Manganese in PDB 4qro: Crystal Structure of Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol

The structure of Crystal Structure of Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol, PDB code: 4qro was solved by Y.Patskovsky, A.Vladimirova, R.Toro, R.Bhosle, J.A.Gerlt, M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.958, 151.058, 143.826, 90.00, 92.15, 90.00
R / Rfree (%)	18.9 / 22.3

The binding sites of Manganese atom in the Crystal Structure of Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol (pdb code 4qro). 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 Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol, PDB code: 4qro:
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 Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol


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 Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:31.3 occ:1.00 OD1 A:ASP287 2.2 34.9 1.0 OE1 A:GLU8 2.2 32.8 1.0 OAI A:38L405 2.2 35.7 1.0 NE2 A:HIS10 2.2 27.4 1.0 NE2 A:HIS164 2.3 37.3 1.0 OAK A:38L405 2.3 37.0 1.0 CG A:ASP287 3.1 53.0 1.0 CD2 A:HIS10 3.2 31.6 1.0 CE1 A:HIS164 3.2 32.1 1.0 CE1 A:HIS10 3.2 38.6 1.0 CD A:GLU8 3.2 31.0 1.0 CAB A:38L405 3.2 35.8 1.0 NAG A:38L405 3.2 94.5 1.0 CD2 A:HIS164 3.2 27.9 1.0 OD2 A:ASP287 3.4 63.3 1.0 CAA A:38L405 3.5 44.3 1.0 CG A:GLU8 3.6 32.5 1.0 O A:HOH556 4.2 34.9 1.0 OAJ A:38L405 4.3 44.2 1.0 ND1 A:HIS10 4.3 32.3 1.0 CG A:HIS10 4.3 29.2 1.0 NE2 A:HIS218 4.3 37.1 1.0 OE2 A:GLU8 4.3 33.1 1.0 ND1 A:HIS164 4.3 29.0 1.0 CG A:HIS164 4.4 31.8 1.0 CB A:ASP287 4.4 35.5 1.0 CE1 A:HIS218 4.5 29.3 1.0 CAC A:38L405 4.5 41.9 1.0 CD2 A:PHE290 4.7 36.8 1.0 CA A:ASP287 4.7 40.1 1.0 CAF A:38L405 4.9 41.2 1.0 CB A:GLU8 4.9 33.3 1.0

Manganese binding site 2 out of 8 in the Crystal Structure of Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol


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 Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:33.6 occ:1.00 OE1 B:GLU8 2.1 32.2 1.0 OAI B:38L404 2.1 34.0 1.0 OD1 B:ASP287 2.2 37.5 1.0 OAK B:38L404 2.3 44.4 1.0 NE2 B:HIS10 2.3 24.9 1.0 NE2 B:HIS164 2.4 31.1 1.0 CD B:GLU8 3.1 37.1 1.0 CD2 B:HIS10 3.1 31.1 1.0 CG B:ASP287 3.2 52.2 1.0 CAB B:38L404 3.2 41.6 1.0 NAG B:38L404 3.2 67.0 1.0 CD2 B:HIS164 3.3 25.1 1.0 CE1 B:HIS10 3.4 42.5 1.0 CE1 B:HIS164 3.4 34.3 1.0 OD2 B:ASP287 3.5 55.6 1.0 CAA B:38L404 3.5 52.5 1.0 CG B:GLU8 3.6 27.6 1.0 OE2 B:GLU8 4.3 35.2 1.0 O B:HOH562 4.3 35.1 1.0 OAJ B:38L404 4.3 57.0 1.0 CG B:HIS10 4.3 33.1 1.0 NE2 B:HIS218 4.3 36.6 1.0 ND1 B:HIS10 4.4 33.1 1.0 CAC B:38L404 4.4 43.9 1.0 CG B:HIS164 4.5 35.5 1.0 ND1 B:HIS164 4.5 39.4 1.0 CB B:ASP287 4.5 46.1 1.0 CE1 B:HIS218 4.5 42.3 1.0 CD2 B:PHE290 4.7 34.0 1.0 CA B:ASP287 4.8 35.9 1.0 CAF B:38L404 4.8 47.2 1.0 CB B:GLU8 4.9 35.3 1.0

