Magnesium in PDB 3hk2: Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand

The structure of Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand, PDB code: 3hk2 was solved by Y.Wang, H.Li, G.Sheng, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.78 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.193, 110.884, 174.339, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.1

The binding sites of Magnesium atom in the Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand (pdb code 3hk2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand, PDB code: 3hk2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg686 b:71.8 occ:1.00 OD2 A:ASP546 2.3 74.9 1.0 O3' D:C9 2.3 54.6 1.0 OD1 A:ASN478 2.3 57.6 1.0 OP1 D:U10 3.0 68.9 1.0 P D:U10 3.3 79.0 1.0 CG A:ASN478 3.4 48.8 1.0 C3' D:C9 3.4 66.8 1.0 CG A:ASP546 3.4 64.1 1.0 O A:ALA479 3.6 45.8 1.0 C4' D:C9 3.6 76.5 1.0 O2' D:C9 3.7 77.5 1.0 ND2 A:ASN478 3.7 72.7 1.0 C5' D:U10 4.1 77.6 1.0 OE2 A:GLU512 4.1 75.3 1.0 C2' D:C9 4.2 71.9 1.0 O5' D:U10 4.2 86.1 1.0 CB A:ASP546 4.2 53.2 1.0 C5' D:C9 4.3 77.5 1.0 OE1 A:GLU512 4.3 61.4 1.0 N A:ALA479 4.3 51.3 1.0 OD1 A:ASP546 4.3 58.1 1.0 O A:ASP546 4.4 71.1 1.0 OP2 D:U10 4.5 60.2 1.0 CD A:GLU512 4.6 60.7 1.0 C A:ALA479 4.6 50.3 1.0 CB A:ASN478 4.7 31.4 1.0 NZ A:LYS575 4.8 57.5 1.0 O4' D:C9 4.9 72.1 1.0 C A:ASP546 5.0 53.2 1.0 CA A:ALA479 5.0 47.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg686 b:75.7 occ:1.00 OD2 B:ASP546 2.3 74.1 1.0 O3' F:C9 2.3 59.5 1.0 OD1 B:ASN478 2.3 60.3 1.0 OP1 F:U10 2.9 64.3 1.0 P F:U10 3.2 74.6 1.0 CG B:ASN478 3.4 49.6 1.0 C3' F:C9 3.4 64.7 1.0 CG B:ASP546 3.4 62.8 1.0 O B:ALA479 3.6 44.4 1.0 C4' F:C9 3.7 74.5 1.0 O2' F:C9 3.7 73.0 1.0 ND2 B:ASN478 3.7 71.1 1.0 C5' F:U10 4.0 75.5 1.0 OE2 B:GLU512 4.1 73.6 1.0 O5' F:U10 4.1 86.1 1.0 C2' F:C9 4.2 71.2 1.0 CB B:ASP546 4.2 51.8 1.0 C5' F:C9 4.3 75.3 1.0 OE1 B:GLU512 4.3 62.4 1.0 OD1 B:ASP546 4.3 58.1 1.0 N B:ALA479 4.3 53.1 1.0 O B:ASP546 4.4 74.6 1.0 OP2 F:U10 4.5 57.3 1.0 CD B:GLU512 4.6 60.1 1.0 C B:ALA479 4.7 47.3 1.0 CB B:ASN478 4.7 32.4 1.0 NZ B:LYS575 4.8 51.1 1.0 O4' F:C9 4.9 75.2 1.0 CA B:ALA479 5.0 46.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg22 b:46.3 occ:1.00 OXT A:VAL685 2.1 68.1 1.0 O A:VAL685 2.1 65.5 1.0 OP1 C:DA3 2.2 39.1 1.0 OP2 C:DT1 2.2 61.3 1.0 C A:VAL685 2.4 47.5 1.0 P C:DT1 3.3 53.3 1.0 OP3 C:DT1 3.3 55.2 1.0 NZ A:LYS457 3.6 48.6 1.0 P C:DA3 3.6 55.5 1.0 OE1 A:GLN433 3.7 53.5 1.0 CA A:VAL685 4.0 55.3 1.0 O3' C:DG2 4.1 44.9 1.0 OP1 C:DT1 4.2 49.6 1.0 O5' C:DT1 4.4 56.4 1.0 CD A:GLN433 4.5 51.6 1.0 NE2 A:GLN433 4.5 46.5 1.0 CE A:LYS457 4.5 41.4 1.0 O5' C:DA3 4.5 46.8 1.0 C5' C:DA3 4.6 55.7 1.0 CB A:VAL685 4.6 53.3 1.0 OP2 C:DA3 4.6 60.5 1.0 CG2 A:VAL685 4.6 49.7 1.0 C5' C:DT1 4.6 50.1 1.0 N A:VAL685 4.8 44.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of T. Thermophilus Argonaute N478 Mutant Protein Complexed with Dna Guide Strand and 19-Nt Rna Target Strand within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg22 b:52.2 occ:1.00 O B:VAL685 2.1 63.5 1.0 OXT B:VAL685 2.1 66.8 1.0 OP1 E:DA3 2.2 42.5 1.0 OP2 E:DT1 2.2 59.3 1.0 C B:VAL685 2.4 46.0 1.0 OP3 E:DT1 3.1 49.1 1.0 P E:DT1 3.2 51.2 1.0 NZ B:LYS457 3.6 49.4 1.0 P E:DA3 3.6 57.4 1.0 OE1 B:GLN433 3.9 57.5 1.0 CA B:VAL685 4.0 55.6 1.0 OP1 E:DT1 4.1 50.8 1.0 O3' E:DG2 4.2 48.0 1.0 O5' E:DT1 4.4 55.2 1.0 O5' E:DA3 4.5 48.8 1.0 C5' E:DT1 4.6 45.5 1.0 OP2 E:DA3 4.6 65.7 1.0 NE2 B:GLN433 4.6 47.5 1.0 C5' E:DA3 4.7 57.2 1.0 CE B:LYS457 4.7 41.6 1.0 CD B:GLN433 4.7 53.5 1.0 CB B:VAL685 4.7 54.0 1.0 N B:VAL685 4.8 45.0 1.0 CG2 B:VAL685 4.8 49.0 1.0

Y.Wang, S.Juranek, H.Li, G.Sheng, G.S.Wardle, T.Tuschl, D.J.Patel. Nucleation, Propagation and Cleavage of Target Rnas in Ago Silencing Complexes. Nature V. 461 754 2009.
ISSN: ISSN 0028-0836
PubMed: 19812667
DOI: 10.1038/NATURE08434