Calcium in PDB 6fb0: Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium

The structure of Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium, PDB code: 6fb0 was solved by R.Molina, J.Prieto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.84 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.437, 67.673, 83.525, 90.00, 96.75, 90.00
R / Rfree (%)	17.6 / 22.9

The binding sites of Calcium atom in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium (pdb code 6fb0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium, PDB code: 6fb0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:23.8 occ:1.00 OP1 D:DC514 2.3 34.5 1.0 OP2 F:DA615 2.3 18.6 1.0 OD2 A:ASP20 2.4 19.4 1.0 O F:HOH715 2.4 32.8 1.0 O B:HOH325 2.4 18.6 1.0 O B:GLY19 2.5 21.1 1.0 OD1 A:ASP20 2.8 17.2 1.0 CG A:ASP20 2.9 18.7 1.0 O B:HOH309 3.3 0.7 1.0 C B:GLY19 3.5 33.0 1.0 O A:HOH302 3.6 16.4 1.0 P F:DA615 3.6 22.4 1.0 P D:DC514 3.7 26.3 1.0 H1 B:ACT202 3.9 55.9 1.0 O3' D:DA513 4.0 26.2 1.0 CA B:GLY19 4.0 29.1 1.0 O5' F:DA615 4.1 20.7 1.0 NE2 A:GLN47 4.2 19.4 1.0 O B:ASP18 4.3 30.8 1.0 OE1 A:GLN47 4.3 24.0 1.0 OP1 F:DA615 4.4 28.6 1.0 H3 B:ACT202 4.4 55.9 1.0 CB A:ASP20 4.4 18.6 1.0 C5' F:DA615 4.4 25.9 1.0 C5' D:DC514 4.5 25.9 1.0 CH3 B:ACT202 4.5 43.3 1.0 C4' D:DC514 4.5 24.7 1.0 H2 B:ACT202 4.6 55.9 1.0 O5' D:DC514 4.6 24.0 1.0 OP2 D:DC514 4.6 26.5 1.0 N B:ASP20 4.7 25.7 1.0 CD A:GLN47 4.7 22.6 1.0 O3' F:DG614 4.7 22.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:51.6 occ:1.00 O B:HOH343 2.4 52.4 1.0 O A:ASN136 2.4 26.4 1.0 O A:ALA134 2.5 35.1 1.0 O A:HOH321 2.5 36.3 1.0 O A:HOH325 2.6 27.1 1.0 O B:HOH302 3.5 57.6 1.0 C A:ASN136 3.6 31.1 1.0 C A:ALA134 3.6 29.3 1.0 O A:LEU135 4.1 34.9 1.0 C A:LEU135 4.1 35.3 1.0 CA A:ASP137 4.3 25.1 1.0 O A:ALA133 4.3 29.5 1.0 N A:ASP137 4.4 28.1 1.0 N A:ASN136 4.4 26.9 1.0 CA A:ALA134 4.4 39.2 1.0 N A:LEU135 4.5 29.9 1.0 N A:SER138 4.5 29.1 1.0 OD1 A:ASP137 4.5 31.6 1.0 CA A:LEU135 4.6 32.9 1.0 CA A:ASN136 4.6 28.2 1.0 OE1 B:GLN50 4.7 63.5 1.0 C A:ASP137 4.9 31.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:21.1 occ:1.00 OP1 F:DG614 2.3 22.0 1.0 O A:SER19 2.3 21.7 1.0 OP2 D:DA515 2.3 24.4 1.0 OD2 B:ASP20 2.5 24.8 1.0 O A:HOH333 2.5 25.4 1.0 O A:HOH315 2.5 15.3 1.0 OD1 B:ASP20 2.7 30.4 1.0 CG B:ASP20 3.0 27.1 1.0 C A:SER19 3.3 22.1 1.0 HO1 A:PGO205 3.5 55.9 1.0 P D:DA515 3.6 21.5 1.0 O A:HOH302 3.6 16.4 1.0 P F:DG614 3.7 23.5 1.0 O A:HOH311 3.8 0.7 1.0 CA A:SER19 3.8 20.6 1.0 O5' D:DA515 4.0 13.2 1.0 O3' F:DG613 4.1 22.6 1.0 C5' D:DA515 4.2 29.1 1.0 OE1 B:GLN47 4.3 22.9 1.0 OP1 D:DA515 4.3 21.1 1.0 O A:ASP18 4.3 22.5 1.0 C5' F:DG614 4.3 16.5 1.0 NE2 B:GLN47 4.4 16.9 1.0 N A:ASP20 4.5 24.1 1.0 O1 A:PGO205 4.5 43.5 1.0 CB B:ASP20 4.5 20.6 1.0 C4' F:DG614 4.6 22.4 1.0 CB A:SER19 4.6 36.5 1.0 O5' F:DG614 4.6 17.8 1.0 OP2 F:DG614 4.7 28.9 1.0 CD B:GLN47 4.7 18.4 1.0 O3' D:DC514 4.8 20.6 1.0 CA A:ASP20 4.9 21.8 1.0 OD1 A:ASP20 4.9 17.2 1.0 N A:SER19 4.9 17.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with Its Target Dna (Haemoglobin Beta Subunit Gene) in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:46.5 occ:1.00 O B:ALA134 2.3 32.7 1.0 O B:ASN136 2.4 35.5 1.0 O B:HOH350 2.4 71.2 1.0 O B:HOH328 2.5 34.4 1.0 O B:HOH311 2.5 35.0 1.0 O A:HOH343 2.7 58.5 1.0 O A:HOH347 3.1 67.7 1.0 C B:ALA134 3.4 38.4 1.0 C B:ASN136 3.6 43.4 1.0 C B:LEU135 4.1 38.7 1.0 CA B:ALA134 4.3 40.8 1.0 O B:ALA133 4.3 44.0 1.0 CA B:ASP137 4.3 32.1 1.0 N B:ASN136 4.3 41.3 1.0 O B:LEU135 4.3 35.3 1.0 N B:ASP137 4.3 37.3 1.0 O B:HOH339 4.4 49.1 1.0 N B:LEU135 4.4 38.2 1.0 N B:SER138 4.4 24.2 1.0 CA B:LEU135 4.5 40.8 1.0 CA B:ASN136 4.6 36.4 1.0 OD1 B:ASP137 4.7 39.8 1.0 OE1 A:GLN50 4.7 64.1 1.0 C B:ASP137 4.9 29.9 1.0

J.Prieto, P.Redondo, B.Lopez-Mendez, M.D'abramo, N.Merino, F.J.Blanco, P.Duchateau, G.Montoya, R.Molina. Understanding the Indirect Dna Read-Out Specificity of I-Crei Meganuclease. Sci Rep V. 8 10286 2018.
ISSN: ESSN 2045-2322
PubMed: 29980759
DOI: 10.1038/S41598-018-28599-0