Manganese binding site 3 out of 8 in the Crystal Structure of Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol


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 Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:32.7 occ:1.00 OD1 C:ASP287 2.1 32.9 1.0 OAH C:38L405 2.2 35.6 1.0 NE2 C:HIS10 2.2 31.3 1.0 OE1 C:GLU8 2.3 32.9 1.0 NE2 C:HIS164 2.3 35.8 1.0 OAK C:38L405 2.4 45.8 1.0 CG C:ASP287 3.1 41.4 1.0 CD2 C:HIS10 3.1 34.8 1.0 CE1 C:HIS10 3.2 38.9 1.0 NAG C:38L405 3.3 71.1 1.0 CAF C:38L405 3.3 41.4 1.0 CE1 C:HIS164 3.3 31.2 1.0 CD2 C:HIS164 3.3 34.5 1.0 CD C:GLU8 3.3 33.2 1.0 OD2 C:ASP287 3.5 60.8 1.0 CAA C:38L405 3.6 45.4 1.0 CG C:GLU8 3.7 33.0 1.0 O C:HOH570 4.2 34.4 1.0 CG C:HIS10 4.3 32.0 1.0 ND1 C:HIS10 4.3 37.5 1.0 OAJ C:38L405 4.3 50.1 1.0 NE2 C:HIS218 4.4 34.9 1.0 ND1 C:HIS164 4.4 34.0 1.0 OE2 C:GLU8 4.4 32.6 1.0 CG C:HIS164 4.5 32.9 1.0 CB C:ASP287 4.5 27.8 1.0 CAE C:38L405 4.5 46.3 1.0 CE1 C:HIS218 4.5 28.3 1.0 CD2 C:PHE290 4.6 33.7 1.0 CA C:ASP287 4.8 34.5 1.0 CAB C:38L405 4.9 41.8 1.0 CE2 C:PHE290 4.9 40.0 1.0 CB C:GLU8 5.0 36.2 1.0

Manganese binding site 4 out of 8 in the Crystal Structure of Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol


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 Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:34.0 occ:1.00 OE1 D:GLU8 2.1 39.3 1.0 OD1 D:ASP287 2.2 33.0 1.0 OAH D:38L403 2.2 33.4 1.0 OAK D:38L403 2.2 38.5 1.0 NE2 D:HIS164 2.3 34.4 1.0 NE2 D:HIS10 2.3 30.6 1.0 NAG D:38L403 3.1 65.4 1.0 CG D:ASP287 3.1 52.7 1.0 CD2 D:HIS10 3.2 36.6 1.0 CD D:GLU8 3.2 34.3 1.0 CAF D:38L403 3.3 37.1 1.0 CD2 D:HIS164 3.3 31.6 1.0 CE1 D:HIS164 3.3 39.7 1.0 CE1 D:HIS10 3.4 39.2 1.0 OD2 D:ASP287 3.4 57.6 1.0 CAA D:38L403 3.5 36.7 1.0 CG D:GLU8 3.6 34.4 1.0 O D:HOH616 4.2 33.4 1.0 OAJ D:38L403 4.2 55.1 1.0 NE2 D:HIS218 4.2 37.2 1.0 OE2 D:GLU8 4.3 40.2 1.0 CG D:HIS10 4.3 37.4 1.0 ND1 D:HIS10 4.4 42.2 1.0 ND1 D:HIS164 4.4 38.4 1.0 CG D:HIS164 4.4 31.7 1.0 CE1 D:HIS218 4.5 48.1 1.0 CAE D:38L403 4.5 37.9 1.0 CB D:ASP287 4.5 39.4 1.0 CD2 D:PHE290 4.7 40.8 1.0 CAB D:38L403 4.8 44.6 1.0 CA D:ASP287 4.9 31.4 1.0 CB D:GLU8 5.0 34.9 1.0

Manganese binding site 5 out of 8 in the Crystal Structure of Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol


