Manganese in PDB 3tr8: Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii

The structure of Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii, PDB code: 3tr8 was solved by J.Cheung, M.C.Franklin, M.Rudolph, M.Cassidy, E.Gary, F.Burshteyn, J.Love, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.03 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.656, 61.300, 58.094, 90.00, 112.41, 90.00
R / Rfree (%)	20.7 / 27.6

The structure of Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii (pdb code 3tr8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii, PDB code: 3tr8:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn184 b:32.1 occ:0.65 OD2 A:ASP12 2.2 21.5 1.0 OE2 A:GLU14 2.2 30.7 1.0 OD2 A:ASP163 2.2 27.1 1.0 MG A:MG186 2.6 23.9 1.0 MN A:MN185 2.9 36.6 0.6 CG A:ASP12 2.9 24.0 1.0 OD1 A:ASP12 3.0 22.7 1.0 CG A:ASP163 3.2 28.3 1.0 CD A:GLU14 3.3 26.2 1.0 O A:LEU13 3.6 20.9 1.0 CB A:ASP163 3.6 27.4 1.0 OE1 A:GLU14 3.9 24.5 1.0 O A:HOH217 4.2 15.2 1.0 OD1 A:ASP163 4.3 26.0 1.0 CB A:ASP12 4.4 20.1 1.0 CG A:GLU14 4.4 18.7 1.0 O A:HOH218 4.4 23.5 1.0 C A:LEU13 4.5 15.7 1.0 CA A:ALA160 4.6 20.6 1.0 CA A:HIS158 4.8 24.1 1.0 N A:ALA160 4.8 25.3 1.0 N A:LEU13 4.8 15.6 1.0 C A:LEU159 4.9 25.0 1.0 C A:HIS158 4.9 23.5 1.0 O A:LEU159 4.9 29.5 1.0

Manganese binding site 2 out of 4 in the Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn185 b:36.6 occ:0.58 OD1 A:ASP12 2.1 22.7 1.0 O A:HOH217 2.4 15.2 1.0 MN A:MN184 2.9 32.1 0.7 CG A:ASP12 3.2 24.0 1.0 MG A:MG186 3.3 23.9 1.0 OD2 A:ASP12 3.6 21.5 1.0 O B:HOH237 3.8 28.8 1.0 O A:LEU13 4.0 20.9 1.0 O A:HOH218 4.2 23.5 1.0 O A:ASN107 4.3 22.9 1.0 O A:HOH192 4.4 15.1 1.0 OD2 A:ASP112 4.4 33.4 1.0 OD1 A:ASP112 4.5 21.9 1.0 CB A:ASP12 4.5 20.1 1.0 N A:LEU13 4.6 15.6 1.0 OD2 A:ASP163 4.6 27.1 1.0 OE2 A:GLU14 4.8 30.7 1.0 CA A:ASP12 4.9 24.2 1.0 CG A:ASP112 4.9 22.4 1.0

Manganese binding site 3 out of 4 in the Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn184 b:33.4 occ:0.70 OD2 B:ASP12 2.1 25.9 1.0 OE2 B:GLU14 2.1 29.2 1.0 OD2 B:ASP163 2.2 27.9 1.0 MG B:MG187 2.5 27.1 1.0 MN B:MN185 2.9 41.4 0.7 CG B:ASP12 2.9 23.7 1.0 OD1 B:ASP12 3.0 22.1 1.0 CG B:ASP163 3.1 25.8 1.0 CD B:GLU14 3.3 25.5 1.0 CB B:ASP163 3.5 22.0 1.0 O B:LEU13 3.6 22.9 1.0 O B:HOH211 3.7 18.4 1.0 OE1 B:GLU14 4.1 23.4 1.0 OD1 B:ASP163 4.2 27.6 1.0 O B:HOH230 4.3 22.9 1.0 CG B:GLU14 4.4 17.8 1.0 CB B:ASP12 4.4 19.1 1.0 O B:HOH226 4.4 15.6 1.0 O B:LEU159 4.5 27.4 1.0 C B:LEU13 4.6 19.8 1.0 CA B:ALA160 4.6 15.1 1.0 CA B:HIS158 4.6 22.3 1.0 C B:LEU159 4.6 25.2 1.0 C B:HIS158 4.7 25.0 1.0 N B:ALA160 4.7 21.7 1.0 N B:LEU159 4.7 23.4 1.0 N B:LEU13 4.9 16.4 1.0 CA B:ASP163 5.0 20.3 1.0

Manganese binding site 4 out of 4 in the Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of An Oligoribonuclease (Orn) From Coxiella Burnetii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn185 b:41.4 occ:0.73 OD1 B:ASP12 2.2 22.1 1.0 O B:HOH211 2.2 18.4 1.0 O B:HOH226 2.5 15.6 1.0 MG B:MG187 2.7 27.1 1.0 MN B:MN184 2.9 33.4 0.7 CG B:ASP12 3.2 23.7 1.0 OD2 B:ASP12 3.6 25.9 1.0 O B:LEU13 3.8 22.9 1.0 O B:HOH230 3.8 22.9 1.0 OD1 B:ASP112 4.5 18.2 1.0 OE2 B:GLU14 4.5 29.2 1.0 CB B:ASP12 4.5 19.1 1.0 N B:LEU13 4.6 16.4 1.0 O B:HOH199 4.6 15.4 1.0 O B:ASN107 4.6 20.9 1.0 OD2 B:ASP163 4.7 27.9 1.0 O B:HOH212 4.7 19.7 1.0 OD2 B:ASP112 4.8 31.5 1.0 C B:LEU13 4.9 19.8 1.0 CA B:ASP12 5.0 23.0 1.0

M.C.Franklin, J.Cheung, M.J.Rudolph, F.Burshteyn, M.Cassidy, E.Gary, B.Hillerich, Z.K.Yao, P.R.Carlier, M.Totrov, J.D.Love. Structural Genomics For Drug Design Against the Pathogen Coxiella Burnetii. Proteins V. 83 2124 2015.
ISSN: ISSN 0887-3585
PubMed: 26033498
DOI: 10.1002/PROT.24841