Magnesium in PDB 8spq: Spry-CAS9:Grna Complex Targeting Tgg Pam Dna

The binding sites of Magnesium atom in the Spry-CAS9:Grna Complex Targeting Tgg Pam Dna (pdb code 8spq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Spry-CAS9:Grna Complex Targeting Tgg Pam Dna, PDB code: 8spq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Spry-CAS9:Grna Complex Targeting Tgg Pam Dna


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 Tgg Pam Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:105.3 occ:1.00 OP1 D:DC34 2.1 121.1 1.0 OD1 A:ASP10 2.5 98.1 1.0 CG A:GLU762 3.2 109.7 1.0 P D:DC34 3.5 116.4 1.0 CG A:ASP10 3.7 95.2 1.0 O5' D:DC34 4.1 119.7 1.0 CB A:GLU762 4.2 106.5 1.0 OD2 A:ASP10 4.3 95.8 1.0 CD A:GLU762 4.3 114.4 1.0 OP2 D:DC34 4.3 109.7 1.0 OG A:SER960 4.5 118.7 1.0 O A:ILE11 4.8 98.6 1.0 CB A:ASP10 4.9 87.5 1.0 OE1 A:GLU762 4.9 115.0 1.0 OE2 A:GLU762 4.9 118.3 1.0 O A:GLU762 4.9 111.5 1.0

Magnesium binding site 2 out of 4 in the Spry-CAS9:Grna Complex Targeting Tgg Pam Dna


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 Tgg Pam Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1402 b:117.0 occ:1.00 OP2 D:DC34 2.0 109.7 1.0 ND1 A:HIS983 2.4 95.8 1.0 OD2 A:ASP10 2.9 95.8 1.0 CE1 A:HIS983 3.1 99.2 1.0 P D:DC34 3.1 116.4 1.0 OD2 A:ASP986 3.1 105.0 1.0 CG A:HIS983 3.4 92.0 1.0 CA A:HIS983 3.4 93.8 1.0 CD2 A:HIS982 3.6 103.3 1.0 OP1 D:DC34 3.8 121.1 1.0 N A:HIS983 3.8 96.8 1.0 CG A:ASP10 3.8 95.2 1.0 CB A:HIS983 3.9 88.0 1.0 CG A:ASP986 3.9 103.4 1.0 O A:HIS982 4.1 110.0 1.0 C A:HIS982 4.2 105.1 1.0 CB A:ASP986 4.2 102.1 1.0 NE2 A:HIS983 4.2 101.8 1.0 OD1 A:ASP10 4.2 98.1 1.0 NE2 A:HIS982 4.2 100.6 1.0 CD2 A:HIS983 4.4 97.3 1.0 NZ A:LYS974 4.4 105.2 1.0 O5' D:DC34 4.4 119.7 1.0 CG A:HIS982 4.5 101.4 1.0 C A:HIS983 4.6 98.5 1.0 NH1 A:ARG976 4.7 129.7 1.0 C5' D:DC34 4.8 120.3 1.0 O A:HIS983 4.8 108.2 1.0 NH2 A:ARG976 4.9 121.5 1.0 OD1 A:ASP986 4.9 103.7 1.0 CB A:HIS982 5.0 100.4 1.0

Magnesium binding site 3 out of 4 in the Spry-CAS9:Grna Complex Targeting Tgg Pam Dna


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 Tgg Pam Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1403 b:90.4 occ:1.00 OP3 E:DT0 2.3 116.3 1.0 OD1 A:ASN863 2.4 116.9 1.0 OD2 A:ASP839 2.7 115.7 1.0 CB A:ASP839 2.9 114.1 1.0 CG A:ASP839 3.2 116.7 1.0 CG A:ASN863 3.5 113.5 1.0 O A:HIS840 3.7 120.0 1.0 P E:DT0 3.7 125.5 1.0 CE A:LYS866 3.8 111.0 1.0 O A:LYS866 3.8 124.5 1.0 NZ A:LYS866 3.9 114.4 1.0 N A:HIS840 3.9 117.2 1.0 CA A:ASP839 3.9 113.2 1.0 O3' C:DG22 3.9 129.6 1.0 C3' C:DG22 4.1 123.7 1.0 ND2 A:ASN863 4.2 118.5 1.0 O5' E:DT0 4.3 117.2 1.0 C A:ASP839 4.3 114.1 1.0 OD1 A:ASP839 4.4 119.7 1.0 O A:ASN863 4.5 122.9 1.0 OP1 E:DT0 4.5 125.5 1.0 OP2 E:DT0 4.5 119.2 1.0 C A:HIS840 4.6 117.9 1.0 CB A:ASN863 4.7 111.4 1.0 CD A:LYS866 4.7 113.8 1.0 CA A:HIS840 4.8 120.4 1.0 CA A:ASN863 5.0 109.1 1.0

Magnesium binding site 4 out of 4 in the Spry-CAS9:Grna Complex Targeting Tgg Pam Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Spry-CAS9:Grna Complex Targeting Tgg Pam Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:109.1 occ:1.00 OP2 B:A65 2.5 136.9 1.0 O4 B:U66 2.9 145.8 1.0 OG1 A:THR1102 3.2 128.7 1.0 P B:A65 3.8 137.5 1.0 C4 B:U66 3.9 147.6 1.0 CG2 A:THR1102 3.9 125.9 1.0 CB A:THR1102 4.1 122.3 1.0 N4 B:C67 4.1 155.4 1.0 C5 B:U66 4.2 149.5 1.0 OP1 B:U64 4.2 126.2 1.0 OP1 B:A65 4.3 133.4 1.0 O5' B:A65 4.4 126.8 1.0 N A:THR1102 4.6 120.1 1.0 O A:VAL1100 4.8 112.2 1.0 N7 B:A65 4.9 142.7 1.0 O A:THR1102 4.9 127.8 1.0 CA A:THR1102 4.9 120.8 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