Magnesium in PDB 8t6x: Spry-CAS9:Grna Complex Targeting Tac Pam Dna with 18 Bp R-Loop

The binding sites of Magnesium atom in the Spry-CAS9:Grna Complex Targeting Tac Pam Dna with 18 Bp R-Loop (pdb code 8t6x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Spry-CAS9:Grna Complex Targeting Tac Pam Dna with 18 Bp R-Loop, PDB code: 8t6x:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Spry-CAS9:Grna Complex Targeting Tac Pam Dna with 18 Bp R-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Spry-CAS9:Grna Complex Targeting Tac Pam Dna with 18 Bp R-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:148.3 occ:1.00 OP2 D:DC34 2.1 210.3 1.0 ND1 A:HIS983 2.1 131.1 1.0 OD2 A:ASP10 2.2 140.9 1.0 CE1 A:HIS983 2.8 136.2 1.0 OG A:SER15 3.0 131.2 1.0 CG A:ASP10 3.2 141.4 1.0 CG A:HIS983 3.3 131.4 1.0 P D:DC34 3.4 217.9 1.0 OD1 A:ASP10 3.6 141.0 1.0 C5' D:DC34 3.8 211.1 1.0 CB A:HIS983 3.8 134.2 1.0 O5' D:DC34 3.9 210.7 1.0 NE2 A:HIS983 4.0 137.3 1.0 CA A:HIS983 4.1 135.3 1.0 CB A:SER15 4.2 133.3 1.0 OP1 D:DC34 4.2 210.8 1.0 CD2 A:HIS983 4.3 130.6 1.0 CB A:ASP10 4.5 137.2 1.0 NH2 A:ARG976 4.5 171.0 1.0 OP2 D:DG35 4.7 234.8 1.0 N A:GLY12 4.7 141.4 1.0 O A:ASP10 4.8 140.8 1.0 O A:SER15 4.9 134.2 1.0 C4' D:DC34 5.0 210.2 1.0 C A:ASP10 5.0 137.4 1.0

Magnesium binding site 2 out of 3 in the Spry-CAS9:Grna Complex Targeting Tac Pam Dna with 18 Bp R-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Spry-CAS9:Grna Complex Targeting Tac Pam Dna with 18 Bp R-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1402 b:111.2 occ:1.00 OG1 A:THR1102 2.3 113.8 1.0 OP2 B:A65 2.8 136.8 1.0 O4 B:U66 3.5 155.1 1.0 OP1 B:U64 3.6 130.2 1.0 CB A:THR1102 3.7 108.2 1.0 OP2 B:U64 4.0 128.3 1.0 P B:A65 4.1 148.3 1.0 P B:U64 4.2 128.8 1.0 C4 B:U66 4.3 151.9 1.0 C5 B:U66 4.4 146.4 1.0 CG2 A:THR1102 4.5 110.4 1.0 O A:THR1102 4.6 101.3 1.0 O5' B:A65 4.6 139.5 1.0 CA A:THR1102 4.6 100.7 1.0 N A:THR1102 4.7 98.8 1.0 N7 B:A65 4.7 140.5 1.0 N4 B:C67 4.8 137.3 1.0 C A:THR1102 4.8 102.4 1.0 O5' B:U64 4.9 118.8 1.0 OP1 B:A65 4.9 139.6 1.0

Magnesium binding site 3 out of 3 in the Spry-CAS9:Grna Complex Targeting Tac Pam Dna with 18 Bp R-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Spry-CAS9:Grna Complex Targeting Tac Pam Dna with 18 Bp R-Loop within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:274.7 occ:1.00 OD1 A:ASP839 2.0 318.2 1.0 OP1 C:DT23 2.1 215.4 1.0 O3' C:DG22 2.1 197.1 1.0 OD1 A:ASN863 2.1 277.3 1.0 P C:DT23 2.4 219.3 1.0 OP2 C:DT23 3.1 210.2 1.0 CG A:ASP839 3.1 318.5 1.0 CG A:ASN863 3.2 276.2 1.0 C3' C:DG22 3.5 191.2 1.0 CA A:ASP839 3.5 318.0 1.0 CB A:ASP839 3.7 318.9 1.0 N A:HIS840 3.7 320.5 1.0 ND2 A:ASN863 3.7 275.3 1.0 O5' C:DT23 3.8 211.3 1.0 C4' C:DG22 4.0 189.0 1.0 OD2 A:ASP839 4.1 318.1 1.0 C A:ASP839 4.2 318.0 1.0 C2' C:DG22 4.3 190.3 1.0 O A:HIS840 4.4 321.7 1.0 O A:ASN863 4.4 274.8 1.0 CB A:ASN863 4.5 276.6 1.0 C5' C:DG22 4.5 190.2 1.0 O A:LYS866 4.5 275.7 1.0 O A:VAL838 4.6 295.1 1.0 C5' C:DT23 4.6 207.9 1.0 N A:ASP839 4.6 317.5 1.0 CA A:HIS840 4.9 321.1 1.0 CA A:ASN863 4.9 276.1 1.0

G.N.Hibshman, J.P.K.Bravo, D.W.Taylor. Unraveling the Mechanisms of Pamless Dna Interrogation By Spry-CAS9 Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-47830-3