Magnesium in PDB 9jt2: Substrate-Bound Nbasparda Complexes

The binding sites of Magnesium atom in the Substrate-Bound Nbasparda Complexes (pdb code 9jt2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Substrate-Bound Nbasparda Complexes, PDB code: 9jt2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Substrate-Bound Nbasparda Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Substrate-Bound Nbasparda Complexes within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:30.0 occ:1.00 OP1 Q:DT6 2.1 169.8 1.0 O B:ILE61 2.7 83.8 1.0 NE2 B:GLN60 2.9 82.8 1.0 P Q:DT6 3.2 169.8 1.0 OP2 Q:DT6 3.6 169.8 1.0 C B:ILE61 3.8 83.8 1.0 OP2 Q:DA7 3.8 170.7 1.0 C5' Q:DT6 3.9 169.8 1.0 O5' Q:DT6 4.1 169.8 1.0 CD B:GLN60 4.2 82.8 1.0 OD2 B:ASP41 4.3 82.1 1.0 N B:ILE61 4.4 83.8 1.0 CA B:ILE61 4.4 83.8 1.0 C4' Q:DT6 4.5 169.8 1.0 O3' Q:DC5 4.5 176.2 1.0 CB B:ILE61 4.5 83.8 1.0 OE2 B:GLU16 4.7 79.0 1.0 N B:LYS62 4.8 95.0 1.0 OE1 B:GLN60 4.9 82.8 1.0 CA B:LYS62 5.0 95.0 1.0

Magnesium binding site 2 out of 6 in the Substrate-Bound Nbasparda Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Substrate-Bound Nbasparda Complexes within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:30.0 occ:1.00 OP1 C:A3 1.9 47.8 1.0 OP3 C:A1 2.3 57.9 1.0 OD1 A:ASN446 2.6 41.7 1.0 OXT A:ILE485 2.6 44.0 1.0 ND2 A:ASN446 3.2 41.7 1.0 CG A:ASN446 3.2 41.7 1.0 P C:A1 3.4 57.9 1.0 P C:A3 3.4 47.8 1.0 OP2 C:A1 3.4 57.9 1.0 C A:ILE485 3.8 44.0 1.0 O3' C:U2 3.9 51.2 1.0 OP1 C:A1 4.1 57.9 1.0 NZ A:LYS240 4.2 35.2 1.0 O5' C:A3 4.2 47.8 1.0 OP2 C:A3 4.4 47.8 1.0 OE1 A:GLN198 4.4 42.4 1.0 OG A:SER236 4.6 35.5 1.0 O5' C:A1 4.6 57.9 1.0 CA A:ILE485 4.7 44.0 1.0 O A:ILE485 4.7 44.0 1.0 CB A:ASN446 4.7 41.7 1.0 CB A:ILE485 4.7 44.0 1.0 C5' C:A1 4.8 57.9 1.0 C5' C:A3 5.0 47.8 1.0

Magnesium binding site 3 out of 6 in the Substrate-Bound Nbasparda Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Substrate-Bound Nbasparda Complexes within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg501 b:30.0 occ:1.00 OP1 G:A3 2.3 62.6 1.0 OP2 G:A1 2.4 40.5 1.0 OD1 E:ASN446 2.7 39.7 1.0 O E:ILE485 2.9 43.7 1.0 OP3 G:A1 2.9 40.5 1.0 ND2 E:ASN446 3.0 39.7 1.0 CG E:ASN446 3.2 39.7 1.0 P G:A1 3.3 40.5 1.0 P G:A3 3.6 62.6 1.0 C E:ILE485 3.9 43.7 1.0 OXT E:ILE485 4.0 43.7 1.0 OE1 E:GLN198 4.2 33.9 1.0 O3' G:U2 4.2 58.8 1.0 OP1 G:A1 4.3 40.5 1.0 O5' G:A1 4.4 40.5 1.0 OP2 G:A3 4.4 62.6 1.0 OG E:SER236 4.5 32.0 1.0 C5' G:A1 4.5 40.5 1.0 CB E:ASN446 4.7 39.7 1.0 O5' G:A3 4.7 62.6 1.0 C5' G:A3 4.9 62.6 1.0 NZ E:LYS240 4.9 34.5 1.0 CG1 E:ILE485 4.9 43.7 1.0

