Manganese in PDB 3v1r: Crystal Structures of the Reverse Transcriptase-Associated Ribonuclease H Domain of Xmrv with Inhibitor Beta-Thujaplicinol

All present enzymatic activity of Crystal Structures of the Reverse Transcriptase-Associated Ribonuclease H Domain of Xmrv with Inhibitor Beta-Thujaplicinol:
3.1.26.4;

The structure of Crystal Structures of the Reverse Transcriptase-Associated Ribonuclease H Domain of Xmrv with Inhibitor Beta-Thujaplicinol, PDB code: 3v1r was solved by D.Zhou, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.17 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	53.677, 84.750, 70.817, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 27.7

The binding sites of Manganese atom in the Crystal Structures of the Reverse Transcriptase-Associated Ribonuclease H Domain of Xmrv with Inhibitor Beta-Thujaplicinol (pdb code 3v1r). 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 Structures of the Reverse Transcriptase-Associated Ribonuclease H Domain of Xmrv with Inhibitor Beta-Thujaplicinol, PDB code: 3v1r:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structures of the Reverse Transcriptase-Associated Ribonuclease H Domain of Xmrv with Inhibitor Beta-Thujaplicinol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structures of the Reverse Transcriptase-Associated Ribonuclease H Domain of Xmrv with Inhibitor Beta-Thujaplicinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn673 b:72.7 occ:1.00 OE2 A:GLU562 2.2 58.9 1.0 OD1 A:ASP524 2.2 50.3 1.0 OD1 A:ASP583 2.2 71.7 1.0 O7 A:JTH675 2.3 98.5 1.0 O1 A:JTH675 2.4 60.1 1.0 OD2 A:ASP583 2.7 50.4 1.0 CG A:ASP583 2.7 56.7 1.0 CD A:GLU562 3.0 55.2 1.0 C7 A:JTH675 3.1 92.4 1.0 C1 A:JTH675 3.1 78.2 1.0 OE1 A:GLU562 3.2 56.5 1.0 CG A:ASP524 3.4 56.1 1.0 MN A:MN674 3.9 64.7 1.0 OD2 A:ASP524 4.1 72.0 1.0 CB A:ASP583 4.2 49.5 1.0 O A:GLY525 4.3 37.8 1.0 CG A:GLU562 4.5 53.3 1.0 CB A:ASP524 4.5 52.1 1.0 C6 A:JTH675 4.5 95.7 1.0 C A:ASP583 4.5 55.4 1.0 N A:SER584 4.5 45.7 1.0 N A:GLY525 4.6 35.5 1.0 C2 A:JTH675 4.6 85.7 1.0 CA A:ASP524 4.6 47.5 1.0 CA A:ASP583 4.7 55.9 1.0 CB A:SER584 4.7 38.6 1.0 N A:ASP583 4.8 59.5 1.0 O2 A:JTH675 4.8 89.3 1.0 O A:ASP583 4.9 65.5 1.0 CA A:SER584 5.0 44.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structures of the Reverse Transcriptase-Associated Ribonuclease H Domain of Xmrv with Inhibitor Beta-Thujaplicinol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structures of the Reverse Transcriptase-Associated Ribonuclease H Domain of Xmrv with Inhibitor Beta-Thujaplicinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn674 b:64.7 occ:1.00 OD1 A:ASP653 2.1 47.8 1.0 O1 A:JTH675 2.2 60.1 1.0 OD2 A:ASP524 2.2 72.0 1.0 O2 A:JTH675 2.3 89.3 1.0 NH1 A:ARG657 2.6 0.1 1.0 CG A:ASP524 2.9 56.1 1.0 C1 A:JTH675 3.0 78.2 1.0 OD1 A:ASP524 3.0 50.3 1.0 C2 A:JTH675 3.2 85.7 1.0 CG A:ASP653 3.2 64.5 1.0 CE1 A:HIS638 3.2 0.1 1.0 CB A:ASP653 3.5 56.1 1.0 CZ A:ARG657 3.6 1.0 1.0 NE2 A:HIS638 3.6 1.0 1.0 O A:GLY525 3.8 37.8 1.0 NH2 A:ARG657 3.9 0.1 1.0 MN A:MN673 3.9 72.7 1.0 CA A:ASP653 4.0 55.9 1.0 OD2 A:ASP653 4.3 78.9 1.0 OD2 A:ASP583 4.3 50.4 1.0 CB A:ASP524 4.4 52.1 1.0 C7 A:JTH675 4.4 92.4 1.0 ND1 A:HIS638 4.4 0.3 1.0 C3 A:JTH675 4.4 88.6 1.0 NE A:ARG657 4.7 89.3 1.0 O7 A:JTH675 4.8 98.5 1.0 C A:ASP653 4.9 63.4 1.0 O A:ASP653 5.0 70.0 1.0 CD2 A:HIS638 5.0 1.0 1.0

D.Zhou, S.Chung, M.Miller, S.F.Le Grice, A.Wlodawer. Crystal Structures of the Reverse Transcriptase-Associated Ribonuclease H Domain of Xenotropic Murine Leukemia-Virus Related Virus. J.Struct.Biol. V. 177 638 2012.
ISSN: ISSN 1047-8477
PubMed: 22366278
DOI: 10.1016/J.JSB.2012.02.006