Manganese in PDB 4qrn: High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid

The structure of High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid, PDB code: 4qrn was solved by Y.Patskovsky, A.Vladimirova, R.Toro, R.Bhosle, J.A.Gerlt, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.14 / 1.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.723, 60.747, 130.517, 90.00, 103.33, 90.00
R / Rfree (%)	13.5 / 15.5

The structure of High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Manganese atom in the High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid (pdb code 4qrn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid, PDB code: 4qrn:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:8.0 occ:0.73 OD1 A:ASP314 2.1 8.8 0.7 O3 A:1DF402 2.1 8.0 0.9 O11 A:1DF402 2.1 12.1 0.9 OE2 A:GLU19 2.2 9.9 1.0 O A:HOH572 2.2 10.1 1.0 OD1 A:ASP314 2.2 9.8 0.3 NE2 A:HIS188 2.2 8.3 1.0 N A:1DF402 2.9 11.0 0.9 CZ A:1DF402 3.1 7.0 0.9 CG A:ASP314 3.1 8.5 0.7 CG A:ASP314 3.2 9.8 0.3 CE1 A:HIS188 3.2 7.9 1.0 CD2 A:HIS188 3.2 8.2 1.0 HE1 A:HIS188 3.3 9.4 1.0 CD A:GLU19 3.3 8.2 1.0 CM1 A:1DF402 3.3 7.3 0.9 HG2 A:GLU19 3.4 10.1 1.0 OD2 A:ASP314 3.4 9.6 0.7 HD2 A:HIS188 3.4 9.8 1.0 OD2 A:ASP314 3.6 10.8 0.3 HE2 A:HIS241 3.6 12.3 1.0 CG A:GLU19 3.9 8.4 1.0 O22 A:1DF402 4.0 12.6 0.9 HE1 A:HIS241 4.1 11.9 1.0 O A:HOH512 4.1 8.1 1.0 HA A:ASP314 4.2 9.7 0.7 HD2 A:TYR317 4.2 8.9 1.0 HA A:ASP314 4.3 10.1 0.3 HB2 A:ASP314 4.3 10.6 0.3 CB A:ASP314 4.3 8.9 0.3 ND1 A:HIS188 4.3 7.7 1.0 NE2 A:HIS241 4.3 10.2 1.0 OE1 A:GLU19 4.3 8.2 1.0 HD2 A:PRO189 4.3 8.7 1.0 O A:GLU19 4.4 9.3 1.0 CM2 A:1DF402 4.4 7.2 0.9 CG A:HIS188 4.4 7.5 1.0 CB A:ASP314 4.5 8.3 0.7 HG3 A:GLU19 4.5 10.1 1.0 HB1 A:ALA21 4.5 9.1 1.0 O A:HOH515 4.5 8.9 1.0 CE1 A:HIS241 4.5 9.9 1.0 CO1 A:1DF402 4.7 7.5 0.9 OM A:1DF402 4.8 7.8 0.9 HB3 A:GLU19 4.8 9.4 1.0 CD2 A:TYR317 4.8 7.4 1.0 CA A:ASP314 4.8 8.1 0.7 CA A:ASP314 4.9 8.4 0.3 HB2 A:SER289 4.9 8.8 1.0 HE2 A:TYR317 4.9 8.4 1.0 HB3 A:ASP314 5.0 10.0 0.7 HG A:SER289 5.0 8.8 1.0 CB A:GLU19 5.0 7.9 1.0

