 OD2 A:ASP44 4.4 34.1 1.0 CA A:ASP44 4.4 30.5 1.0 N A:ASP44 4.4 33.4 1.0 OP1 D:DC17 4.4 36.2 1.0 O5' D:DT16 4.4 45.1 1.0 C3' B:DA14 4.5 35.2 1.0 C4' D:DT16 4.5 40.0 1.0 CB A:ASP44 4.6 32.7 1.0 O5' D:DC17 4.6 40.3 1.0 CA A:ASP145 4.7 32.8 1.0 O A:ASN163 4.7 36.3 1.0 CA A:GLY43 4.7 32.8 1.0 C3' D:DT16 4.7 38.6 1.0 O A:ASP144 4.7 33.4 1.0 C5' C:DC15 4.8 37.2 1.0 O A:HOH402 4.8 44.0 1.0 OP2 D:DT16 4.8 44.2 1.0 C A:ASP144 5.0 34.4 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