Calcium in PDB 9f38: Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna

The structure of Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna, PDB code: 9f38 was solved by R.Sieskind, S.Missoury, C.Madru, I.Commenge, G.Niogret, M.Hollenstein, Y.Rondelez, A.Haouz, L.Sauguet, P.Legrand, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.70 / 2.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.735, 129.885, 100.733, 90, 95.5, 90
R / Rfree (%)	27.4 / 29.3

The structure of Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna (pdb code 9f38). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna, PDB code: 9f38:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:24.0 occ:1.00 OD2 A:ASP9 2.1 40.1 1.0 OD1 A:ASP91 2.4 43.7 1.0 O3' E:DG5 2.8 36.1 1.0 CG A:ASP9 2.9 38.0 1.0 OP1 E:DC6 2.9 36.1 1.0 OD1 A:ASP9 3.2 38.7 1.0 P E:DC6 3.5 36.2 1.0 CG A:ASP91 3.6 42.8 1.0 C3' E:DG5 4.0 35.8 1.0 O A:GLY497 4.0 70.4 1.0 CB A:ASP9 4.1 33.4 1.0 C5' E:DC6 4.1 36.3 1.0 C4' E:DG5 4.2 36.1 1.0 CA A:ASP91 4.3 35.0 1.0 O5' E:DC6 4.4 36.4 1.0 OD2 A:ASP91 4.4 45.0 1.0 CB A:ASP91 4.4 37.2 1.0 C2' E:DG5 4.6 35.4 1.0 CA A:CA702 4.7 35.2 1.0 O A:THR89 4.7 33.9 1.0 N A:ASP91 4.7 34.7 1.0 OP2 E:DC6 4.7 36.1 1.0 O A:PRO90 4.8 34.7 1.0 OE1 A:GLU109 4.8 31.9 1.0 C5' E:DG5 4.8 36.9 1.0 C A:PRO90 4.9 34.7 1.0 OE2 A:GLU109 5.0 33.3 1.0

Calcium binding site 2 out of 6 in the Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:35.2 occ:1.00 O A:PHE110 2.2 27.6 1.0 OD2 A:ASP91 2.6 45.0 1.0 OP1 E:DC6 2.8 36.1 1.0 OD1 A:ASP499 2.9 77.6 1.0 OD2 A:ASP499 3.0 79.2 1.0 CG A:ASP499 3.3 77.1 1.0 OE1 A:GLU109 3.3 31.9 1.0 CG A:ASP91 3.4 42.8 1.0 C A:PHE110 3.4 27.1 1.0 NH2 A:ARG123 3.4 37.9 1.0 OD1 A:ASP91 3.5 43.7 1.0 P E:DC6 4.1 36.2 1.0 CD A:GLU109 4.2 31.5 1.0 N A:PHE110 4.2 25.0 1.0 CA A:PHE110 4.3 25.9 1.0 N A:CYS111 4.4 27.3 1.0 O5' E:DC6 4.4 36.4 1.0 C5' E:DC6 4.4 36.3 1.0 CA A:CYS111 4.4 28.0 1.0 OP1 E:DA7 4.4 36.4 1.0 CB A:PHE110 4.5 25.8 1.0 CA A:CA701 4.7 24.0 1.0 CB A:ASP499 4.7 73.0 1.0 CZ A:ARG123 4.7 37.6 1.0 OE1 A:GLU13 4.8 42.4 1.0 CB A:ASP91 4.8 37.2 1.0 CG A:GLU109 4.8 27.7 1.0 O3' E:DC6 4.9 36.0 1.0 OE2 A:GLU109 4.9 33.3 1.0 P E:DA7 5.0 36.4 1.0 OP2 E:DA7 5.0 36.6 1.0 OP2 E:DC6 5.0 36.1 1.0

Calcium binding site 3 out of 6 in the Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:50.4 occ:1.00 OD2 A:ASP528 2.1 71.2 1.0 OE1 A:GLU470 2.5 56.4 1.0 CG A:ASP528 2.5 69.3 1.0 OD1 A:ASP528 2.6 69.7 1.0 CD A:GLU470 3.6 55.1 1.0 O A:SER547 3.6 60.5 1.0 CB A:ASP528 3.7 65.7 1.0 OG A:SER547 3.8 65.1 1.0 O A:ASN494 4.1 68.8 1.0 OE2 A:GLU470 4.3 57.4 1.0 CG A:GLU470 4.4 48.0 1.0 N A:SER547 4.5 61.6 1.0 OP1 F:DG11 4.5 64.5 1.0 C A:SER547 4.6 60.4 1.0 OD2 A:ASP474 4.7 42.5 1.0 CA A:ASP528 4.9 64.3 1.0 CB A:SER547 4.9 62.8 1.0 CA A:SER547 4.9 61.3 1.0 CE A:LYS548 5.0 71.0 1.0 OE1 A:GLU546 5.0 79.8 1.0