Manganese binding site 2 out of 4 in the High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:7.9 occ:0.72 OD1 B:ASP314 2.1 10.4 0.8 O11 B:1DF402 2.1 13.1 0.9 O3 B:1DF402 2.1 8.4 0.9 OE2 B:GLU19 2.1 10.0 1.0 OD1 B:ASP314 2.2 10.0 0.2 O B:HOH564 2.2 10.4 1.0 NE2 B:HIS188 2.2 8.3 1.0 N B:1DF402 2.9 11.6 0.9 CG B:ASP314 3.1 10.0 0.8 CZ B:1DF402 3.1 7.9 0.9 CE1 B:HIS188 3.2 8.4 1.0 CG B:ASP314 3.2 10.0 0.2 CD2 B:HIS188 3.3 7.9 1.0 CD B:GLU19 3.3 9.0 1.0 HE1 B:HIS188 3.3 10.0 1.0 CM1 B:1DF402 3.4 8.8 0.9 OD2 B:ASP314 3.4 10.0 0.8 HG2 B:GLU19 3.4 10.8 1.0 HD2 B:HIS188 3.4 9.5 1.0 HE2 B:HIS241 3.6 13.3 1.0 OD2 B:ASP314 3.7 9.7 0.2 CG B:GLU19 3.9 9.0 1.0 O22 B:1DF402 4.0 13.3 0.9 HE1 B:HIS241 4.1 12.5 1.0 O B:HOH512 4.1 8.1 1.0 HD2 B:TYR317 4.1 9.6 1.0 HA B:ASP314 4.2 11.2 0.8 HA B:ASP314 4.2 11.0 0.2 NE2 B:HIS241 4.3 11.1 1.0 ND1 B:HIS188 4.3 7.6 1.0 OE1 B:GLU19 4.3 8.4 1.0 O B:GLU19 4.3 10.1 1.0 CB B:ASP314 4.3 9.5 0.2 HB2 B:ASP314 4.3 11.4 0.2 HD2 B:PRO189 4.4 8.9 1.0 CG B:HIS188 4.4 7.5 1.0 CM2 B:1DF402 4.4 7.5 0.9 CB B:ASP314 4.5 9.8 0.8 O B:HOH519 4.5 9.2 1.0 HG3 B:GLU19 4.5 10.8 1.0 CE1 B:HIS241 4.5 10.4 1.0 HB3 B:ALA21 4.6 9.3 1.0 CO1 B:1DF402 4.7 8.3 0.9 CD2 B:TYR317 4.7 8.0 1.0 HB3 B:GLU19 4.7 10.1 1.0 OM B:1DF402 4.8 8.1 0.9 CA B:ASP314 4.8 9.3 0.8 HB2 B:SER289 4.8 9.1 1.0 CA B:ASP314 4.9 9.2 0.2 HE2 B:TYR317 4.9 9.3 1.0 HG B:SER289 5.0 8.9 1.0 HB3 B:ASP314 5.0 11.7 0.8 CB B:GLU19 5.0 8.4 1.0

Manganese binding site 3 out of 4 in the High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:8.8 occ:0.72 OD1 C:ASP314 2.1 10.9 0.7 O11 C:1DF402 2.1 14.0 0.9 O3 C:1DF402 2.1 9.3 0.9 OE2 C:GLU19 2.1 10.4 1.0 OD1 C:ASP314 2.2 11.5 0.3 O C:HOH575 2.2 11.3 1.0 NE2 C:HIS188 2.2 9.1 1.0 N C:1DF402 2.9 12.9 0.9 CG C:ASP314 3.1 10.6 0.7 CZ C:1DF402 3.1 9.0 0.9 CE1 C:HIS188 3.2 9.1 1.0 CG C:ASP314 3.2 10.9 0.3 CD2 C:HIS188 3.3 8.8 1.0 CD C:GLU19 3.3 9.1 1.0 HE1 C:HIS188 3.3 10.9 1.0 CM1 C:1DF402 3.4 9.8 0.9 OD2 C:ASP314 3.4 11.6 0.7 HG2 C:GLU19 3.4 11.4 1.0 HD2 C:HIS188 3.4 10.5 1.0 HE2 C:HIS241 3.6 14.3 1.0 OD2 C:ASP314 3.7 11.2 0.3 CG C:GLU19 3.9 9.5 1.0 O22 C:1DF402 4.0 14.6 0.9 O C:HOH512 4.1 9.2 1.0 HE1 C:HIS241 4.1 13.7 1.0 HD2 C:TYR317 4.1 11.2 1.0 HA C:ASP314 4.2 11.4 0.7 HA C:ASP314 4.2 11.7 0.3 NE2 C:HIS241 4.3 11.9 1.0 ND1 C:HIS188 4.3 8.7 1.0 OE1 C:GLU19 4.3 9.2 1.0 CB C:ASP314 4.3 10.1 0.3 HB2 C:ASP314 4.3 12.1 0.3 O C:GLU19 4.4 10.7 1.0 HD2 C:PRO189 4.4 9.9 1.0 CG C:HIS188 4.4 8.2 1.0 CM2 C:1DF402 4.4 8.5 0.9 CB C:ASP314 4.5 10.2 0.7 HG3 C:GLU19 4.5 11.4 1.0 O C:HOH550 4.5 10.1 1.0 CE1 C:HIS241 4.5 11.4 1.0 HB2 C:ALA21 4.6 10.4 1.0 CD2 C:TYR317 4.7 9.3 1.0 CO1 C:1DF402 4.7 9.6 0.9 HB3 C:GLU19 4.8 11.0 1.0 OM C:1DF402 4.8 9.4 0.9 CA C:ASP314 4.8 9.5 0.7 HB2 C:SER289 4.8 10.2 1.0 CA C:ASP314 4.9 9.8 0.3 HE2 C:TYR317 4.9 10.5 1.0 HB3 C:ASP314 4.9 12.2 0.7 HG C:SER289 5.0 10.1 1.0 CB C:GLU19 5.0 9.2 1.0

