Magnesium in PDB 8jay: Crtsparta Octamer Bound with Guide-Target

The binding sites of Magnesium atom in the Crtsparta Octamer Bound with Guide-Target (pdb code 8jay). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crtsparta Octamer Bound with Guide-Target, PDB code: 8jay:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crtsparta Octamer Bound with Guide-Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crtsparta Octamer Bound with Guide-Target within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg601 b:72.1 occ:1.00 OP3 O:U1 2.1 82.2 1.0 OP1 O:U1 2.1 82.2 1.0 P O:U1 2.5 82.2 1.0 CG1 M:ILE507 2.6 68.0 1.0 OP1 O:A3 2.8 100.9 1.0 ND2 M:ASN468 2.9 68.5 1.0 OD1 M:ASN468 2.9 68.5 1.0 CG M:ASN468 3.2 68.5 1.0 CD1 M:ILE507 3.2 68.0 1.0 OP2 O:U1 3.2 82.2 1.0 O5' O:U1 3.9 82.2 1.0 CB M:ILE507 3.9 68.0 1.0 O M:ILE507 4.1 68.0 1.0 P O:A3 4.1 100.9 1.0 NZ M:LYS263 4.1 52.0 1.0 CG2 M:ILE507 4.2 68.0 1.0 C M:ILE507 4.5 68.0 1.0 O3' O:G2 4.5 92.1 1.0 CB M:ASN468 4.6 68.5 1.0 C5' O:U1 4.6 82.2 1.0 CA M:ILE507 4.8 68.0 1.0 OP2 O:A3 4.9 100.9 1.0

Magnesium binding site 2 out of 4 in the Crtsparta Octamer Bound with Guide-Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crtsparta Octamer Bound with Guide-Target within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:71.5 occ:1.00 OP1 E:A3 2.0 88.0 1.0 OP3 E:U1 2.1 87.0 1.0 OP1 E:U1 2.1 87.0 1.0 OD1 A:ASN468 2.4 69.4 1.0 P E:U1 2.5 87.0 1.0 ND2 A:ASN468 2.5 69.4 1.0 CG A:ASN468 2.8 69.4 1.0 CD1 A:ILE507 3.0 66.8 1.0 CG1 A:ILE507 3.1 66.8 1.0 P E:A3 3.1 88.0 1.0 OP2 E:U1 3.3 87.0 1.0 OP2 E:A3 3.4 88.0 1.0 O5' E:U1 3.9 87.0 1.0 O3' E:G2 4.1 90.3 1.0 O5' E:A3 4.3 88.0 1.0 CB A:ASN468 4.3 69.4 1.0 CB A:ILE507 4.5 66.8 1.0 O A:ASN468 4.7 69.4 1.0 C5' E:A3 4.8 88.0 1.0 C5' E:U1 4.9 87.0 1.0

Magnesium binding site 3 out of 4 in the Crtsparta Octamer Bound with Guide-Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crtsparta Octamer Bound with Guide-Target within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:77.9 occ:1.00 OP2 G:U1 2.1 99.8 1.0 OP1 G:U1 2.2 99.8 1.0 P G:U1 2.5 99.8 1.0 OP3 G:U1 3.4 99.8 1.0 OD1 C:ASN468 3.8 76.4 1.0 O5' G:U1 3.8 99.8 1.0 NZ C:LYS263 3.9 54.4 1.0 OP1 G:A3 4.0 106.3 1.0 NE2 C:GLN222 4.0 72.3 1.0 OE1 C:GLN222 4.4 72.3 1.0 ND2 C:ASN468 4.4 76.4 1.0 CG C:ASN468 4.5 76.4 1.0 CG2 C:ILE507 4.6 80.2 1.0 CD C:GLN222 4.6 72.3 1.0 C5' G:U1 4.7 99.8 1.0 P G:A3 4.9 106.3 1.0 NZ C:LYS211 4.9 83.2 1.0 OP2 G:A3 5.0 106.3 1.0

Magnesium binding site 4 out of 4 in the Crtsparta Octamer Bound with Guide-Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crtsparta Octamer Bound with Guide-Target within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg101 b:72.1 occ:1.00 OP1 K:A3 2.0 83.6 1.0 OP3 K:U1 2.0 86.8 1.0 OP2 K:A3 2.3 83.6 1.0 ND2 I:ASN468 2.4 75.0 1.0 P K:A3 2.5 83.6 1.0 OP1 K:U1 2.7 86.8 1.0 P K:U1 2.9 86.8 1.0 OD1 I:ASN468 3.1 75.0 1.0 CG I:ASN468 3.1 75.0 1.0 O5' K:A3 3.5 83.6 1.0 O3' K:G2 3.8 91.2 1.0 O I:ILE507 3.8 67.3 1.0 C5' K:U1 3.9 86.8 1.0 O5' K:U1 3.9 86.8 1.0 OP2 K:U1 4.1 86.8 1.0 C5' K:A3 4.4 83.6 1.0 CB I:ASN468 4.5 75.0 1.0 C3' K:G2 4.6 91.2 1.0 C I:ILE507 4.9 67.3 1.0

L.Guo, P.Huang, Z.Li, Y.C.Shin, P.Yan, M.Lu, M.Chen, Y.Xiao. Auto-Inhibition and Activation of A Short Argonaute-Associated Tir-Apaz Defense System. Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
PubMed: 37932527
DOI: 10.1038/S41589-023-01478-0