Manganese in PDB 5hrm: Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1

The structure of Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1, PDB code: 5hrm was solved by M.F.Mabanglo, F.M.Raushel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.93 / 2.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.977, 91.273, 96.328, 78.90, 73.60, 89.86
R / Rfree (%)	17.4 / 20.9

The binding sites of Manganese atom in the Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1 (pdb code 5hrm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1, PDB code: 5hrm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1


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 Phosphotriesterase From Sphingobium Sp. TCM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:33.1 occ:1.00 OE2 A:GLU201 2.1 33.7 1.0 O A:HOH864 2.1 38.4 1.0 NE2 A:HIS475 2.1 28.5 1.0 NE2 A:HIS389 2.3 29.5 1.0 OE1 A:GLU407 2.6 40.5 1.0 O A:HOH932 3.0 49.6 1.0 CE1 A:HIS475 3.0 32.7 1.0 CD2 A:HIS475 3.0 30.8 1.0 CD A:GLU201 3.1 33.6 1.0 CE1 A:HIS389 3.1 30.9 1.0 CD2 A:HIS389 3.3 28.6 1.0 CD A:GLU407 3.4 40.6 1.0 OE1 A:GLU201 3.5 31.6 1.0 MN A:MN602 3.5 31.0 1.0 OE2 A:GLU407 3.6 38.2 1.0 NE2 A:HIS317 4.0 32.9 1.0 ND1 A:HIS475 4.1 28.3 1.0 CE1 A:HIS317 4.1 30.9 1.0 CG A:HIS475 4.1 32.4 1.0 ND1 A:HIS389 4.3 31.9 1.0 CG A:GLU201 4.3 30.8 1.0 CG A:HIS389 4.3 28.1 1.0 O A:HOH858 4.5 49.1 1.0 CG A:GLU407 4.6 34.4 1.0 CB A:GLU407 4.7 30.1 1.0

Manganese binding site 2 out of 8 in the Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1


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 Phosphotriesterase From Sphingobium Sp. TCM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:31.0 occ:1.00 OE1 A:GLU201 2.0 31.6 1.0 NE2 A:HIS317 2.0 32.9 1.0 O A:HOH864 2.1 38.4 1.0 NE2 A:HIS258 2.1 31.9 1.0 CD2 A:HIS317 2.9 27.8 1.0 CD A:GLU201 3.0 33.6 1.0 CD2 A:HIS258 3.0 34.3 1.0 O A:HOH858 3.0 49.1 1.0 CE1 A:HIS317 3.1 30.9 1.0 CE1 A:HIS258 3.1 30.9 1.0 O A:HOH939 3.4 50.6 1.0 OE2 A:GLU201 3.4 33.7 1.0 MN A:MN601 3.5 33.1 1.0 CG A:HIS317 4.1 28.3 1.0 ND1 A:HIS317 4.1 31.5 1.0 CG A:HIS258 4.2 34.0 1.0 ND1 A:HIS258 4.2 29.6 1.0 OH A:TYR219 4.2 36.3 1.0 NE2 A:HIS389 4.3 29.5 1.0 CG A:GLU201 4.3 30.8 1.0 CE2 A:TYR219 4.5 34.7 1.0 CD2 A:HIS389 4.5 28.6 1.0 OE2 A:GLU407 4.5 38.2 1.0 O A:HOH932 4.8 49.6 1.0 CB A:GLU201 4.8 31.6 1.0 CZ A:TYR219 4.9 34.8 1.0

Manganese binding site 3 out of 8 in the Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1


