Magnesium in PDB 7vti: Crystal Structure of the CAS13BT3-Crrna Binary Complex

The structure of Crystal Structure of the CAS13BT3-Crrna Binary Complex, PDB code: 7vti was solved by R.Nakagawa, N.S.Takeda, A.Tomita, H.Hirano, T.Kusakizako, T.Nishizawa, K.Yamashita, H.Nishimasu, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.99 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.434, 95.452, 125.283, 90, 90, 90
R / Rfree (%)	19.6 / 24.3

The structure of Crystal Structure of the CAS13BT3-Crrna Binary Complex also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Chlorine	(Cl)	5 atoms

The binding sites of Magnesium atom in the Crystal Structure of the CAS13BT3-Crrna Binary Complex (pdb code 7vti). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the CAS13BT3-Crrna Binary Complex, PDB code: 7vti:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the CAS13BT3-Crrna Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the CAS13BT3-Crrna Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:34.1 occ:1.00 O6 B:G10 2.2 29.4 1.0 O2' B:G7 2.3 31.8 1.0 O6 B:G26 2.3 29.9 1.0 O B:HOH219 2.4 44.3 1.0 O B:HOH247 2.5 31.7 1.0 O4 B:U27 2.6 31.2 1.0 C6 B:G10 3.3 26.8 1.0 N3 B:U27 3.4 34.0 1.0 C6 B:G26 3.4 27.8 1.0 C4 B:U27 3.4 34.1 1.0 C2' B:G7 3.4 30.5 1.0 O B:HOH201 3.6 36.2 1.0 N4 B:C11 3.7 31.5 1.0 O B:HOH278 3.9 36.4 1.0 NH2 A:ARG374 3.9 75.8 1.0 N7 B:G10 4.0 29.0 1.0 C5 B:G10 4.0 28.4 1.0 N1 B:G26 4.1 29.4 1.0 O A:HOH933 4.3 41.3 1.0 C5 B:G26 4.3 33.7 1.0 O3' B:G7 4.4 32.7 1.0 OP2 B:C8 4.4 32.0 1.0 N7 B:A9 4.4 30.8 1.0 N1 B:G10 4.5 28.6 1.0 C4 B:C11 4.5 32.9 1.0 C3' B:G7 4.5 29.9 1.0 C1' B:G7 4.5 32.1 1.0 C2 B:U27 4.6 30.2 1.0 N6 B:A9 4.6 28.3 1.0 OP2 B:A9 4.7 31.3 1.0 N3 B:C11 4.7 31.2 1.0 N7 B:G26 4.7 34.7 1.0 C5 B:U27 4.8 32.5 1.0 CZ A:ARG374 4.9 68.7 1.0 O2 B:U27 5.0 29.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the CAS13BT3-Crrna Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the CAS13BT3-Crrna Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:51.3 occ:1.00 N7 B:G4 2.1 36.3 1.0 O B:HOH286 2.2 49.6 1.0 O B:HOH283 2.4 47.8 1.0 O B:HOH235 2.6 41.0 1.0 O B:HOH281 2.7 45.7 1.0 O B:HOH212 2.9 43.8 1.0 C8 B:G4 2.9 33.1 1.0 C5 B:G4 3.2 38.1 1.0 MG B:MG103 3.5 47.3 1.0 O6 B:G4 3.8 33.0 1.0 C6 B:G4 3.9 34.2 1.0 O B:HOH263 4.0 48.6 1.0 C5 B:U3 4.1 38.3 1.0 N9 B:G4 4.1 38.1 1.0 C4 B:U3 4.2 34.9 1.0 C4 B:G4 4.3 36.3 1.0 O4 B:U3 4.4 37.0 1.0 C6 B:U3 4.4 38.5 1.0 OP2 B:G4 4.5 44.1 1.0 N3 B:U3 4.6 35.4 1.0 N7 B:G5 4.6 34.7 1.0 O B:HOH246 4.7 36.9 1.0 N1 B:U3 4.8 38.4 1.0 NZ A:LYS511 4.9 53.5 1.0 C2 B:U3 4.9 39.7 1.0 OP2 B:A29 4.9 35.7 1.0 O B:HOH260 5.0 45.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the CAS13BT3-Crrna Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the CAS13BT3-Crrna Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:47.3 occ:1.00 O6 B:G5 2.2 31.8 1.0 O6 B:G4 2.2 33.0 1.0 O4 B:U31 2.2 34.7 1.0 O B:HOH283 2.3 47.8 1.0 O B:HOH286 2.7 49.6 1.0 O B:HOH263 2.8 48.6 1.0 C6 B:G4 3.1 34.2 1.0 C4 B:U31 3.2 32.8 1.0 N3 B:U31 3.3 32.0 1.0 C6 B:G5 3.3 30.9 1.0 MG B:MG102 3.5 51.3 1.0 N6 B:A6 3.8 34.2 1.0 C5 B:G4 3.9 38.1 1.0 N4 B:C33 3.9 36.0 1.0 N7 B:G5 4.0 34.7 1.0 C5 B:G5 4.0 32.4 1.0 N7 B:G4 4.0 36.3 1.0 N1 B:G4 4.1 34.7 1.0 O B:HOH212 4.2 43.8 1.0 O2' B:A29 4.4 34.3 1.0 N1 B:G5 4.5 29.5 1.0 O B:HOH246 4.5 36.9 1.0 C6 B:A6 4.5 34.3 1.0 C5 B:U31 4.6 37.5 1.0 C2 B:U31 4.6 31.9 1.0 O4 B:U3 4.7 37.0 1.0 C4 B:C33 4.8 40.0 1.0 N3 B:C33 4.9 34.9 1.0

R.Nakagawa, S.Kannan, H.Altae-Tran, S.N.Takeda, A.Tomita, H.Hirano, T.Kusakizako, T.Nishizawa, K.Yamashita, F.Zhang, H.Nishimasu, O.Nureki. Structure and Engineering of the Minimal Type VI Crispr-CAS13BT3. Mol.Cell V. 82 3178 2022.
ISSN: ISSN 1097-2765
PubMed: 36027912
DOI: 10.1016/J.MOLCEL.2022.08.001