Magnesium in PDB 8j12: Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex

The structure of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex (pdb code 8j12). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex, PDB code: 8j12:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:60.7 occ:1.00 OD2 A:ASP141 2.5 83.6 1.0 OD1 A:ASP141 2.8 85.8 1.0 CG A:ASP141 3.0 83.8 1.0 OP1 C:C-88 4.1 63.8 1.0 OP1 C:C-87 4.4 75.2 1.0 CB A:ASP141 4.5 76.2 1.0 OP2 C:C-87 4.8 72.2 1.0

Magnesium binding site 2 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:75.2 occ:1.00 NH2 B:ARG214 3.7 88.3 1.0 OE1 B:GLU316 4.3 82.8 1.0 OE2 B:GLU316 4.5 83.4 1.0 C5 C:U16 4.6 68.7 1.0 CZ B:ARG214 4.6 89.1 1.0 NH1 B:ARG214 4.6 90.1 1.0 O4 C:U16 4.7 80.9 1.0 CD B:GLU316 4.8 82.7 1.0 C4 C:U16 4.9 73.5 1.0 O6 C:G17 5.0 78.5 1.0 OP2 C:U16 5.0 74.1 1.0

Magnesium binding site 3 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:34.6 occ:1.00 N6 C:A-182 4.4 68.0 1.0 O6 C:G-187 4.6 74.0 1.0 N7 C:A-182 4.9 68.7 1.0

Magnesium binding site 4 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:26.7 occ:1.00 O4 C:U-5 3.9 69.6 1.0 O6 C:G-4 4.1 70.4 1.0 O4 C:U-185 4.3 77.6 1.0 N6 C:A-3 4.3 66.5 1.0 C4 C:U-5 4.4 64.7 1.0 C5 C:U-5 4.8 63.8 1.0 N7 C:G-4 4.9 61.3 1.0 O6 C:G-186 4.9 69.5 1.0 O4 C:U-184 4.9 77.6 1.0

Magnesium binding site 5 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg103 b:54.5 occ:1.00 O6 C:G-122 4.2 74.8 1.0 N7 C:G-122 4.2 58.8 1.0 O2' C:C-188 4.7 71.5 1.0 C4' C:C-188 4.8 63.9 1.0 OP1 C:A-89 4.8 76.6 1.0 OP2 C:A-89 4.8 76.4 1.0 C6 C:G-122 5.0 71.5 1.0 C5 C:G-122 5.0 62.2 1.0

Magnesium binding site 6 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg104 b:65.8 occ:1.00 N7 C:G-82 4.3 86.8 1.0 N7 C:G-81 4.4 85.6 1.0 O6 C:G-81 4.5 97.1 1.0 O6 C:G-82 4.6 86.9 1.0 C5 C:G-82 5.0 79.8 1.0

Magnesium binding site 7 out of 7 in the Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of the ASCAS12F-Sgrna-Target Dna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg105 b:30.0 occ:1.00 OP2 C:A-106 2.9 65.6 1.0 P C:A-106 4.2 78.3 1.0 N7 C:A-105 4.2 63.1 1.0 N6 C:A-105 4.2 72.0 1.0 O2' C:G-107 4.3 82.9 1.0 O5' C:A-106 4.4 75.8 1.0 OP2 C:A-105 4.5 72.9 1.0 C8 C:A-106 4.8 71.6 1.0 O3' C:G-107 4.8 77.5 1.0 N7 C:A-106 4.9 70.5 1.0 C5 C:A-105 5.0 57.4 1.0

T.Hino, N.S.Omura, R.Nakagawa, T.Togashi, N.S.Takeda, T.Hiramoto, S.Tasaka, H.Hirano, T.Tokuyama, H.Uosaki, H.Ishiguro, H.Yamano, Y.Ozaki, D.Motooka, H.Mori, Y.Kirita, Y.Kise, Y.Itoh, S.Matoba, H.Aburatani, N.Yachie, V.Siksnys, T.Ohmori, A.Hoshino, O.Nureki. Minimal and Most Efficient Genome Editing Cas Enzyme To Be Published.