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 Phosphotriesterase From Sphingobium Sp. TCM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:28.1 occ:1.00 OE1 B:GLU201 2.0 20.0 1.0 NE2 B:HIS258 2.1 27.6 1.0 O B:HOH712 2.1 38.4 1.0 NE2 B:HIS317 2.2 28.4 1.0 CD2 B:HIS258 2.9 29.8 1.0 CD2 B:HIS317 3.0 23.2 1.0 CD B:GLU201 3.0 20.0 1.0 CE1 B:HIS258 3.2 29.4 1.0 CE1 B:HIS317 3.3 31.0 1.0 OE2 B:GLU201 3.3 20.0 1.0 MN B:MN602 3.6 31.1 1.0 CG B:HIS258 4.1 29.4 1.0 CG B:HIS317 4.2 29.3 1.0 OH B:TYR219 4.2 35.1 1.0 ND1 B:HIS258 4.2 30.2 1.0 ND1 B:HIS317 4.3 27.0 1.0 NE2 B:HIS389 4.3 30.9 1.0 CG B:GLU201 4.3 20.0 1.0 CE2 B:TYR219 4.4 28.2 1.0 CD2 B:HIS389 4.6 28.0 1.0 OE2 B:GLU407 4.6 39.2 1.0 CB B:GLU201 4.7 20.0 1.0 CZ B:TYR219 4.8 34.3 1.0

Manganese binding site 4 out of 8 in the Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:31.1 occ:1.00 OE2 B:GLU201 1.8 20.0 1.0 O B:HOH712 2.1 38.4 1.0 NE2 B:HIS475 2.1 25.2 1.0 NE2 B:HIS389 2.2 30.9 1.0 OE1 B:GLU407 2.7 38.0 1.0 CD B:GLU201 2.9 20.0 1.0 CD2 B:HIS475 3.0 25.6 1.0 CE1 B:HIS389 3.1 29.8 1.0 CE1 B:HIS475 3.1 27.9 1.0 CD2 B:HIS389 3.2 28.0 1.0 CD B:GLU407 3.4 35.5 1.0 OE1 B:GLU201 3.5 20.0 1.0 OE2 B:GLU407 3.6 39.2 1.0 MN B:MN601 3.6 28.1 1.0 NE2 B:HIS317 4.0 28.4 1.0 CG B:HIS475 4.2 24.9 1.0 CE1 B:HIS317 4.2 31.0 1.0 ND1 B:HIS475 4.2 27.6 1.0 ND1 B:HIS389 4.2 26.9 1.0 CG B:GLU201 4.2 20.0 1.0 CG B:HIS389 4.3 27.8 1.0 CG B:GLU407 4.7 29.6 1.0 CB B:GLU407 4.8 29.9 1.0 CZ B:PHE476 5.0 33.7 1.0

Manganese binding site 5 out of 8 in the Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn601 b:30.1 occ:1.00 OE1 C:GLU201 2.0 36.1 1.0 NE2 C:HIS317 2.1 30.8 1.0 NE2 C:HIS258 2.1 31.5 1.0 O C:HOH803 2.2 42.4 1.0 CD C:GLU201 3.0 36.5 1.0 CD2 C:HIS317 3.0 27.8 1.0 CD2 C:HIS258 3.1 31.7 1.0 CE1 C:HIS317 3.1 29.0 1.0 CE1 C:HIS258 3.2 31.2 1.0 OE2 C:GLU201 3.3 31.7 1.0 MN C:MN602 3.6 31.0 1.0 ND1 C:HIS317 4.2 30.7 1.0 CG C:HIS317 4.2 29.8 1.0 OH C:TYR219 4.2 38.4 1.0 ND1 C:HIS258 4.2 34.2 1.0 CG C:HIS258 4.2 33.9 1.0 NE2 C:HIS389 4.3 33.8 1.0 CG C:GLU201 4.3 35.4 1.0 CE2 C:TYR219 4.5 32.8 1.0 CD2 C:HIS389 4.5 31.0 1.0 OE2 C:GLU407 4.6 39.4 1.0 CB C:GLU201 4.8 34.5 1.0 CZ C:TYR219 4.8 35.9 1.0

