Magnesium in PDB 7yf6: Crystal Structure of Hiv-1 Protease in Complex with Macrocyclic Peptide

The structure of Crystal Structure of Hiv-1 Protease in Complex with Macrocyclic Peptide, PDB code: 7yf6 was solved by Y.Kusumoto, S.Sato, T.Yamada, I.Kozono, Z.Nakata, N.Asada, S.Mitsuki, C.Wakasa-Morimoto, M.Tohru, A.Watanabe, K.Hayashi, H.Mikamiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.39 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.877, 49.325, 122.078, 90, 90, 90
R / Rfree (%)	19.2 / 23.4

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Protease in Complex with Macrocyclic Peptide (pdb code 7yf6). 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 Crystal Structure of Hiv-1 Protease in Complex with Macrocyclic Peptide, PDB code: 7yf6:

Magnesium binding site 1 out of 1 in the Crystal Structure of Hiv-1 Protease in Complex with Macrocyclic Peptide


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 Hiv-1 Protease in Complex with Macrocyclic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:13.6 occ:1.00 N B:THR12 3.2 17.9 1.0 OG1 B:THR12 3.4 19.5 1.0 CB B:THR12 3.7 19.0 1.0 CA B:VAL11 3.9 18.2 1.0 SG B:CYS67 3.9 38.5 1.0 CB B:VAL11 3.9 17.8 1.0 C B:VAL11 4.0 17.8 1.0 CA B:THR12 4.0 18.2 1.0 CG1 B:VAL11 4.5 18.2 1.0 CB B:CYS67 4.6 32.0 1.0 CA B:CYS67 4.6 30.1 1.0 O B:THR12 4.7 16.8 1.0 C B:THR12 4.9 17.9 1.0

Y.Kusumoto, K.Hayashi, S.Sato, T.Yamada, I.Kozono, Z.Nakata, N.Asada, S.Mitsuki, A.Watanabe, C.Wakasa-Morimoto, K.Uemura, S.Arita, S.Miki, T.Mizutare, H.Mikamiyama. Highly Potent and Oral Macrocyclic Peptides As A Hiv-1 Protease Inhibitor: Mrna Display-Derived Hit-to-Lead Optimization. Acs Med.Chem.Lett. V. 13 1634 2022.
ISSN: ISSN 1948-5875
PubMed: 36262395
DOI: 10.1021/ACSMEDCHEMLETT.2C00310