Calcium binding site 4 out of 6 in the Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ca701 b:20.8 occ:1.00 O Z:PHE110 2.1 30.6 1.0 OD2 Z:ASP91 2.2 35.3 1.0 OP1 V:DC6 2.7 37.6 1.0 OE2 Z:GLU109 2.7 40.3 1.0 CG Z:ASP91 3.0 33.7 1.0 OD1 Z:ASP91 3.2 34.2 1.0 OD1 Z:ASP499 3.3 74.3 1.0 C Z:PHE110 3.3 30.3 1.0 OD2 Z:ASP499 3.4 76.1 1.0 NH2 Z:ARG123 3.5 37.2 1.0 CD Z:GLU109 3.6 38.5 1.0 CG Z:ASP499 3.7 74.0 1.0 N Z:PHE110 3.8 28.9 1.0 P V:DC6 4.0 37.4 1.0 CA Z:PHE110 4.0 29.6 1.0 N Z:CYS111 4.3 30.8 1.0 CG Z:GLU109 4.3 32.7 1.0 CB Z:PHE110 4.4 29.4 1.0 CA Z:CA702 4.4 31.6 1.0 OE1 Z:GLU109 4.4 40.0 1.0 CA Z:CYS111 4.5 31.9 1.0 CB Z:ASP91 4.5 30.5 1.0 O5' V:DC6 4.5 37.3 1.0 C5' V:DC6 4.6 37.6 1.0 CZ Z:ARG123 4.7 36.9 1.0 OE1 Z:GLU13 4.8 42.3 1.0 C Z:GLU109 4.8 28.5 1.0 OP2 V:DC6 4.8 37.2 1.0 OP1 V:DA7 4.9 39.1 1.0 CB Z:CYS111 4.9 33.4 1.0

Calcium binding site 5 out of 6 in the Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ca702 b:31.6 occ:1.00 OD2 Z:ASP9 2.1 42.2 1.0 OD1 Z:ASP91 2.2 34.2 1.0 OP1 V:DC6 2.8 37.6 1.0 O3' V:DG5 2.8 37.7 1.0 O Z:HOH809 2.9 16.5 1.0 CG Z:ASP9 3.0 39.7 1.0 OD1 Z:ASP9 3.4 40.5 1.0 CG Z:ASP91 3.4 33.7 1.0 P V:DC6 3.4 37.4 1.0 O Z:GLY497 4.0 66.0 1.0 C5' V:DC6 4.0 37.6 1.0 C3' V:DG5 4.1 37.9 1.0 CA Z:ASP91 4.1 29.5 1.0 OD2 Z:ASP91 4.2 35.3 1.0 CB Z:ASP9 4.2 34.4 1.0 CB Z:ASP91 4.2 30.5 1.0 O5' V:DC6 4.3 37.3 1.0 C4' V:DG5 4.3 38.1 1.0 CA Z:CA701 4.4 20.8 1.0 N Z:ASP91 4.6 28.6 1.0 OE2 Z:GLU109 4.6 40.3 1.0 C2' V:DG5 4.6 37.8 1.0 O Z:THR89 4.7 28.3 1.0 OP2 V:DC6 4.7 37.2 1.0 O Z:PRO90 4.8 28.1 1.0 OE1 Z:GLU109 4.8 40.0 1.0 OD1 Z:ASP499 4.9 74.3 1.0 C Z:PRO90 4.9 28.3 1.0 OE1 Z:GLU13 4.9 42.3 1.0 C5' V:DG5 4.9 38.4 1.0

Calcium binding site 6 out of 6 in the Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Bsmi (Wild-Type) Crystallized with CA2+ and Cognate Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ca703 b:68.2 occ:1.00 OE1 Z:GLU470 2.2 48.5 1.0 OD2 Z:ASP528 2.3 69.3 1.0 CG Z:ASP528 2.9 67.2 1.0 O Z:SER547 3.0 48.2 1.0 CD Z:GLU470 3.1 47.4 1.0 OD1 Z:ASP528 3.2 67.5 1.0 OP1 U:DG11 3.7 53.9 1.0 OG Z:SER547 3.7 52.3 1.0 OE2 Z:GLU470 3.8 49.4 1.0 CG Z:GLU470 4.0 41.7 1.0 C Z:SER547 4.1 48.1 1.0 CB Z:ASP528 4.2 63.3 1.0 N Z:SER547 4.3 48.4 1.0 CE Z:LYS548 4.3 61.7 1.0 C5' U:DG11 4.5 55.6 1.0 CA Z:SER547 4.6 48.5 1.0 CB Z:SER547 4.8 49.9 1.0 O Z:ASN494 4.9 64.9 1.0 OD2 Z:ASP474 4.9 39.1 1.0 CD Z:GLU546 4.9 61.2 1.0 CD Z:LYS548 5.0 57.9 1.0 P U:DG11 5.0 53.9 1.0

R.Sieskind, S.Missoury, C.Madru, I.Commenge, G.Niogret, M.Hollenstein, Y.Rondelez, L.Sauguet, A.Haouz, P.Legrand, M.Delarue. Crystal Structures of Monomeric Bsmi Restriction Endonuclease Reveal Coordinated Sequential Cleavage of Two Dna Strands. Commun Biol V. 8 387 2025.
ISSN: ESSN 2399-3642
PubMed: 40055548
DOI: 10.1038/S42003-025-07612-Z