Manganese in PDB 3lp3: P15 Hiv Rnaseh Domain with Inhibitor MK3

The structure of P15 Hiv Rnaseh Domain with Inhibitor MK3, PDB code: 3lp3 was solved by Y.Yan, S.K.Munshi, G.S.Prasad, H.P.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.88 / 2.80
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	51.256, 51.256, 112.773, 90.00, 90.00, 120.00
R / Rfree (%)	22.9 / 28.8

The binding sites of Manganese atom in the P15 Hiv Rnaseh Domain with Inhibitor MK3 (pdb code 3lp3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the P15 Hiv Rnaseh Domain with Inhibitor MK3, PDB code: 3lp3:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the P15 Hiv Rnaseh Domain with Inhibitor MK3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of P15 Hiv Rnaseh Domain with Inhibitor MK3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1 b:46.8 occ:1.00 OD2 A:ASP549 1.9 50.5 1.0 O11 A:LP93 2.0 73.0 1.0 O A:HOH4 2.4 17.2 1.0 OD2 A:ASP443 2.5 33.7 1.0 O12 A:LP93 2.7 73.0 1.0 C6 A:LP93 2.9 73.0 1.0 OD1 A:ASP443 3.1 33.6 1.0 CG A:ASP549 3.1 50.6 1.0 CG A:ASP443 3.1 33.3 1.0 N5 A:LP93 3.2 73.0 1.0 MN A:MN2 3.5 39.0 1.0 O A:GLY444 3.8 37.0 1.0 CB A:ASP549 3.9 50.8 1.0 OD1 A:ASP549 4.1 50.4 1.0 NE2 A:HIS539 4.2 41.4 1.0 C7 A:LP93 4.2 73.1 1.0 OD2 A:ASP498 4.2 23.2 1.0 CA A:ASP549 4.3 50.9 1.0 OG A:SER553 4.4 54.6 1.0 O25 A:LP93 4.4 73.2 1.0 C3 A:LP93 4.5 73.1 1.0 CB A:ASP443 4.6 33.1 1.0 C9 A:LP93 4.7 73.1 1.0 C26 A:LP93 4.7 73.1 1.0 CG2 A:VAL552 4.8 53.4 1.0 CE1 A:HIS539 4.9 41.5 1.0 OD1 A:ASP498 4.9 23.6 1.0 CD2 A:HIS539 4.9 41.1 1.0 CG A:ASP498 5.0 23.1 1.0

Manganese binding site 2 out of 4 in the P15 Hiv Rnaseh Domain with Inhibitor MK3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of P15 Hiv Rnaseh Domain with Inhibitor MK3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2 b:39.0 occ:1.00 O12 A:LP93 1.7 73.0 1.0 OE2 A:GLU478 1.9 29.9 1.0 OD1 A:ASP498 2.0 23.6 1.0 OD1 A:ASP443 2.4 33.6 1.0 CG A:ASP498 2.9 23.1 1.0 N5 A:LP93 2.9 73.0 1.0 CD A:GLU478 3.0 30.4 1.0 OD2 A:ASP498 3.1 23.2 1.0 N A:LP93 3.1 73.0 1.0 CG A:ASP443 3.3 33.3 1.0 C3 A:LP93 3.4 73.1 1.0 OE1 A:GLU478 3.5 30.5 1.0 MN A:MN1 3.5 46.8 1.0 OD2 A:ASP443 3.7 33.7 1.0 O A:HOH4 3.9 17.2 1.0 C6 A:LP93 4.0 73.0 1.0 O A:GLY444 4.0 37.0 1.0 C2 A:LP93 4.2 73.1 1.0 CB A:ASP498 4.3 22.8 1.0 O11 A:LP93 4.3 73.0 1.0 CG A:GLU478 4.3 31.3 1.0 N A:GLY444 4.4 34.9 1.0 CB A:ASP443 4.6 33.1 1.0 O A:ASP498 4.6 23.1 1.0 C A:ASP498 4.7 22.8 1.0 CA A:ASP443 4.7 33.2 1.0 C4 A:LP93 4.8 73.1 1.0 CA A:ASP498 4.9 22.9 1.0

