Calcium in PDB 6bci: Wild-Type I-Ltri Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex)

The structure of Wild-Type I-Ltri Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex), PDB code: 6bci was solved by C.Brown, K.Zhang, T.A.Mcmurrough, G.B.Gloor, D.R.Edgell, M.Junop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.88 / 2.28
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.530, 43.610, 105.710, 90.00, 105.94, 90.00
R / Rfree (%)	23.7 / 26.8

The binding sites of Calcium atom in the Wild-Type I-Ltri Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex) (pdb code 6bci). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Wild-Type I-Ltri Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex), PDB code: 6bci:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Wild-Type I-Ltri Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Wild-Type I-Ltri Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:56.6 occ:1.00 OE2 A:GLU184 2.3 39.6 1.0 OP1 D:DC15 2.3 50.9 1.0 O A:ALA28 2.4 40.8 1.0 O B:HOH106 2.4 50.6 1.0 OP2 B:DA17 2.5 44.5 1.0 CD A:GLU184 3.4 46.2 1.0 C A:ALA28 3.5 44.9 1.0 OE1 A:GLN211 3.7 49.8 1.0 OE1 A:GLU184 3.7 47.8 1.0 P B:DA17 3.7 48.5 1.0 P D:DC15 3.8 50.2 1.0 CA A:ALA28 4.1 37.8 1.0 C5' B:DA17 4.1 47.4 1.0 OE2 A:GLU29 4.2 47.5 1.0 CA A:CA403 4.2 59.8 1.0 O5' B:DA17 4.3 49.6 1.0 OP1 B:DA17 4.4 43.1 1.0 O3' D:DC14 4.4 55.2 1.0 O A:ASP27 4.4 44.0 1.0 OP2 D:DC15 4.5 57.2 1.0 CD A:GLN211 4.5 51.7 1.0 NE2 A:GLN211 4.6 41.6 1.0 CG A:GLU184 4.7 47.2 1.0 N A:GLU29 4.7 37.1 1.0 C5' D:DC15 4.7 50.1 1.0 O5' D:DC15 4.8 58.4 1.0 C4' D:DC15 4.9 52.5 1.0 C4' B:DA17 5.0 50.2 1.0 CB A:ALA28 5.0 43.1 1.0 CA A:GLU29 5.0 34.0 1.0 O3' B:DT16 5.0 37.6 1.0

Calcium binding site 2 out of 3 in the Wild-Type I-Ltri Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Wild-Type I-Ltri Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:47.4 occ:1.00 OP2 D:DG16 2.3 47.0 1.0 O A:HOH516 2.4 50.1 1.0 OP1 B:DT16 2.5 48.8 1.0 O A:GLY183 2.5 44.1 1.0 OE1 A:GLU29 2.5 47.9 1.0 O D:HOH106 2.5 52.0 1.0 CD A:GLU29 3.5 42.7 1.0 C A:GLY183 3.6 44.9 1.0 P D:DG16 3.7 38.0 1.0 CA A:CA403 3.8 59.8 1.0 P B:DT16 3.9 52.4 1.0 OE2 A:GLU29 4.0 47.5 1.0 CA A:GLY183 4.1 38.2 1.0 C5' D:DG16 4.2 50.3 1.0 C4' B:DT16 4.3 52.9 1.0 C5' B:DT16 4.3 49.8 1.0 O5' D:DG16 4.3 55.2 1.0 OP1 D:DG16 4.3 45.3 1.0 NZ A:LYS274 4.5 54.9 1.0 O3' B:DT15 4.5 54.7 1.0 CG A:GLU29 4.6 44.9 1.0 O5' B:DT16 4.6 52.0 1.0 O A:ALA182 4.7 39.1 1.0 N A:GLU184 4.7 43.0 1.0 OE1 A:GLU184 4.8 47.8 1.0 O3' D:DC15 4.9 41.9 1.0 C4' D:DG16 4.9 48.0 1.0 OP2 B:DT16 4.9 50.6 1.0

Calcium binding site 3 out of 3 in the Wild-Type I-Ltri Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Wild-Type I-Ltri Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:59.8 occ:1.00 OE1 A:GLU184 2.3 47.8 1.0 OP2 D:DG16 2.4 47.0 1.0 OE2 A:GLU29 2.4 47.5 1.0 OP2 B:DA17 2.5 44.5 1.0 O3' D:DC15 2.6 41.9 1.0 O3' B:DT16 2.7 37.6 1.0 P D:DG16 3.0 38.0 1.0 P B:DA17 3.1 48.5 1.0 CD A:GLU29 3.2 42.7 1.0 OE1 A:GLU29 3.2 47.9 1.0 CD A:GLU184 3.5 46.2 1.0 C3' B:DT16 3.6 48.9 1.0 C3' D:DC15 3.7 52.4 1.0 O A:GLY183 3.7 44.1 1.0 CA A:CA402 3.8 47.4 1.0 C4' B:DT16 3.9 52.9 1.0 OE2 A:GLU184 3.9 39.6 1.0 O5' D:DG16 4.0 55.2 1.0 OP1 D:DG16 4.1 45.3 1.0 C4' D:DC15 4.1 52.5 1.0 O5' B:DA17 4.2 49.6 1.0 OP1 B:DA17 4.2 43.1 1.0 CA A:CA401 4.2 56.6 1.0 O A:ALA28 4.4 40.8 1.0 C A:GLY183 4.5 44.9 1.0 CG A:GLU29 4.6 44.9 1.0 CG A:GLU184 4.7 47.2 1.0 OP1 D:DC15 4.7 50.9 1.0 CA A:GLU184 4.8 46.6 1.0 O4' B:DT16 4.9 54.8 1.0 C5' B:DT16 4.9 49.8 1.0 C A:ALA28 5.0 44.9 1.0 C2' D:DC15 5.0 57.8 1.0 C2' B:DT16 5.0 51.7 1.0

T.A.Mcmurrough, C.M.Brown, K.Zhang, G.Hausner, M.S.Junop, G.B.Gloor, D.R.Edgell. Active Site Residue Identity Regulates Cleavage Preference of Laglidadg Homing Endonucleases. Nucleic Acids Res. V. 46 11990 2018.
ISSN: ESSN 1362-4962
PubMed: 30357419
DOI: 10.1093/NAR/GKY976