Manganese in PDB 4qs5: Crystal Structure of 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant

The structure of Crystal Structure of 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant, PDB code: 4qs5 was solved by Y.Patskovsky, A.Vladimirova, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, 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 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	97.159, 60.590, 123.473, 90.00, 112.84, 90.00
R / Rfree (%)	15.6 / 21

The structure of Crystal Structure of 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant (pdb code 4qs5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant, PDB code: 4qs5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant


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 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:23.1 occ:1.00 O3 A:1DF402 2.1 20.3 1.0 O11 A:1DF402 2.2 53.6 1.0 OE2 A:GLU19 2.2 21.1 1.0 OD1 A:ASN314 2.3 28.6 1.0 NE2 A:HIS188 2.3 17.1 1.0 O A:HOH695 2.3 22.7 1.0 N A:1DF402 2.8 34.1 1.0 CZ A:1DF402 3.1 22.8 1.0 CG A:ASN314 3.2 25.8 1.0 CD2 A:HIS188 3.2 15.5 1.0 CE1 A:HIS188 3.3 22.5 1.0 CM1 A:1DF402 3.3 26.5 1.0 CD A:GLU19 3.4 37.7 1.0 ND2 A:ASN314 3.6 49.9 1.0 O22 A:1DF402 3.8 81.7 1.0 O A:HOH513 4.0 17.8 1.0 CG A:GLU19 4.0 24.3 1.0 OE1 A:GLU19 4.3 19.1 1.0 ND1 A:HIS188 4.4 19.3 1.0 CG A:HIS188 4.4 16.0 1.0 CM2 A:1DF402 4.4 18.1 1.0 CB A:ASN314 4.5 22.4 1.0 O A:GLU19 4.5 26.9 1.0 O A:HOH530 4.5 23.2 1.0 NE2 A:HIS241 4.6 27.8 1.0 CO1 A:1DF402 4.6 24.6 1.0 CD2 A:TYR317 4.7 16.3 1.0 CE1 A:HIS241 4.8 45.7 1.0 OM A:1DF402 4.9 24.0 1.0 CA A:ASN314 4.9 14.8 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant


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 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:20.8 occ:1.00 O11 B:1DF402 2.1 32.5 1.0 O B:HOH708 2.2 23.8 1.0 OD1 B:ASN314 2.2 20.8 1.0 O3 B:1DF402 2.2 21.2 1.0 OE2 B:GLU19 2.2 23.5 1.0 NE2 B:HIS188 2.2 15.2 1.0 N B:1DF402 2.9 39.0 1.0 CE1 B:HIS188 3.2 18.8 1.0 CZ B:1DF402 3.2 17.4 1.0 CG B:ASN314 3.2 41.4 1.0 CD2 B:HIS188 3.3 24.9 1.0 CD B:GLU19 3.4 27.9 1.0 CM1 B:1DF402 3.4 17.1 1.0 ND2 B:ASN314 3.7 50.5 1.0 CG B:GLU19 3.9 24.8 1.0 O22 B:1DF402 4.0 55.8 1.0 O B:HOH509 4.0 16.5 1.0 ND1 B:HIS188 4.3 16.5 1.0 O B:GLU19 4.4 27.5 1.0 OE1 B:GLU19 4.4 22.3 1.0 CG B:HIS188 4.4 7.9 1.0 CB B:ASN314 4.5 13.6 1.0 CM2 B:1DF402 4.5 21.9 1.0 O B:HOH605 4.6 22.8 1.0 NE2 B:HIS241 4.7 38.0 1.0 CO1 B:1DF402 4.8 17.4 1.0 CD2 B:TYR317 4.9 18.2 1.0 CE1 B:HIS241 4.9 40.6 1.0 CA B:ASN314 4.9 14.8 1.0 OM B:1DF402 4.9 23.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant


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 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:22.7 occ:1.00 OE2 C:GLU19 2.1 18.8 1.0 O3 C:1DF402 2.2 19.1 1.0 O11 C:1DF402 2.2 54.5 1.0 OD1 C:ASN314 2.3 23.4 1.0 NE2 C:HIS188 2.3 21.5 1.0 O C:HOH726 2.3 20.6 1.0 N C:1DF402 2.9 36.8 1.0 CZ C:1DF402 3.2 21.3 1.0 CG C:ASN314 3.2 30.2 1.0 CD C:GLU19 3.2 24.1 1.0 CE1 C:HIS188 3.2 21.2 1.0 CD2 C:HIS188 3.3 17.6 1.0 CM1 C:1DF402 3.4 27.8 1.0 ND2 C:ASN314 3.6 36.7 1.0 CG C:GLU19 3.8 17.4 1.0 O22 C:1DF402 3.9 65.6 1.0 O C:HOH524 4.0 17.5 1.0 OE1 C:GLU19 4.3 18.3 1.0 O C:GLU19 4.3 23.4 1.0 ND1 C:HIS188 4.4 16.1 1.0 CG C:HIS188 4.4 12.3 1.0 CM2 C:1DF402 4.4 18.9 1.0 CB C:ASN314 4.5 18.0 1.0 O C:HOH517 4.6 20.3 1.0 NE2 C:HIS241 4.7 34.5 1.0 CD2 C:TYR317 4.7 22.6 1.0 CO1 C:1DF402 4.8 14.8 1.0 CE1 C:HIS241 4.9 34.1 1.0 OM C:1DF402 4.9 29.1 1.0 CA C:ASN314 4.9 14.8 1.0 CB C:GLU19 4.9 16.5 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant


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 5-Carboxyvanillate Decarboxylase LIGW2 From Novosphingobium Aromaticivorans Dsm 12444 (Target Efi-505250) with Bound Manganese and 3-Methoxy-4-Hydroxy-5-Nitrobenzoic Acid, the D314N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:19.5 occ:1.00 O11 D:1DF402 2.1 35.0 1.0 O D:HOH710 2.2 19.0 1.0 O3 D:1DF402 2.2 15.6 1.0 OD1 D:ASN314 2.2 18.8 1.0 OE2 D:GLU19 2.2 23.7 1.0 NE2 D:HIS188 2.3 17.4 1.0 N D:1DF402 3.0 32.9 1.0 CE1 D:HIS188 3.2 18.0 1.0 CZ D:1DF402 3.2 15.4 1.0 CG D:ASN314 3.3 23.8 1.0 CD2 D:HIS188 3.3 22.9 1.0 CD D:GLU19 3.3 30.9 1.0 CM1 D:1DF402 3.4 24.5 1.0 ND2 D:ASN314 3.7 34.5 1.0 CG D:GLU19 3.9 21.4 1.0 O D:HOH527 4.0 17.4 1.0 O22 D:1DF402 4.1 57.5 1.0 ND1 D:HIS188 4.3 16.1 1.0 OE1 D:GLU19 4.3 21.6 1.0 O D:GLU19 4.4 25.1 1.0 CM2 D:1DF402 4.4 19.8 1.0 CG D:HIS188 4.4 17.2 1.0 CB D:ASN314 4.5 16.6 1.0 O D:HOH605 4.6 19.9 1.0 NE2 D:HIS241 4.6 31.3 1.0 CO1 D:1DF402 4.8 17.1 1.0 CD2 D:TYR317 4.8 18.0 1.0 OM D:1DF402 4.8 19.6 1.0 CE1 D:HIS241 4.9 53.5 1.0 CA D:ASN314 5.0 19.3 1.0 O D:HOH515 5.0 18.8 1.0

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