Manganese in PDB 3hyf: Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Active Site Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Active Site Inhibitor:
3.1.26.4;

The structure of Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Active Site Inhibitor, PDB code: 3hyf was solved by E.B.Lansdon, T.A.Kirschberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.10 / 1.70
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.717, 90.326, 113.334, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 26.6

The structure of Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Active Site Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Active Site Inhibitor (pdb code 3hyf). 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 Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Active Site Inhibitor, PDB code: 3hyf:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Active Site Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Active Site Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:15.4 occ:1.00 OD2 A:ASP498 2.1 15.7 1.0 O1 A:ON1701 2.1 15.3 1.0 OD1 A:ASP443 2.1 15.2 1.0 OE1 A:GLU478 2.1 17.4 1.0 O4 A:ON1701 2.2 15.8 1.0 CG A:ASP498 3.0 15.7 1.0 CD A:GLU478 3.0 19.5 1.0 C10 A:ON1701 3.1 17.8 1.0 C12 A:ON1701 3.2 19.1 1.0 CG A:ASP443 3.2 12.5 1.0 OD1 A:ASP498 3.3 16.4 1.0 OE2 A:GLU478 3.3 17.6 1.0 C9 A:ON1701 3.5 18.5 1.0 OD2 A:ASP443 3.7 13.7 1.0 MN A:MN602 3.7 23.7 1.0 O A:HOH5 3.8 16.3 1.0 O A:HOH26 3.9 27.0 1.0 O A:HOH604 4.1 16.4 1.0 O A:GLY444 4.3 15.8 1.0 O3 A:ON1701 4.3 19.6 1.0 O A:HOH4 4.4 16.7 1.0 CB A:ASP498 4.4 13.0 1.0 C11 A:ON1701 4.4 16.7 1.0 CG A:GLU478 4.4 13.9 1.0 O A:HOH603 4.4 15.0 1.0 CB A:ASP443 4.4 12.2 1.0 C A:ASP498 4.4 13.2 1.0 N A:GLY444 4.5 12.8 1.0 N A:SER499 4.6 13.2 1.0 O A:ASP498 4.6 15.0 1.0 CA A:ASP443 4.6 12.8 1.0 O2 A:ON1701 4.8 13.0 1.0 CB A:SER499 4.8 16.7 1.0 CA A:SER499 4.8 14.9 1.0 CA A:ASP498 4.8 15.3 1.0 O A:HOH145 4.9 50.7 1.0 N1 A:ON1701 4.9 18.3 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Active Site Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Active Site Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:23.7 occ:1.00 OD2 A:ASP443 2.1 13.7 1.0 OD2 A:ASP549 2.1 16.5 1.0 O A:HOH603 2.2 15.0 1.0 O2 A:ON1701 2.2 13.0 1.0 O A:HOH604 2.2 16.4 1.0 O1 A:ON1701 2.2 15.3 1.0 C11 A:ON1701 2.9 16.7 1.0 C10 A:ON1701 3.0 17.8 1.0 CG A:ASP443 3.1 12.5 1.0 CG A:ASP549 3.2 18.8 1.0 OD1 A:ASP443 3.3 15.2 1.0 CB A:ASP549 3.6 16.1 1.0 MN A:MN601 3.7 15.4 1.0 OD1 A:ASP498 4.0 16.4 1.0 NH1 A:ARG557 4.0 21.9 1.0 NE2 A:HIS539 4.1 19.8 1.0 O A:HOH52 4.1 31.8 1.0 N2 A:ON1701 4.3 17.5 1.0 CA A:ASP549 4.3 16.7 1.0 O A:GLY444 4.3 15.8 1.0 OD1 A:ASP549 4.3 21.7 1.0 C9 A:ON1701 4.4 18.5 1.0 CB A:ASP443 4.4 12.2 1.0 O A:HOH9 4.7 18.0 1.0 OG A:SER553 4.7 25.6 0.5 CE1 A:HIS539 4.7 17.9 1.0 OD2 A:ASP498 4.8 15.7 1.0 CG A:ASP498 4.8 15.7 1.0 CD2 A:HIS539 5.0 20.0 1.0

T.A.Kirschberg, M.Balakrishnan, N.H.Squires, T.Barnes, K.M.Brendza, X.Chen, E.J.Eisenberg, W.Jin, N.Kutty, S.Leavitt, A.Liclican, Q.Liu, X.Liu, J.Mak, J.K.Perry, M.Wang, W.J.Watkins, E.B.Lansdon. Rnase H Active Site Inhibitors of Human Immunodeficiency Virus Type 1 Reverse Transcriptase: Design, Biochemical Activity, and Structural Information. J.Med.Chem. V. 52 5781 2009.
ISSN: ISSN 0022-2623
PubMed: 19791799
DOI: 10.1021/JM900597Q