Manganese in PDB 8xk3: Structure of the Argonaute Protein From Kurthia Massiliensis in Complex with Guide Dna and 19-Mer Target Dna in Target-Cleaved State

The binding sites of Manganese atom in the Structure of the Argonaute Protein From Kurthia Massiliensis in Complex with Guide Dna and 19-Mer Target Dna in Target-Cleaved State (pdb code 8xk3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of the Argonaute Protein From Kurthia Massiliensis in Complex with Guide Dna and 19-Mer Target Dna in Target-Cleaved State, PDB code: 8xk3:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of the Argonaute Protein From Kurthia Massiliensis in Complex with Guide Dna and 19-Mer Target Dna in Target-Cleaved State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Argonaute Protein From Kurthia Massiliensis in Complex with Guide Dna and 19-Mer Target Dna in Target-Cleaved State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:35.5 occ:1.00 OD2 A:ASP596 2.4 18.5 1.0 OP3 C:DT7 3.0 20.0 1.0 OD1 A:ASP527 3.0 20.4 1.0 CG A:ASP596 3.4 18.5 1.0 O A:ASP596 3.9 23.5 1.0 CG A:ASP527 3.9 20.4 1.0 C5' c:DC6 4.0 30.9 1.0 MN A:MN802 4.0 37.0 1.0 O A:VAL528 4.0 24.3 1.0 OD2 A:ASP527 4.1 20.4 1.0 CB A:ASP596 4.1 18.5 1.0 P C:DT7 4.2 28.7 1.0 OD1 A:ASP596 4.3 18.5 1.0 C3' c:DC6 4.3 30.9 1.0 OP2 C:DT7 4.3 28.7 1.0 C A:ASP596 4.4 23.5 1.0 C4' c:DC6 4.5 30.9 1.0 OP1 c:DC6 4.5 30.9 1.0 C5' C:DT7 4.6 28.7 1.0 NZ A:LYS624 4.7 23.5 1.0 O3' c:DC6 4.7 30.9 1.0 N A:VAL528 4.8 24.3 1.0 CA A:ASP596 4.9 23.5 1.0 N A:GLY597 5.0 23.5 1.0 O5' C:DT7 5.0 28.7 1.0

Manganese binding site 2 out of 3 in the Structure of the Argonaute Protein From Kurthia Massiliensis in Complex with Guide Dna and 19-Mer Target Dna in Target-Cleaved State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Argonaute Protein From Kurthia Massiliensis in Complex with Guide Dna and 19-Mer Target Dna in Target-Cleaved State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:37.0 occ:1.00 OD1 A:ASP713 1.8 23.5 1.0 OP2 C:DT7 2.1 28.7 1.0 OD2 A:ASP527 2.6 20.4 1.0 CG A:ASP713 2.9 23.5 1.0 P C:DT7 3.4 28.7 1.0 CG A:ASP527 3.5 20.4 1.0 CB A:ASP713 3.6 23.5 1.0 OD1 A:ASP527 3.6 20.4 1.0 OD2 A:ASP596 3.7 18.5 1.0 OD2 A:ASP713 3.8 23.5 1.0 OP3 C:DT7 3.9 20.0 1.0 MN A:MN801 4.0 35.5 1.0 CA A:ASP713 4.1 23.5 1.0 O5' C:DT7 4.2 28.7 1.0 NZ A:LYS624 4.3 23.5 1.0 C5' C:DT7 4.4 28.7 1.0 O C:HOH102 4.4 24.6 1.0 OP1 C:DT7 4.5 28.7 1.0 CG A:ASP596 4.8 18.5 1.0 O A:VAL528 4.8 24.3 1.0 CB A:ASP527 4.9 20.4 1.0 O A:HOH903 4.9 21.2 1.0 CE A:LYS624 5.0 23.5 1.0

Manganese binding site 3 out of 3 in the Structure of the Argonaute Protein From Kurthia Massiliensis in Complex with Guide Dna and 19-Mer Target Dna in Target-Cleaved State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the Argonaute Protein From Kurthia Massiliensis in Complex with Guide Dna and 19-Mer Target Dna in Target-Cleaved State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:37.1 occ:1.00 OP1 B:DA3 2.2 23.5 1.0 OP1 B:DT1 2.4 23.5 1.0 P B:DT1 3.7 23.5 1.0 P B:DA3 3.7 23.5 1.0 O A:HOH906 3.8 23.3 1.0 CG1 A:VAL737 3.8 21.1 1.0 CB A:VAL737 3.9 21.1 1.0 OP3 B:DT1 3.9 20.0 1.0 NZ A:LYS506 3.9 23.5 1.0 O B:HOH203 3.9 20.6 1.0 O A:PHE736 4.1 23.5 1.0 O A:VAL737 4.1 21.1 1.0 O A:HOH915 4.2 11.8 1.0 OE1 A:GLN450 4.3 23.5 1.0 C5' B:DA3 4.3 23.5 1.0 O3' B:DG2 4.4 23.5 1.0 O5' B:DA3 4.4 23.5 1.0 C5' B:DT1 4.6 23.5 1.0 O5' B:DT1 4.6 23.5 1.0 OP2 B:DA3 4.7 23.5 1.0 OP2 B:DT1 4.7 23.5 1.0 CG2 A:VAL737 4.8 21.1 1.0 C A:VAL737 4.9 21.1 1.0 CA A:VAL737 4.9 21.1 1.0

X.Tao, H.Ding, S.Wu, F.Wang, H.Xu, J.Li, C.Zhai, S.Li, K.Chen, S.Wu, Y.Liu, L.Ma. Structural and Mechanistic Insights Into A Mesophilic Prokaryotic Argonaute Nucleic Acids Res. V. 52 11895 2024.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAE820