Calcium in PDB 6bct: I-Ltri E184D Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex)

The structure of I-Ltri E184D Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex), PDB code: 6bct 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)	33.55 / 2.73
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.611, 43.440, 105.210, 90.00, 106.95, 90.00
R / Rfree (%)	22.7 / 28.2

The binding sites of Calcium atom in the I-Ltri E184D Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex) (pdb code 6bct). 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-Ltri E184D Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex), PDB code: 6bct:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the I-Ltri E184D 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 I-Ltri E184D Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:70.7 occ:1.00 OP2 B:DA17 2.2 58.5 1.0 OP1 D:DC15 2.4 77.1 1.0 O A:ALA28 2.4 64.7 1.0 OD2 A:ASP184 3.0 64.3 1.0 OD1 A:ASP184 3.1 76.0 1.0 CG A:ASP184 3.5 72.0 1.0 C A:ALA28 3.5 62.3 1.0 P B:DA17 3.6 74.0 1.0 CA A:CA403 3.7 98.7 1.0 OE1 A:GLN211 3.8 77.4 1.0 P D:DC15 3.8 72.2 1.0 CA A:ALA28 3.9 61.4 1.0 OE1 A:GLU29 3.9 76.1 1.0 C5' B:DA17 3.9 65.5 1.0 O5' B:DA17 4.0 72.7 1.0 OP1 B:DA17 4.3 62.9 1.0 O3' D:DC14 4.4 77.4 1.0 CB A:ALA28 4.5 62.1 1.0 CD A:GLN211 4.5 73.4 1.0 NE2 A:GLN211 4.6 77.9 1.0 OP2 D:DC15 4.6 73.9 1.0 C4' D:DC15 4.6 73.8 1.0 N A:GLU29 4.7 61.5 1.0 C5' D:DC15 4.7 73.0 1.0 O A:ASP27 4.7 70.0 1.0 O3' B:DT16 4.7 68.3 1.0 O5' D:DC15 4.8 79.5 1.0 C4' B:DA17 4.9 66.7 1.0 CB A:ASP184 5.0 69.9 1.0

Calcium binding site 2 out of 3 in the I-Ltri E184D 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 I-Ltri E184D Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:72.5 occ:1.00 O A:GLY183 2.4 70.9 1.0 OP1 B:DT16 2.4 66.8 1.0 OE2 A:GLU29 2.5 77.8 1.0 OP2 D:DG16 2.5 78.4 1.0 C A:GLY183 3.4 67.9 1.0 CD A:GLU29 3.7 73.8 1.0 P B:DT16 3.8 76.5 1.0 P D:DG16 3.8 78.9 1.0 CA A:GLY183 3.8 66.9 1.0 C5' D:DG16 4.1 75.0 1.0 CA A:CA403 4.1 98.7 1.0 O5' D:DG16 4.3 74.5 1.0 OE1 A:GLU29 4.3 76.1 1.0 O3' B:DT15 4.4 76.0 1.0 C5' B:DT16 4.4 70.4 1.0 OP1 D:DG16 4.5 73.6 1.0 C4' B:DT16 4.5 73.1 1.0 N A:ASP184 4.6 65.0 1.0 NZ A:LYS274 4.6 76.7 1.0 O A:ALA182 4.6 68.2 1.0 O5' B:DT16 4.6 75.1 1.0 CG A:GLU29 4.7 68.6 1.0 C4' D:DG16 4.8 77.7 1.0 OP2 B:DT16 4.8 71.7 1.0 N A:GLY183 4.9 67.1 1.0 O3' D:DC15 5.0 66.0 1.0

Calcium binding site 3 out of 3 in the I-Ltri E184D 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 I-Ltri E184D Bound to Non-Cognate C4 Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:98.7 occ:1.00 OE1 A:GLU29 2.4 76.1 1.0 OP2 B:DA17 2.5 58.5 1.0 O3' D:DC15 2.5 66.0 1.0 OD1 A:ASP184 2.5 76.0 1.0 OP2 D:DG16 2.5 78.4 1.0 O3' B:DT16 2.6 68.3 1.0 P B:DA17 3.0 74.0 1.0 P D:DG16 3.1 78.9 1.0 CD A:GLU29 3.1 73.8 1.0 OE2 A:GLU29 3.2 77.8 1.0 C3' D:DC15 3.6 77.5 1.0 O A:GLY183 3.7 70.9 1.0 C3' B:DT16 3.7 66.1 1.0 CA A:CA401 3.7 70.7 1.0 CG A:ASP184 3.7 72.0 1.0 C4' D:DC15 4.0 73.8 1.0 OP1 B:DA17 4.1 62.9 1.0 O5' B:DA17 4.1 72.7 1.0 O5' D:DG16 4.1 74.5 1.0 C4' B:DT16 4.1 73.1 1.0 CA A:CA402 4.1 72.5 1.0 OP1 D:DG16 4.1 73.6 1.0 O A:ALA28 4.2 64.7 1.0 C A:GLY183 4.4 67.9 1.0 CA A:ASP184 4.5 71.2 1.0 OD2 A:ASP184 4.5 64.3 1.0 OP1 D:DC15 4.6 77.1 1.0 CG A:GLU29 4.6 68.6 1.0 CB A:ASP184 4.7 69.9 1.0 N A:ASP184 4.8 65.0 1.0 C2' D:DC15 4.9 79.0 1.0 C A:ALA28 4.9 62.3 1.0 C5' D:DC15 4.9 73.0 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