Manganese in PDB 8dip: The Crystal Structure of I38T Mutant Pa Endonuclease (2009/H1N1/California) in Complex with Compound SJ001023030

The structure of The Crystal Structure of I38T Mutant Pa Endonuclease (2009/H1N1/California) in Complex with Compound SJ001023030, PDB code: 8dip was solved by M.G.Cuypers, J.P.Slavish, Z.Rankovic, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.98 / 2.50
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.316, 89.316, 134.121, 90, 90, 90
R / Rfree (%)	22.8 / 27

The structure of The Crystal Structure of I38T Mutant Pa Endonuclease (2009/H1N1/California) in Complex with Compound SJ001023030 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Manganese atom in the The Crystal Structure of I38T Mutant Pa Endonuclease (2009/H1N1/California) in Complex with Compound SJ001023030 (pdb code 8dip). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Crystal Structure of I38T Mutant Pa Endonuclease (2009/H1N1/California) in Complex with Compound SJ001023030, PDB code: 8dip:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The Crystal Structure of I38T Mutant Pa Endonuclease (2009/H1N1/California) in Complex with Compound SJ001023030


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of I38T Mutant Pa Endonuclease (2009/H1N1/California) in Complex with Compound SJ001023030 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:67.5 occ:1.00 O15 A:SE9204 2.0 63.0 1.0 OD2 A:ASP108 2.1 73.1 1.0 O A:ILE120 2.2 88.0 1.0 OE2 A:GLU119 2.2 78.4 1.0 O13 A:SE9204 2.3 85.3 1.0 NE2 A:HIS41 2.4 85.9 1.0 C14 A:SE9204 2.8 90.0 1.0 CG A:ASP108 2.9 73.5 1.0 C12 A:SE9204 2.9 85.1 1.0 CE1 A:HIS41 2.9 76.7 1.0 OD1 A:ASP108 3.1 70.6 1.0 CD A:GLU119 3.3 82.2 1.0 C A:ILE120 3.3 67.4 1.0 CD2 A:HIS41 3.5 88.1 1.0 N A:ILE120 3.6 67.2 1.0 MN A:MN202 3.8 85.7 1.0 OE1 A:GLU119 3.8 94.4 1.0 CA A:ILE120 3.8 66.7 1.0 CB A:ILE120 4.1 73.4 1.0 ND1 A:HIS41 4.1 78.2 1.0 N16 A:SE9204 4.2 102.1 1.0 CB A:ASP108 4.3 73.5 1.0 C11 A:SE9204 4.4 109.9 1.0 CG A:GLU119 4.4 72.2 1.0 N A:GLY121 4.4 79.9 1.0 CG A:HIS41 4.4 64.2 1.0 C A:GLU119 4.5 77.9 1.0 CA A:GLY121 4.7 70.3 1.0 CA A:GLU119 4.9 69.8 1.0 O A:HOH301 4.9 66.6 1.0 CG2 A:ILE120 4.9 71.8 1.0 SG A:CYS45 5.0 65.9 1.0 O10 A:SE9204 5.0 96.3 1.0

Manganese binding site 2 out of 2 in the The Crystal Structure of I38T Mutant Pa Endonuclease (2009/H1N1/California) in Complex with Compound SJ001023030


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of I38T Mutant Pa Endonuclease (2009/H1N1/California) in Complex with Compound SJ001023030 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:85.7 occ:1.00 OD1 A:ASP108 2.2 70.6 1.0 O13 A:SE9204 2.3 85.3 1.0 O10 A:SE9204 2.4 96.3 1.0 OE1 A:GLU80 2.5 92.4 1.0 CG A:ASP108 3.3 73.5 1.0 C12 A:SE9204 3.3 85.1 1.0 C09 A:SE9204 3.4 109.0 1.0 CD A:GLU80 3.6 86.0 1.0 O A:PRO107 3.7 74.1 1.0 C11 A:SE9204 3.8 109.9 1.0 MN A:MN201 3.8 67.5 1.0 OD2 A:ASP108 3.9 73.1 1.0 CE1 A:HIS41 3.9 76.7 1.0 O A:LEU106 4.0 89.8 1.0 C A:PRO107 4.1 84.1 1.0 OE2 A:GLU80 4.3 103.3 1.0 N A:ASP108 4.4 80.6 1.0 CB A:ASP108 4.4 73.5 1.0 CA A:ASP108 4.4 70.4 1.0 OE1 A:GLU119 4.5 94.4 1.0 CB A:GLU80 4.5 60.5 1.0 OE2 A:GLU119 4.5 78.4 1.0 CG A:GLU80 4.6 57.4 1.0 C14 A:SE9204 4.6 90.0 1.0 N08 A:SE9204 4.7 116.3 1.0 NE2 A:HIS41 4.7 85.9 1.0 CA A:PRO107 4.8 79.6 1.0 C A:LEU106 4.8 87.4 1.0 ND1 A:HIS41 4.9 78.2 1.0 O15 A:SE9204 4.9 63.0 1.0 CD A:GLU119 5.0 82.2 1.0

P.J.Slavish, M.G.Cuypers, M.A.Rimmer, A.Abdolvahabi, T.Jeevan, G.Kumar, J.A.Jarusiewicz, S.Vaithiyalingam, J.C.Jones, J.J.Bowling, J.E.Price, R.M.Dubois, J.Min, R.J.Webby, Z.Rankovic, S.W.White. Chemical Scaffold Recycling: Structure-Guided Conversion of An Hiv Integrase Inhibitor Into A Potent Influenza Virus Rna-Dependent Rna Polymerase Inhibitor Designed to Minimize Resistance Potential. Eur.J.Med.Chem. V. 247 15035 2023.
ISSN: ISSN 0223-5234
PubMed: 36603507
DOI: 10.1016/J.EJMECH.2022.115035