Manganese binding site 4 out of 4 in the High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of High-Resolution Crystal Structure of 5-Carboxyvanillate Decarboxylase (Target Efi-505250) From Novosphingobium Aromaticivorans Dsm 12444 Complexed with Manganese and 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:8.7 occ:0.71 OD1 D:ASP314 2.1 11.6 0.7 O11 D:1DF402 2.1 13.7 0.9 O3 D:1DF402 2.1 9.1 0.9 OE2 D:GLU19 2.2 10.9 1.0 O D:HOH542 2.2 11.3 1.0 OD1 D:ASP314 2.2 11.7 0.3 NE2 D:HIS188 2.2 9.5 1.0 N D:1DF402 2.9 12.1 0.9 CZ D:1DF402 3.1 8.8 0.9 CG D:ASP314 3.1 10.5 0.7 CE1 D:HIS188 3.2 9.5 1.0 CG D:ASP314 3.2 11.2 0.3 CD2 D:HIS188 3.3 9.2 1.0 HE1 D:HIS188 3.3 11.4 1.0 CD D:GLU19 3.3 9.8 1.0 CM1 D:1DF402 3.3 9.7 0.9 HG2 D:GLU19 3.4 12.6 1.0 OD2 D:ASP314 3.4 10.6 0.7 HD2 D:HIS188 3.5 11.0 1.0 HE2 D:HIS241 3.6 13.8 1.0 OD2 D:ASP314 3.7 12.0 0.3 CG D:GLU19 3.9 10.5 1.0 O22 D:1DF402 4.0 13.8 0.9 O D:HOH509 4.1 9.8 1.0 HE1 D:HIS241 4.1 13.3 1.0 HA D:ASP314 4.2 10.4 0.7 HD2 D:TYR317 4.2 10.9 1.0 HA D:ASP314 4.3 10.9 0.3 ND1 D:HIS188 4.3 9.0 1.0 HB2 D:ASP314 4.3 12.0 0.3 NE2 D:HIS241 4.3 11.5 1.0 OE1 D:GLU19 4.3 9.2 1.0 CB D:ASP314 4.3 10.0 0.3 HD2 D:PRO189 4.3 10.6 1.0 O D:GLU19 4.4 11.0 1.0 CM2 D:1DF402 4.4 9.1 0.9 CG D:HIS188 4.4 8.5 1.0 HG3 D:GLU19 4.5 12.6 1.0 CB D:ASP314 4.5 9.9 0.7 O D:HOH513 4.5 11.2 1.0 HB3 D:ALA21 4.5 11.0 1.0 CE1 D:HIS241 4.6 11.1 1.0 CO1 D:1DF402 4.7 9.1 0.9 OM D:1DF402 4.8 9.8 0.9 HB3 D:GLU19 4.8 11.3 1.0 CD2 D:TYR317 4.8 9.1 1.0 CA D:ASP314 4.8 8.6 0.7 CA D:ASP314 4.9 9.1 0.3 HB2 D:SER289 4.9 9.7 1.0 HE2 D:TYR317 5.0 10.7 1.0 HB3 D:ASP314 5.0 11.9 0.7 CB D:GLU19 5.0 9.4 1.0 HG D:SER289 5.0 10.2 1.0

Y.Patskovsky, A.Vladimirova, R.Toro, R.Bhosle, F.M.Raushel, S.C.Almo. Crystal Structure of 5-Carboxyvanillate Decarboxylase From Novosphingobium Aromaticivorans To Be Published.