Magnesium binding site 4 out of 6 in the Substrate-Bound Nbasparda Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Substrate-Bound Nbasparda Complexes within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg501 b:30.0 occ:1.00 OP1 R:DC5 2.2 164.9 1.0 O F:ILE61 2.2 81.3 1.0 OE1 F:GLN60 2.5 77.8 1.0 OD2 F:ASP41 2.8 83.9 1.0 C F:ILE61 3.4 81.3 1.0 P R:DC5 3.5 164.9 1.0 CG F:ASP41 3.7 83.9 1.0 CD F:GLN60 3.7 77.8 1.0 OD1 F:ASP41 4.0 83.9 1.0 N F:ILE61 4.1 81.3 1.0 OP2 R:DC5 4.1 164.9 1.0 O5' R:DC5 4.2 164.9 1.0 CA F:ILE61 4.2 81.3 1.0 C5' R:DC5 4.4 164.9 1.0 N F:LYS62 4.5 93.2 1.0 NE2 F:GLN60 4.5 77.8 1.0 CB F:ILE61 4.5 81.3 1.0 O3' R:DA4 4.6 171.3 1.0 CA F:LYS62 4.7 93.2 1.0 CG F:GLN60 4.7 77.8 1.0 CB F:ASP41 4.8 83.9 1.0 NZ F:LYS62 5.0 93.2 1.0 OP2 R:DT6 5.0 170.3 1.0

Magnesium binding site 5 out of 6 in the Substrate-Bound Nbasparda Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Substrate-Bound Nbasparda Complexes within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg501 b:34.7 occ:1.00 OP1 K:A3 2.1 38.7 1.0 OP3 K:A1 2.1 35.6 1.0 OD1 I:ASN446 2.4 37.9 1.0 O I:ILE485 2.6 35.6 1.0 CG I:ASN446 3.1 37.9 1.0 ND2 I:ASN446 3.2 37.9 1.0 P K:A3 3.5 38.7 1.0 P K:A1 3.6 35.6 1.0 C I:ILE485 3.8 35.6 1.0 O3' K:U2 4.0 35.0 1.0 OP1 K:A1 4.0 35.6 1.0 O5' K:A3 4.2 38.7 1.0 OXT I:ILE485 4.3 35.6 1.0 O5' K:A1 4.4 35.6 1.0 CB I:ASN446 4.4 37.9 1.0 OP2 K:A1 4.5 35.6 1.0 NE2 I:GLN198 4.6 34.6 1.0 OP2 K:A3 4.6 38.7 1.0 NZ I:LYS240 4.7 37.7 1.0 OE1 I:GLN198 4.8 34.6 1.0 CG1 I:ILE485 4.8 35.6 1.0 OG I:SER236 4.9 37.8 1.0 C5' K:A3 4.9 38.7 1.0 CA I:ILE485 4.9 35.6 1.0 CA I:ASN446 5.0 37.9 1.0

Magnesium binding site 6 out of 6 in the Substrate-Bound Nbasparda Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Substrate-Bound Nbasparda Complexes within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg501 b:38.6 occ:1.00 OD1 M:ASN446 2.3 42.8 1.0 OP1 O:A3 2.4 43.2 1.0 OP1 O:A1 2.5 31.5 1.0 ND2 M:ASN446 2.6 42.8 1.0 CG M:ASN446 2.8 42.8 1.0 O M:ILE485 2.8 37.8 1.0 OP3 O:A1 3.5 31.5 1.0 P O:A1 3.6 31.5 1.0 P O:A3 3.8 43.2 1.0 C M:ILE485 4.0 37.8 1.0 CB M:ASN446 4.2 42.8 1.0 O5' O:A3 4.3 43.2 1.0 OG M:SER236 4.4 46.4 1.0 OP2 O:A1 4.5 31.5 1.0 O3' O:U2 4.5 37.2 1.0 CA M:ILE485 4.6 37.8 1.0 CB M:ILE485 4.6 37.8 1.0 C5' O:A3 4.6 43.2 1.0 O5' O:A1 4.7 31.5 1.0 C5' O:A1 4.9 31.5 1.0 OXT M:ILE485 4.9 37.8 1.0 CE M:LYS240 4.9 58.8 1.0 CA M:ASN446 4.9 42.8 1.0 OP2 O:A3 5.0 43.2 1.0

F.Wang, H.Xu, C.Zhang, J.Xue, Z.Li. Target Dna-Induced Filament Formation and Nuclease Activation of Sparda Complex. Cell Res. 2025.
ISSN: ISSN 1001-0602
PubMed: 40122999
DOI: 10.1038/S41422-025-01100-Z