Manganese binding site 6 out of 8 in the Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn602 b:31.0 occ:1.00 OE2 C:GLU201 2.0 31.7 1.0 NE2 C:HIS475 2.1 26.9 1.0 O C:HOH803 2.1 42.4 1.0 NE2 C:HIS389 2.2 33.8 1.0 OE1 C:GLU407 2.7 41.5 1.0 CD2 C:HIS475 3.0 31.1 1.0 CD C:GLU201 3.1 36.5 1.0 CE1 C:HIS475 3.1 30.6 1.0 CE1 C:HIS389 3.1 31.9 1.0 CD2 C:HIS389 3.2 31.0 1.0 CD C:GLU407 3.4 41.7 1.0 OE2 C:GLU407 3.5 39.4 1.0 OE1 C:GLU201 3.5 36.1 1.0 MN C:MN601 3.6 30.1 1.0 NE2 C:HIS317 4.1 30.8 1.0 ND1 C:HIS475 4.1 30.0 1.0 CG C:HIS475 4.1 32.9 1.0 CE1 C:HIS317 4.1 29.0 1.0 ND1 C:HIS389 4.2 31.8 1.0 CG C:HIS389 4.3 31.6 1.0 CG C:GLU201 4.3 35.4 1.0 CG C:GLU407 4.7 35.6 1.0 CB C:GLU407 4.9 33.4 1.0

Manganese binding site 7 out of 8 in the Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn601 b:35.6 occ:1.00 OE2 D:GLU201 2.0 31.0 1.0 NE2 D:HIS475 2.1 31.3 1.0 NE2 D:HIS389 2.2 31.1 1.0 O D:HOH858 2.2 43.3 1.0 OE1 D:GLU407 2.6 43.1 1.0 CE1 D:HIS475 3.0 36.1 1.0 CD2 D:HIS475 3.0 30.9 1.0 CD D:GLU201 3.0 33.6 1.0 CE1 D:HIS389 3.1 32.1 1.0 O D:HOH864 3.2 57.5 1.0 CD2 D:HIS389 3.2 28.6 1.0 CD D:GLU407 3.4 42.8 1.0 OE1 D:GLU201 3.4 32.2 1.0 MN D:MN602 3.6 35.0 1.0 OE2 D:GLU407 3.6 42.0 1.0 NE2 D:HIS317 4.0 34.4 1.0 ND1 D:HIS475 4.1 32.1 1.0 CG D:HIS475 4.1 34.5 1.0 CE1 D:HIS317 4.2 33.2 1.0 ND1 D:HIS389 4.2 33.6 1.0 CG D:HIS389 4.3 31.1 1.0 CG D:GLU201 4.3 37.9 1.0 CG D:GLU407 4.7 35.6 1.0 CB D:GLU407 4.9 31.4 1.0 O D:HOH838 4.9 52.8 1.0

Manganese binding site 8 out of 8 in the Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Phosphotriesterase From Sphingobium Sp. TCM1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn602 b:35.0 occ:1.00 OE1 D:GLU201 2.0 32.2 1.0 NE2 D:HIS258 2.0 33.9 1.0 NE2 D:HIS317 2.0 34.4 1.0 O D:HOH858 2.2 43.3 1.0 CD2 D:HIS317 2.9 31.0 1.0 CD2 D:HIS258 2.9 35.0 1.0 O D:HOH878 3.0 53.4 1.0 CE1 D:HIS258 3.1 31.4 1.0 CD D:GLU201 3.1 33.6 1.0 CE1 D:HIS317 3.1 33.2 1.0 O D:HOH838 3.3 52.8 1.0 OE2 D:GLU201 3.4 31.0 1.0 MN D:MN601 3.6 35.6 1.0 CG D:HIS317 4.1 36.1 1.0 CG D:HIS258 4.1 35.1 1.0 ND1 D:HIS258 4.1 33.0 1.0 ND1 D:HIS317 4.1 31.5 1.0 NE2 D:HIS389 4.3 31.1 1.0 OH D:TYR219 4.4 39.7 1.0 CG D:GLU201 4.4 37.9 1.0 CD2 D:HIS389 4.5 28.6 1.0 CE1 D:TYR219 4.5 35.4 1.0 OE2 D:GLU407 4.6 42.0 1.0 CB D:GLU201 4.9 32.9 1.0 CZ D:TYR219 5.0 37.9 1.0

M.F.Mabanglo, D.F.Xiang, A.N.Bigley, F.M.Raushel. Structure of A Novel Phosphotriesterase From Sphingobium Sp. TCM1: A Familiar Binuclear Metal Center Embedded in A Seven-Bladed Beta-Propeller Protein Fold. Biochemistry V. 55 3963 2016.
ISSN: ISSN 0006-2960
PubMed: 27353520
DOI: 10.1021/ACS.BIOCHEM.6B00364