Magnesium in PDB 9izs: Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State

The binding sites of Magnesium atom in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State (pdb code 9izs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State, PDB code: 9izs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State


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 CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:29.9 occ:1.00 OD1 A:ASP499 2.1 30.7 1.0 OP1 B:G-30 2.1 36.0 1.0 CG A:ASP499 3.1 27.2 1.0 OD2 A:ASP499 3.4 31.1 1.0 P B:G-30 3.5 33.9 1.0 OP2 B:G-30 4.1 28.1 1.0 NE2 A:GLN498 4.1 35.8 1.0 O5' B:G-30 4.2 39.1 1.0 CB A:ASP499 4.4 21.2 1.0 O A:ASN495 4.5 33.3 1.0 O3' B:U-31 4.6 30.4 1.0 C5' B:G-30 4.6 26.7 1.0 CD A:GLN498 4.6 28.7 1.0 OP2 B:U-29 4.7 23.8 1.0 CG A:GLN498 4.8 27.6 1.0 CA A:ASP499 4.8 27.4 1.0 N A:ASP499 4.8 29.3 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State


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 CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:48.4 occ:1.00 OD1 A:ASP324 2.0 42.4 1.0 OP1 D:GS-1 2.1 49.8 1.0 OE1 A:GLU526 2.1 41.9 1.0 OE2 A:GLU526 2.5 54.0 1.0 CD A:GLU526 2.6 49.6 1.0 CG A:ASP324 3.2 38.0 1.0 P D:GS-1 3.5 47.7 1.0 OD2 A:ASP324 3.7 32.9 1.0 O A:VAL325 3.8 41.0 1.0 N A:VAL325 4.1 35.3 1.0 CG A:GLU526 4.1 43.0 1.0 C4' D:GS-2 4.2 43.8 1.0 S2P D:GS-1 4.2 74.1 1.0 O3' D:GS-2 4.3 49.5 1.0 CB A:ASP324 4.4 33.5 1.0 OG1 A:THR638 4.5 50.7 1.0 CA A:ASP324 4.6 28.8 1.0 O5' D:GS-1 4.6 47.7 1.0 C A:VAL325 4.7 38.8 1.0 C3' D:GS-2 4.7 48.8 1.0 C5' D:GS-1 4.7 45.3 1.0 MG A:MG803 4.8 67.7 1.0 C A:ASP324 4.9 33.9 1.0 CA A:VAL325 4.9 35.7 1.0 C2' D:GS-2 4.9 46.8 1.0 CB A:GLU526 4.9 39.7 1.0 OD1 A:ASN326 4.9 41.0 1.0 O4' D:GS-2 5.0 43.7 1.0 C5' D:GS-2 5.0 42.4 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State


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 CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:67.7 occ:1.00 OD2 A:ASP324 2.0 32.9 1.0 OD1 A:ASN326 2.1 41.0 1.0 OD1 A:ASP680 2.2 55.1 1.0 S2P D:GS-1 2.5 74.1 1.0 CG A:ASN326 3.2 34.6 1.0 CG A:ASP324 3.2 38.0 1.0 CG A:ASP680 3.3 45.1 1.0 CA A:ASP680 3.9 41.1 1.0 OD1 A:ASP324 3.9 42.4 1.0 ND2 A:ASN326 4.0 37.2 1.0 CB A:ASP680 4.0 40.4 1.0 CB A:ASN326 4.2 31.9 1.0 CB A:ALA683 4.2 40.7 1.0 N A:ASP680 4.2 46.6 1.0 OD2 A:ASP680 4.3 46.0 1.0 P D:GS-1 4.3 47.7 1.0 CB A:ASP324 4.3 33.5 1.0 OP1 D:GS-1 4.4 49.8 1.0 NH2 A:ARG667 4.5 50.0 1.0 O A:ALA679 4.6 42.7 1.0 C A:ALA679 4.6 45.2 1.0 O A:VAL325 4.7 41.0 1.0 MG A:MG802 4.8 48.4 1.0 CB A:SER639 4.8 42.9 1.0 O5' D:GS-1 5.0 47.7 1.0 CA A:ASN326 5.0 33.8 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State


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 CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:30.9 occ:1.00 O6 B:G-30 3.2 23.0 1.0 O4 B:U-31 3.3 17.0 1.0 O4 B:U-29 3.4 35.0 1.0 N6 B:A-5 4.1 25.1 1.0 C4 B:U-31 4.1 15.3 1.0 C6 B:G-30 4.2 19.1 1.0 N7 B:G-30 4.2 20.7 1.0 N6 B:A-3 4.3 11.9 1.0 C4 B:U-29 4.5 26.2 1.0 C5 B:G-30 4.6 18.0 1.0 N4 B:C-4 4.6 29.9 1.0 C5 B:U-31 4.6 16.3 1.0 N3 B:U-31 4.9 14.4 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State


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 CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Ts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:20.9 occ:1.00 OP2 B:U-31 2.3 25.1 1.0 C5 B:U-31 3.5 16.3 1.0 O5' B:U-32 3.6 27.3 1.0 OP2 B:U-32 3.6 28.3 1.0 P B:U-31 3.6 28.6 1.0 C3' B:U-32 3.9 23.4 1.0 C6 B:U-31 4.0 17.5 1.0 P B:U-32 4.0 30.5 1.0 O5' B:U-31 4.1 26.9 1.0 O3' B:U-32 4.2 24.2 1.0 OP1 B:U-32 4.5 28.6 1.0 C6 B:U-32 4.5 15.8 1.0 C5' B:U-32 4.6 26.0 1.0 C4 B:U-31 4.7 15.3 1.0 C2' B:U-32 4.8 23.5 1.0 C4' B:U-32 4.8 24.1 1.0 C5 B:U-32 4.8 13.0 1.0 OP1 B:U-31 4.8 25.9 1.0 O4 B:U-31 5.0 17.0 1.0 N1 B:U-32 5.0 17.1 1.0

S.N.Omura, H.Hirano, Y.Itoh, O.Nureki. Structural Basis For the Target Dna Cleavage and Guide Rna Processing By the Crispr-CASLAMBDA2 To Be Published.