Magnesium in PDB 6qzk: Structure of Clostridium Butyricum Argonaute Bound to A Guide Dna (5' Deoxycytidine) and A 19-Mer Target Dna

The structure of Structure of Clostridium Butyricum Argonaute Bound to A Guide Dna (5' Deoxycytidine) and A 19-Mer Target Dna, PDB code: 6qzk was solved by D.C.Swarts, M.Jinek, J.W.Hegge, J.Van Der Oost, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.61 / 3.55
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	181.450, 181.450, 142.990, 90.00, 90.00, 120.00
R / Rfree (%)	24.7 / 27.6

The binding sites of Magnesium atom in the Structure of Clostridium Butyricum Argonaute Bound to A Guide Dna (5' Deoxycytidine) and A 19-Mer Target Dna (pdb code 6qzk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of Clostridium Butyricum Argonaute Bound to A Guide Dna (5' Deoxycytidine) and A 19-Mer Target Dna, PDB code: 6qzk:

Magnesium binding site 1 out of 1 in the Structure of Clostridium Butyricum Argonaute Bound to A Guide Dna (5' Deoxycytidine) and A 19-Mer Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Clostridium Butyricum Argonaute Bound to A Guide Dna (5' Deoxycytidine) and A 19-Mer Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:97.9 occ:1.00 OP1 B:DC1 2.0 0.4 1.0 O A:LEU748 2.2 0.5 1.0 C A:LEU748 2.2 0.2 1.0 OP3 B:DC1 2.5 0.7 1.0 ND2 A:ASN515 2.6 0.8 1.0 P B:DC1 2.7 0.4 1.0 OP1 B:DA3 3.1 0.2 1.0 NZ A:LYS519 3.2 0.3 1.0 OD1 A:ASN515 3.3 0.8 1.0 CG A:ASN515 3.3 0.7 1.0 CE A:LYS519 3.3 0.7 1.0 OP2 B:DC1 3.4 0.2 1.0 CA A:LEU748 3.7 0.6 1.0 O A:PHE747 4.0 0.5 1.0 O5' B:DC1 4.0 0.8 1.0 NE2 A:GLN487 4.1 0.2 1.0 N A:LEU748 4.3 0.8 1.0 C A:PHE747 4.4 0.3 1.0 CB A:LEU748 4.5 0.1 1.0 C5' B:DC1 4.5 0.8 1.0 P B:DA3 4.6 0.1 1.0 CD A:LYS519 4.6 0.7 1.0 CB A:ASN515 4.7 0.4 1.0

J.W.Hegge, D.C.Swarts, S.D.Chandradoss, T.J.Cui, J.Kneppers, M.Jinek, C.Joo, J.Van Der Oost. Dna-Guided Dna Cleavage at Moderate Temperatures By Clostridium Butyricum Argonaute. Nucleic Acids Res. V. 47 5809 2019.
ISSN: ESSN 1362-4962
PubMed: 31069393
DOI: 10.1093/NAR/GKZ306