Manganese in PDB 7ug9: Crystal Structure of Rnase Am Php Domain

The structure of Crystal Structure of Rnase Am Php Domain, PDB code: 7ug9 was solved by S.K.Doamekpor, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.19 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.289, 74.389, 40.079, 90, 118.98, 90
R / Rfree (%)	18.2 / 21.5

The binding sites of Manganese atom in the Crystal Structure of Rnase Am Php Domain (pdb code 7ug9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Rnase Am Php Domain, PDB code: 7ug9:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Rnase Am Php Domain


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 Rnase Am Php Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:15.3 occ:1.00 OE2 A:GLU72 2.0 17.1 1.0 ND1 A:HIS83 2.1 16.1 1.0 NE2 A:HIS198 2.1 19.5 1.0 O2 A:SO4304 2.1 18.3 1.0 O1 A:SO4304 2.4 20.9 1.0 S A:SO4304 2.8 21.6 1.0 CD A:GLU72 3.0 17.4 1.0 CE1 A:HIS198 3.0 16.2 1.0 CE1 A:HIS83 3.0 19.3 1.0 CG A:HIS83 3.1 18.2 1.0 CD2 A:HIS198 3.2 16.4 1.0 OE1 A:GLU72 3.4 14.3 1.0 CB A:HIS83 3.5 16.9 1.0 MN A:MN303 3.6 14.4 1.0 O3 A:SO4304 3.9 20.6 1.0 O4 A:SO4304 3.9 20.8 1.0 NH2 A:ARG201 4.0 31.7 1.0 ND1 A:HIS198 4.1 16.4 1.0 NE2 A:HIS83 4.2 18.3 1.0 CD2 A:HIS83 4.2 22.8 1.0 CG A:GLU72 4.2 15.7 1.0 CG A:HIS198 4.3 17.3 1.0 CE1 A:HIS45 4.3 16.4 1.0 CE1 A:HIS13 4.3 17.8 1.0 NE2 A:HIS13 4.5 17.8 1.0 NH1 A:ARG201 4.5 31.1 1.0 CZ A:ARG201 4.5 31.4 1.0 OD2 A:ASP255 4.6 28.4 1.0 CB A:ALA197 4.9 13.2 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Rnase Am Php Domain


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 Rnase Am Php Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:17.6 occ:1.00 O A:HOH464 2.1 26.5 1.0 O3 A:SO4304 2.1 20.6 1.0 OD2 A:ASP20 2.2 18.1 1.0 NE2 A:HIS257 2.2 15.7 1.0 NE2 A:HIS45 2.2 17.4 1.0 OD1 A:ASP20 2.7 16.6 1.0 CG A:ASP20 2.8 19.2 1.0 CE1 A:HIS257 3.1 14.9 1.0 CD2 A:HIS45 3.1 14.7 1.0 CD2 A:HIS257 3.2 17.0 1.0 CE1 A:HIS45 3.3 16.4 1.0 S A:SO4304 3.4 21.6 1.0 CE1 A:HIS15 3.7 13.5 1.0 NE2 A:HIS15 3.9 14.8 1.0 O4 A:SO4304 3.9 20.8 1.0 O1 A:SO4304 4.0 20.9 1.0 ND1 A:HIS15 4.0 16.9 1.0 ND1 A:HIS257 4.2 17.5 1.0 CD2 A:HIS15 4.3 13.4 1.0 CB A:ASP20 4.3 17.8 1.0 CG A:HIS45 4.3 17.6 1.0 CG A:HIS257 4.3 16.0 1.0 MN A:MN303 4.3 14.4 1.0 ND1 A:HIS45 4.3 15.1 1.0 CG A:HIS15 4.4 14.7 1.0 O A:HOH413 4.4 32.7 1.0 O2 A:SO4304 4.5 18.3 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Rnase Am Php Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Rnase Am Php Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:14.4 occ:1.00 O2 A:SO4304 2.1 18.3 1.0 NE2 A:HIS15 2.1 14.8 1.0 NE2 A:HIS13 2.2 17.8 1.0 OE1 A:GLU72 2.3 14.3 1.0 OD1 A:ASP255 2.4 16.0 1.0 O3 A:SO4304 2.7 20.6 1.0 S A:SO4304 2.9 21.6 1.0 CE1 A:HIS15 3.0 13.5 1.0 CD2 A:HIS13 3.1 16.1 1.0 CD A:GLU72 3.2 17.4 1.0 CE1 A:HIS13 3.2 17.8 1.0 CD2 A:HIS15 3.2 13.4 1.0 CG A:ASP255 3.2 20.3 1.0 OE2 A:GLU72 3.4 17.1 1.0 OD2 A:ASP255 3.6 28.4 1.0 MN A:MN301 3.6 15.3 1.0 O4 A:SO4304 3.9 20.8 1.0 O1 A:SO4304 4.0 20.9 1.0 CE1 A:HIS45 4.1 16.4 1.0 CE1 A:HIS257 4.2 14.9 1.0 ND1 A:HIS15 4.2 16.9 1.0 CG A:HIS13 4.3 15.4 1.0 ND1 A:HIS13 4.3 17.7 1.0 NE2 A:HIS45 4.3 17.4 1.0 CG A:HIS15 4.3 14.7 1.0 MN A:MN302 4.3 17.6 1.0 CG A:GLU72 4.5 15.7 1.0 CB A:ASP255 4.5 16.1 1.0 NE2 A:HIS257 4.6 15.7 1.0 O A:THR43 4.8 16.4 1.0 NE2 A:HIS198 4.8 19.5 1.0 CB A:GLU72 4.8 14.6 1.0 CA A:ASP255 4.8 14.8 1.0 CD2 A:HIS198 4.9 16.4 1.0 OG1 A:THR43 5.0 17.4 1.0 ND1 A:HIS45 5.0 15.1 1.0

S.Sharma, J.Yang, S.K.Doamekpor, E.Grudizen-Nogalska, L.Tong, M.Kiledjian. Identification of A Novel Defadding Activity in Human, Yeast and Bacterial 5' to 3' Exoribonucleases. Nucleic Acids Res. V. 50 8807 2022.
ISSN: ESSN 1362-4962
PubMed: 35904778
DOI: 10.1093/NAR/GKAC617