Magnesium in PDB 9jsz: Active Nbasparda Complexes

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

Magnesium binding site 1 out of 4 in the Active Nbasparda Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Active Nbasparda Complexes within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg501 b:44.6 occ:1.00 OP3 O:A1 2.1 43.6 1.0 OP1 O:A1 2.1 43.6 1.0 O M:ILE485 2.3 40.9 1.0 OP1 O:A3 2.4 51.5 1.0 P O:A1 2.6 43.6 1.0 ND2 M:ASN446 3.0 39.9 1.0 OD1 M:ASN446 3.4 39.9 1.0 C M:ILE485 3.5 40.9 1.0 CG M:ASN446 3.6 39.9 1.0 OP2 O:A1 3.7 43.6 1.0 O5' O:A1 3.7 43.6 1.0 P O:A3 3.9 51.5 1.0 C5' O:A1 3.9 43.6 1.0 OXT M:ILE485 4.1 40.9 1.0 NH2 M:ARG183 4.1 44.1 1.0 NE M:ARG183 4.4 44.1 1.0 O5' O:A3 4.5 51.5 1.0 OE1 M:GLN198 4.5 40.4 1.0 O3' O:U2 4.6 53.5 1.0 CA M:ILE485 4.6 40.9 1.0 CZ M:ARG183 4.7 44.1 1.0 C5' O:A3 4.8 51.5 1.0 CB M:ILE485 4.9 40.9 1.0 OP2 O:A3 5.0 51.5 1.0

Magnesium binding site 2 out of 4 in the Active Nbasparda Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Active Nbasparda Complexes within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:61.2 occ:1.00 OP3 G:A1 1.8 70.6 1.0 O3' G:U2 2.1 77.0 1.0 O E:ILE485 2.7 62.3 1.0 C3' G:U2 3.1 77.0 1.0 OP1 G:A3 3.2 77.2 1.0 P G:A3 3.2 77.2 1.0 C4' G:U2 3.2 77.0 1.0 P G:A1 3.2 70.6 1.0 O2' G:U2 3.4 77.0 1.0 OP1 G:A1 3.7 70.6 1.0 O5' G:A3 3.7 77.2 1.0 C E:ILE485 3.8 62.3 1.0 C2' G:U2 3.9 77.0 1.0 C5' G:U2 3.9 77.0 1.0 OP2 G:A1 4.0 70.6 1.0 OXT E:ILE485 4.0 62.3 1.0 C5' G:A1 4.2 70.6 1.0 O5' G:A1 4.2 70.6 1.0 OD1 E:ASN446 4.4 64.8 1.0 NE2 E:GLN198 4.4 64.1 1.0 O4' G:U2 4.4 77.0 1.0 OP2 G:A3 4.4 77.2 1.0 OG E:SER236 4.7 66.5 1.0 CB E:SER236 4.7 66.5 1.0 CG E:GLN198 4.7 64.1 1.0 C1' G:U2 4.8 77.0 1.0 O5' G:U2 4.9 77.0 1.0

Magnesium binding site 3 out of 4 in the Active Nbasparda Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Active Nbasparda Complexes within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg501 b:41.0 occ:1.00 OP3 K:A1 2.1 39.2 1.0 OP2 K:A1 2.1 39.2 1.0 OP1 K:A3 2.3 48.3 1.0 OXT I:ILE485 2.5 40.2 1.0 P K:A1 2.5 39.2 1.0 OD1 I:ASN446 3.0 38.0 1.0 ND2 I:ASN446 3.1 38.0 1.0 CG I:ASN446 3.4 38.0 1.0 OP1 K:A1 3.5 39.2 1.0 C I:ILE485 3.6 40.2 1.0 P K:A3 3.8 48.3 1.0 O5' K:A1 3.8 39.2 1.0 NZ I:LYS240 3.9 35.9 1.0 C5' K:A1 4.1 39.2 1.0 O I:ILE485 4.2 40.2 1.0 OE1 I:GLN198 4.2 36.5 1.0 O3' K:U2 4.4 47.9 1.0 O5' K:A3 4.4 48.3 1.0 NH2 I:ARG183 4.5 40.1 1.0 CA I:ILE485 4.8 40.2 1.0 NE2 I:GLN198 4.8 36.5 1.0 C5' K:A3 4.8 48.3 1.0 OP2 K:A3 4.8 48.3 1.0 CD I:GLN198 4.9 36.5 1.0 CB I:ASN446 4.9 38.0 1.0 CB I:ILE485 5.0 40.2 1.0

Magnesium binding site 4 out of 4 in the Active Nbasparda Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Active Nbasparda Complexes within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:43.1 occ:1.00 OP1 C:A3 2.1 62.5 1.0 OP2 C:A1 2.7 52.8 1.0 OXT A:ILE485 2.8 43.7 1.0 O3' C:U2 2.9 55.4 1.0 P C:A3 3.0 62.5 1.0 ND2 A:ASN446 3.0 45.4 1.0 OE1 A:GLN198 3.2 45.7 1.0 P C:A1 3.7 52.8 1.0 OP3 C:A1 3.7 52.8 1.0 O5' C:A3 3.9 62.5 1.0 C A:ILE485 3.9 43.7 1.0 CD A:GLN198 4.0 45.7 1.0 NE2 A:GLN198 4.1 45.7 1.0 CG A:ASN446 4.1 45.4 1.0 OP2 C:A3 4.2 62.5 1.0 C3' C:U2 4.2 55.4 1.0 OP1 C:A1 4.2 52.8 1.0 OG A:SER236 4.3 44.4 1.0 O A:ILE485 4.4 43.7 1.0 OD1 A:ASN446 4.4 45.4 1.0 CB A:SER236 4.6 44.4 1.0 O2' C:U2 4.6 55.4 1.0 C4' C:U2 4.8 55.4 1.0 NZ A:LYS240 5.0 41.4 1.0 C5' C:A3 5.0 62.5 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