Manganese binding site 3 out of 4 in the P15 Hiv Rnaseh Domain with Inhibitor MK3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of P15 Hiv Rnaseh Domain with Inhibitor MK3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2 b:56.0 occ:1.00 OD2 B:ASP549 1.9 51.1 1.0 O12 B:LP91 2.1 67.0 1.0 OD1 B:ASP443 2.3 33.7 1.0 O11 B:LP91 2.4 67.0 1.0 N5 B:LP91 3.0 67.0 1.0 O B:HOH5 3.0 29.7 1.0 C6 B:LP91 3.0 67.1 1.0 CG B:ASP549 3.1 51.2 1.0 CG B:ASP443 3.3 33.4 1.0 OD2 B:ASP443 3.5 33.2 1.0 MN B:MN3 3.8 29.9 1.0 OD1 B:ASP498 3.9 23.4 1.0 CB B:ASP549 3.9 51.2 1.0 O B:GLY444 4.0 37.2 1.0 OD1 B:ASP549 4.1 51.1 1.0 NE2 B:HIS539 4.2 42.0 1.0 C3 B:LP91 4.2 67.0 1.0 CA B:ASP549 4.3 51.3 1.0 C7 B:LP91 4.4 67.0 1.0 CB B:ASP443 4.7 33.4 1.0 N B:LP91 4.8 67.0 1.0 CE1 B:HIS539 4.9 42.0 1.0 CG B:ASP498 4.9 23.2 1.0 CD2 B:HIS539 4.9 41.8 1.0

Manganese binding site 4 out of 4 in the P15 Hiv Rnaseh Domain with Inhibitor MK3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of P15 Hiv Rnaseh Domain with Inhibitor MK3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn3 b:29.9 occ:1.00 OE1 B:GLU478 2.1 30.1 1.0 OD2 B:ASP498 2.1 23.0 1.0 O12 B:LP91 2.2 67.0 1.0 OD2 B:ASP443 2.2 33.2 1.0 N B:LP91 2.4 67.0 1.0 CG B:ASP498 2.8 23.2 1.0 OD1 B:ASP498 2.8 23.4 1.0 CD B:GLU478 2.9 30.5 1.0 N5 B:LP91 3.1 67.0 1.0 C3 B:LP91 3.2 67.0 1.0 OE2 B:GLU478 3.2 30.6 1.0 CG B:ASP443 3.3 33.4 1.0 C2 B:LP91 3.4 67.0 1.0 O B:GLY444 3.8 37.2 1.0 MN B:MN2 3.8 56.0 1.0 OD1 B:ASP443 3.8 33.7 1.0 O B:HOH18 3.9 21.3 1.0 N B:GLY444 4.3 35.1 1.0 CB B:ASP498 4.3 22.9 1.0 CG B:GLU478 4.3 31.6 1.0 C6 B:LP91 4.4 67.1 1.0 C4 B:LP91 4.5 67.0 1.0 CB B:ASP443 4.6 33.4 1.0 O B:HOH5 4.6 29.7 1.0 C1 B:LP91 4.7 67.1 1.0 C B:ASP498 4.7 22.9 1.0 O B:ASP498 4.7 23.1 1.0 C B:GLY444 4.8 37.2 1.0 CA B:ASP443 4.8 33.5 1.0 O11 B:LP91 4.9 67.0 1.0 CA B:ASP498 4.9 23.0 1.0

H.P.Su, Y.Yan, G.S.Prasad, R.F.Smith, C.L.Daniels, P.D.Abeywickrema, J.C.Reid, H.M.Loughran, M.Kornienko, S.Sharma, J.A.Grobler, B.Xu, V.Sardana, T.J.Allison, P.D.Williams, P.L.Darke, D.J.Hazuda, S.Munshi. Structural Basis For the Inhibition of Rnase H Activity of Hiv-1 Reverse Transcriptase By Rnase H Active Site-Directed Inhibitors. J.Virol. V. 84 7625 2010.
ISSN: ISSN 0022-538X
PubMed: 20484498
DOI: 10.1128/JVI.00353-10