Magnesium in PDB 8u3y: Spg CAS9 with Ngg Pam Dna Target

The binding sites of Magnesium atom in the Spg CAS9 with Ngg Pam Dna Target (pdb code 8u3y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Spg CAS9 with Ngg Pam Dna Target, PDB code: 8u3y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Spg CAS9 with Ngg Pam Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Spg CAS9 with Ngg Pam Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:75.3 occ:1.00 OD1 A:ASP10 2.0 43.9 1.0 OE1 A:GLU762 2.1 52.7 1.0 OE2 A:GLU762 2.3 52.7 1.0 CD A:GLU762 2.4 52.7 1.0 CG A:ASP10 3.0 43.9 1.0 OD2 A:ASP10 3.6 43.9 1.0 CG A:GLU762 3.9 52.7 1.0 CB A:ASP10 4.2 43.9 1.0 CB A:GLU762 4.4 52.7 1.0 OG A:SER960 4.5 58.1 1.0 MG A:MG1402 4.6 56.0 1.0 OD2 A:ASP986 4.6 43.4 1.0 CA A:ASP10 4.7 43.9 1.0 O A:ILE11 4.9 42.7 1.0 C A:ASP10 5.0 43.9 1.0

Magnesium binding site 2 out of 5 in the Spg CAS9 with Ngg Pam Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Spg CAS9 with Ngg Pam Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1402 b:56.0 occ:1.00 ND1 A:HIS983 2.1 42.5 1.0 CE1 A:HIS983 2.5 42.5 1.0 OD2 A:ASP10 2.5 43.9 1.0 CG A:HIS983 3.4 42.5 1.0 CG A:ASP10 3.5 43.9 1.0 NE2 A:HIS983 3.8 42.5 1.0 OD1 A:ASP10 3.9 43.9 1.0 CB A:HIS983 4.2 42.5 1.0 CD2 A:HIS983 4.2 42.5 1.0 OG A:SER15 4.3 37.4 1.0 CA A:HIS983 4.3 42.5 1.0 NZ A:LYS974 4.5 59.6 1.0 CE1 A:HIS982 4.5 46.1 1.0 OD2 A:ASP986 4.5 43.4 1.0 ND1 A:HIS982 4.5 46.1 1.0 MG A:MG1401 4.6 75.3 1.0 O A:ASP10 4.7 43.9 1.0 CB A:ASP10 4.8 43.9 1.0 N A:HIS983 5.0 42.5 1.0

Magnesium binding site 3 out of 5 in the Spg CAS9 with Ngg Pam Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Spg CAS9 with Ngg Pam Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1403 b:40.9 occ:1.00 OD1 A:ASP839 2.2 51.6 1.0 ND2 A:ASN863 2.3 56.1 1.0 OP2 c:DT23 2.3 64.3 1.0 O3' C:DG22 2.7 65.2 1.0 CG A:ASP839 3.4 51.6 1.0 CG A:ASN863 3.4 56.1 1.0 O A:LYS866 3.7 56.6 1.0 P c:DT23 3.7 64.3 1.0 NZ A:LYS866 3.8 56.6 1.0 OD1 A:ASN863 3.8 56.1 1.0 O A:HIS840 3.9 53.2 1.0 O A:ASN863 3.9 56.1 1.0 C3' C:DG22 4.0 65.2 1.0 CB A:ASP839 4.2 51.6 1.0 N A:HIS840 4.2 53.2 1.0 O5' c:DT23 4.2 64.3 1.0 OD2 A:ASP839 4.4 51.6 1.0 CE A:LYS866 4.4 56.6 1.0 CA A:ASP839 4.4 51.6 1.0 C4' C:DG22 4.5 65.2 1.0 C5' C:DG22 4.6 65.2 1.0 C A:ASN863 4.6 56.1 1.0 OP1 c:DT23 4.6 64.3 1.0 CB A:ASN863 4.7 56.1 1.0 C A:ASP839 4.8 51.6 1.0 CA A:ASN863 4.8 56.1 1.0 C A:HIS840 4.8 53.2 1.0 C A:LYS866 4.9 56.6 1.0

Magnesium binding site 4 out of 5 in the Spg CAS9 with Ngg Pam Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Spg CAS9 with Ngg Pam Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:84.8 occ:1.00 OP2 B:A65 2.1 74.2 1.0 OG1 A:THR1102 2.9 46.2 1.0 P B:A65 3.4 74.2 1.0 OP1 B:U64 3.9 61.5 1.0 OP1 B:A65 3.9 74.2 1.0 O5' B:A65 4.1 74.2 1.0 CB A:THR1102 4.3 46.2 1.0 O3' B:U64 4.6 61.5 1.0 P B:U64 4.8 61.5 1.0 OP2 B:U66 4.8 83.5 1.0 O4 B:U66 4.8 83.5 1.0 OP2 B:U64 4.8 61.5 1.0 O A:THR1102 4.9 46.2 1.0 C5 B:U66 5.0 83.5 1.0

Magnesium binding site 5 out of 5 in the Spg CAS9 with Ngg Pam Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Spg CAS9 with Ngg Pam Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ c:Mg101 b:67.0 occ:1.00 OP2 c:DA33 3.4 59.3 1.0 OP2 c:DT32 4.0 57.6 1.0 NE A:ARG765 4.3 59.0 1.0 O5' c:DT32 4.4 57.6 1.0 P c:DT32 4.6 57.6 1.0 CD A:ARG765 4.7 59.0 1.0 OP2 B:A2 4.8 63.0 1.0 P c:DA33 4.8 59.3 1.0 OP1 c:DT32 5.0 57.6 1.0 CZ A:ARG765 5.0 59.0 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