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 Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn401 b:21.1 occ:1.00 OAK E:38L404 2.1 23.1 1.0 OAH E:38L404 2.2 24.9 1.0 NE2 E:HIS10 2.2 17.9 1.0 OE1 E:GLU8 2.2 24.7 1.0 OD1 E:ASP287 2.2 27.7 1.0 NE2 E:HIS164 2.3 25.3 1.0 CD2 E:HIS10 3.0 20.6 1.0 NAG E:38L404 3.1 72.0 1.0 CG E:ASP287 3.1 35.1 1.0 CE1 E:HIS164 3.2 22.4 1.0 CD E:GLU8 3.2 21.3 1.0 CAF E:38L404 3.2 24.2 1.0 CE1 E:HIS10 3.3 25.4 1.0 CD2 E:HIS164 3.4 22.9 1.0 OD2 E:ASP287 3.4 43.7 1.0 CAA E:38L404 3.5 27.4 1.0 CG E:GLU8 3.6 23.0 1.0 OAJ E:38L404 4.1 32.0 1.0 O E:HOH583 4.2 23.8 1.0 CG E:HIS10 4.2 20.6 1.0 ND1 E:HIS10 4.3 22.9 1.0 OE2 E:GLU8 4.3 22.2 1.0 ND1 E:HIS164 4.3 21.3 1.0 NE2 E:HIS218 4.3 22.8 1.0 CG E:HIS164 4.5 18.6 1.0 CB E:ASP287 4.5 23.6 1.0 CAE E:38L404 4.5 29.3 1.0 CE1 E:HIS218 4.6 25.6 1.0 CD2 E:PHE290 4.7 21.3 1.0 CA E:ASP287 4.8 21.9 1.0 CAB E:38L404 4.9 30.2 1.0 CB E:GLU8 5.0 19.5 1.0

Manganese binding site 6 out of 8 in the Crystal Structure of Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol


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 Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn402 b:22.9 occ:1.00 OAI F:38L404 2.1 27.9 1.0 OD1 F:ASP287 2.2 29.9 1.0 OE1 F:GLU8 2.2 26.3 1.0 OAK F:38L404 2.3 26.6 1.0 NE2 F:HIS10 2.3 22.2 1.0 NE2 F:HIS164 2.3 26.7 1.0 CD2 F:HIS10 3.1 22.5 1.0 CG F:ASP287 3.1 34.9 1.0 CAB F:38L404 3.2 26.2 1.0 NAG F:38L404 3.2 57.3 1.0 CD F:GLU8 3.2 24.0 1.0 CE1 F:HIS164 3.3 25.5 1.0 CD2 F:HIS164 3.3 22.9 1.0 CE1 F:HIS10 3.4 28.8 1.0 OD2 F:ASP287 3.4 42.0 1.0 CAA F:38L404 3.5 35.9 1.0 CG F:GLU8 3.6 20.9 1.0 O F:HOH543 4.2 24.8 1.0 OAJ F:38L404 4.3 31.4 1.0 CG F:HIS10 4.3 25.4 1.0 NE2 F:HIS218 4.3 27.2 1.0 OE2 F:GLU8 4.3 23.5 1.0 ND1 F:HIS10 4.4 27.4 1.0 ND1 F:HIS164 4.4 22.5 1.0 CAC F:38L404 4.4 29.0 1.0 CG F:HIS164 4.5 20.0 1.0 CB F:ASP287 4.5 19.8 1.0 CE1 F:HIS218 4.5 30.6 1.0 CD2 F:PHE290 4.6 24.4 1.0 CA F:ASP287 4.8 20.0 1.0 CAF F:38L404 4.8 29.4 1.0 CB F:GLU8 4.9 23.7 1.0 CE2 F:PHE290 5.0 27.8 1.0

Manganese binding site 7 out of 8 in the Crystal Structure of Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol


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 Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn401 b:21.4 occ:1.00 OAK G:38L403 2.1 26.9 1.0 OAH G:38L403 2.1 25.4 1.0 OE1 G:GLU8 2.2 24.1 1.0 NE2 G:HIS10 2.2 24.1 1.0 OD1 G:ASP287 2.3 26.8 1.0 NE2 G:HIS164 2.3 28.4 1.0 NAG G:38L403 3.1 79.2 1.0 CD2 G:HIS10 3.1 23.5 1.0 CAF G:38L403 3.2 21.7 1.0 CD G:GLU8 3.2 20.9 1.0 CG G:ASP287 3.2 38.3 1.0 CE1 G:HIS164 3.2 25.5 1.0 CE1 G:HIS10 3.3 25.4 1.0 CD2 G:HIS164 3.3 23.0 1.0 CAA G:38L403 3.5 29.2 1.0 OD2 G:ASP287 3.5 42.4 1.0 CG G:GLU8 3.6 22.6 1.0 OAJ G:38L403 4.1 29.4 1.0 O G:HOH735 4.2 25.1 1.0 CG G:HIS10 4.3 21.7 1.0 OE2 G:GLU8 4.3 21.6 1.0 ND1 G:HIS10 4.3 24.5 1.0 NE2 G:HIS218 4.4 22.9 1.0 ND1 G:HIS164 4.4 22.4 1.0 CAE G:38L403 4.4 28.4 1.0 CG G:HIS164 4.5 21.7 1.0 CB G:ASP287 4.5 22.3 1.0 CE1 G:HIS218 4.6 24.5 1.0 CD2 G:PHE290 4.7 23.3 1.0 CA G:ASP287 4.8 21.8 1.0 CAB G:38L403 4.8 28.6 1.0 CB G:GLU8 4.9 24.0 1.0

Manganese binding site 8 out of 8 in the Crystal Structure of Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol


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 Dihydroxybenzoic Acid Decarbboxylase BPRO_2061 (Target Efi-500288) From Polaromonas Sp. JS666 with Bound Manganese and An Inhibitor, 2-Nitroresorcinol within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn402 b:23.8 occ:1.00 OE1 H:GLU8 2.2 25.8 1.0 OAK H:38L405 2.2 35.4 1.0 OD1 H:ASP287 2.2 28.2 1.0 OAI H:38L405 2.2 25.6 1.0 NE2 H:HIS10 2.3 24.4 1.0 NE2 H:HIS164 2.3 27.4 1.0 CD2 H:HIS10 3.1 22.6 1.0 CG H:ASP287 3.1 36.1 1.0 NAG H:38L405 3.1 68.0 1.0 CD H:GLU8 3.2 25.0 1.0 CAB H:38L405 3.2 27.9 1.0 CD2 H:HIS164 3.3 22.0 1.0 CE1 H:HIS164 3.3 29.6 1.0 CE1 H:HIS10 3.3 28.1 1.0 OD2 H:ASP287 3.4 39.3 1.0 CAA H:38L405 3.5 30.0 1.0 CG H:GLU8 3.6 20.9 1.0 OAJ H:38L405 4.2 31.8 1.0 O H:HOH608 4.3 25.9 1.0 CG H:HIS10 4.3 22.2 1.0 OE2 H:GLU8 4.3 24.6 1.0 ND1 H:HIS10 4.4 24.5 1.0 NE2 H:HIS218 4.4 28.5 1.0 ND1 H:HIS164 4.4 26.6 1.0 CG H:HIS164 4.5 22.4 1.0 CB H:ASP287 4.5 21.1 1.0 CAC H:38L405 4.5 30.2 1.0 CE1 H:HIS218 4.6 27.1 1.0 CD2 H:PHE290 4.6 24.4 1.0 CA H:ASP287 4.8 19.2 1.0 CAF H:38L405 4.8 28.6 1.0 CB H:GLU8 4.9 27.9 1.0

Y.Patskovsky, A.Vladimirova, R.Toro, R.Bhosle, F.M.Raushel, S.C.Almo. Crystal Structure of Dihydroxybenzoate Decarboxylase From Frompolaromonas Sp with Bound Manganese and 2-Nitroresorcinol To Be Published.