Manganese in PDB 8u7b: Crystal Structure of Apo Form of Short Prokaryotic Argonaute Tir-Apaz (Sparta) Heterodimer

The structure of Crystal Structure of Apo Form of Short Prokaryotic Argonaute Tir-Apaz (Sparta) Heterodimer, PDB code: 8u7b was solved by J.Kottur, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.71 / 2.66
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	197.181, 197.181, 183.407, 90, 90, 120
R / Rfree (%)	17.9 / 23.9

The binding sites of Manganese atom in the Crystal Structure of Apo Form of Short Prokaryotic Argonaute Tir-Apaz (Sparta) Heterodimer (pdb code 8u7b). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Apo Form of Short Prokaryotic Argonaute Tir-Apaz (Sparta) Heterodimer, PDB code: 8u7b:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Apo Form of Short Prokaryotic Argonaute Tir-Apaz (Sparta) Heterodimer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Apo Form of Short Prokaryotic Argonaute Tir-Apaz (Sparta) Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn601 b:66.1 occ:1.00 N C:THR110 3.3 57.9 1.0 CD2 C:HIS111 3.8 61.0 1.0 CA C:SER109 3.9 48.2 1.0 C C:SER109 4.1 56.9 1.0 CB C:SER109 4.1 60.6 1.0 CB C:THR110 4.1 49.2 1.0 CE2 C:TYR200 4.1 62.9 1.0 N C:HIS111 4.2 53.6 1.0 CA C:THR110 4.2 48.6 1.0 OG1 C:THR110 4.2 65.6 1.0 OH C:TYR200 4.3 69.3 1.0 O C:HOH734 4.5 64.5 1.0 CZ C:TYR200 4.6 61.9 1.0 OG C:SER109 4.7 57.8 1.0 NE2 C:HIS111 4.7 65.8 1.0 CE C:LYS170 4.7 76.2 1.0 C C:THR110 4.7 49.0 1.0 CG C:HIS111 4.7 56.4 1.0 O C:HOH709 4.8 37.5 1.0 O C:HOH741 4.8 64.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Apo Form of Short Prokaryotic Argonaute Tir-Apaz (Sparta) Heterodimer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Apo Form of Short Prokaryotic Argonaute Tir-Apaz (Sparta) Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn602 b:67.9 occ:1.00 NZ C:LYS211 2.5 66.5 1.0 N C:ILE223 3.7 42.5 1.0 NE2 C:HIS207 3.8 71.8 1.0 CE C:LYS211 3.9 56.0 1.0 O C:ILE223 4.1 51.0 1.0 O C:ILE507 4.1 53.5 1.0 NZ C:LYS263 4.3 73.3 1.0 CB C:ILE223 4.4 36.1 1.0 CA C:GLN222 4.4 45.4 1.0 CA C:ILE223 4.4 35.2 1.0 CD2 C:HIS207 4.5 55.7 1.0 O C:THR221 4.5 65.6 1.0 C C:GLN222 4.5 44.8 1.0 CG C:GLN222 4.6 37.8 1.0 C C:ILE223 4.7 38.6 1.0 CE C:LYS263 4.7 63.6 1.0 C C:ILE507 4.7 53.6 1.0 ND2 C:ASN468 4.7 86.0 1.0 CD C:LYS211 4.9 48.3 1.0 CE1 C:HIS207 4.9 102.2 1.0 CD1 C:ILE223 4.9 44.3 1.0

J.Kottur, R.Malik, A.K.Aggarwal. Nucleic Acid Mediated Activation of A Short Prokaryotic Argonaute Immune System Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-49271-4