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

The binding sites of Magnesium atom in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-Cleaving State (pdb code 9izr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-Cleaving State, PDB code: 9izr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-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 Nts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:24.2 occ:1.00 OD1 A:ASP499 2.1 31.9 1.0 OP1 B:G-30 2.1 37.1 1.0 CG A:ASP499 3.2 26.9 1.0 P B:G-30 3.4 33.7 1.0 OD2 A:ASP499 3.7 32.1 1.0 O5' B:G-30 4.0 28.4 1.0 OP2 B:G-30 4.2 27.9 1.0 NE2 A:GLN498 4.2 35.8 1.0 CB A:ASP499 4.4 22.9 1.0 C5' B:G-30 4.5 21.2 1.0 O A:ASN495 4.5 28.0 1.0 OP2 B:U-29 4.6 28.9 1.0 O3' B:U-31 4.6 26.4 1.0 CA A:ASP499 4.8 24.9 1.0 N A:ASP499 4.8 27.0 1.0 CD A:GLN498 4.9 29.6 1.0

Magnesium binding site 2 out of 8 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-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 Nts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:49.1 occ:1.00 OE2 A:GLU526 1.8 63.8 1.0 OD1 A:ASP324 2.0 41.4 1.0 OE1 A:GLU526 2.1 49.9 1.0 CD A:GLU526 2.2 59.7 1.0 OP1 A:AS806 3.1 45.7 1.0 CG A:ASP324 3.2 37.5 1.0 O3' A:SC805 3.3 55.0 1.0 CG A:GLU526 3.7 46.5 1.0 P A:AS806 3.8 48.2 1.0 OD2 A:ASP324 3.8 32.8 1.0 O A:VAL325 4.0 42.5 1.0 N A:VAL325 4.1 33.8 1.0 O5' A:AS806 4.1 49.5 1.0 CB A:ASP324 4.4 30.2 1.0 C4' A:SC805 4.5 41.7 1.0 C3' A:SC805 4.5 43.7 1.0 CA A:ASP324 4.5 26.6 1.0 CB A:GLU526 4.6 38.3 1.0 C5' A:AS806 4.7 54.6 1.0 C A:VAL325 4.8 35.1 1.0 C A:ASP324 4.8 29.1 1.0 CZ A:PHE612 5.0 46.5 1.0 CA A:VAL325 5.0 30.9 1.0 C5' A:SC805 5.0 44.7 1.0

Magnesium binding site 3 out of 8 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-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 Nts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:50.2 occ:1.00 OD2 A:ASP324 2.1 32.8 1.0 OD1 A:ASP680 2.1 61.2 1.0 OD1 A:ASN326 2.2 45.5 1.0 CG A:ASP680 3.0 50.9 1.0 CG A:ASN326 3.2 35.4 1.0 CG A:ASP324 3.3 37.5 1.0 OP1 A:AS806 3.3 45.7 1.0 CB A:ASP680 3.5 37.0 1.0 CA A:ASP680 3.5 37.6 1.0 ND2 A:ASN326 3.6 31.2 1.0 O A:ALA679 3.8 41.2 1.0 OD1 A:ASP324 4.0 41.4 1.0 OD2 A:ASP680 4.0 51.9 1.0 N A:ASP680 4.1 43.7 1.0 C A:ALA679 4.3 42.9 1.0 CB A:ASP324 4.3 30.2 1.0 CB A:ALA683 4.5 25.9 1.0 CB A:ASN326 4.5 33.5 1.0 P A:AS806 4.6 48.2 1.0 O5' A:AS806 4.7 49.5 1.0 NH1 A:ARG667 4.8 56.9 1.0 C A:ASP680 4.8 36.7 1.0 O A:ASP680 4.9 40.6 1.0

Magnesium binding site 4 out of 8 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-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 Nts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:46.8 occ:1.00 MG B:MG103 4.2 15.3 1.0 O4 B:U-31 4.4 16.0 1.0 C5 B:U-31 4.7 15.9 1.0 C4 B:U-31 4.9 15.4 1.0

Magnesium binding site 5 out of 8 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-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 Nts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:43.1 occ:1.00 O4 B:U-23 2.2 50.2 1.0 C4 B:U-23 3.4 51.5 1.0 C5 B:U-23 4.3 58.2 1.0 N3 B:U-23 4.4 51.0 1.0 N6 B:A-24 4.9 57.4 1.0 N7 B:A-24 4.9 66.4 1.0 O6 B:G-13 5.0 28.7 1.0

Magnesium binding site 6 out of 8 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-Cleaving State


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 CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:15.3 occ:1.00 OP2 B:U-31 2.0 25.6 1.0 O5' B:U-32 3.2 23.8 1.0 P B:U-31 3.4 28.9 1.0 OP2 B:U-32 3.4 26.3 1.0 C3' B:U-32 3.6 21.0 1.0 P B:U-32 3.8 26.3 1.0 C5 B:U-31 3.9 15.9 1.0 O3' B:U-32 3.9 23.7 1.0 O5' B:U-31 4.1 29.8 1.0 OP1 B:U-32 4.2 31.1 1.0 MG B:MG101 4.2 46.8 1.0 C5' B:U-32 4.3 19.8 1.0 C6 B:U-31 4.3 14.2 1.0 C6 B:U-32 4.4 14.6 1.0 C4' B:U-32 4.5 19.3 1.0 C2' B:U-32 4.5 21.0 1.0 OP1 B:U-31 4.5 34.7 1.0 C5 B:U-32 4.8 14.0 1.0 N1 B:U-32 4.9 15.8 1.0

Magnesium binding site 7 out of 8 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-Cleaving State


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 CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:43.0 occ:1.00 O2 B:U-19 2.2 34.2 1.0 OP2 B:A-16 2.3 37.6 1.0 P B:A-16 3.3 37.4 1.0 O5' B:A-16 3.4 30.4 1.0 C2 B:U-19 3.5 33.3 1.0 C8 B:A-16 3.8 29.2 1.0 CD1 A:ILE442 4.0 34.5 1.0 OP1 B:A-16 4.0 31.8 1.0 C2' B:A-16 4.1 35.7 1.0 C1' B:U-19 4.2 43.5 1.0 N1 B:U-19 4.3 37.0 1.0 N7 B:A-16 4.3 31.1 1.0 N3 B:U-19 4.4 30.9 1.0 N9 B:A-16 4.5 26.6 1.0 C5' B:A-16 4.6 28.4 1.0 O3' B:U-17 4.6 36.1 1.0 O2' B:A-16 4.7 43.7 1.0 C1' B:A-16 4.8 28.2 1.0 C3' B:A-16 4.9 33.5 1.0 O2' B:U-19 5.0 40.7 1.0 O4' B:U-19 5.0 43.8 1.0 C3' B:U-17 5.0 33.0 1.0

Magnesium binding site 8 out of 8 in the Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-Cleaving State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of CASLAMBDA2-Crrna-Target Dna Ternary Complex in the Nts-Cleaving State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:46.1 occ:1.00 OP1 D:DA15 3.6 51.8 1.0 O5' D:DA15 4.3 52.5 1.0 OP2 D:DT16 4.4 53.1 1.0 P D:DA15 4.4 49.5 1.0 OD1 A:ASN527 4.5 43.6 1.0 CE A:LYS616 4.5 39.7 1.0 OD2 A:ASP715 4.7 69.1 1.0 OP2 D:DA15 4.8 47.4 1.0 C5' D:DA15 4.8 39.5 1.0 C3' D:DA15 4.9 38.5 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.