Manganese in PDB 4ni8: Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid

The structure of Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid, PDB code: 4ni8 was solved by A.A.Fedorov, E.V.Fedorov, A.Vladimirova, 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)	39.97 / 1.64
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	80.523, 99.896, 100.427, 67.04, 88.44, 68.07
R / Rfree (%)	14.8 / 17.5

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid (pdb code 4ni8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid, PDB code: 4ni8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid


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 Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:8.4 occ:0.85 MN A:MN401 0.0 8.4 0.8 O A:HOH827 2.1 22.0 0.8 OE2 A:GLU7 2.1 9.2 1.0 OD1 A:ASP296 2.2 10.1 1.0 NE2 A:HIS173 2.2 11.0 1.0 O11 A:1WB402 2.2 14.4 1.0 O A:HOH727 2.2 15.6 1.0 MN A:MN401 2.6 5.7 0.1 CG A:ASP296 3.1 12.3 1.0 CD2 A:HIS173 3.1 9.6 1.0 CD A:GLU7 3.2 8.0 1.0 CE1 A:HIS173 3.2 9.2 1.0 CCC A:1WB402 3.3 21.7 1.0 OD2 A:ASP296 3.3 13.7 1.0 CZ A:1WB402 3.6 16.5 1.0 CG A:GLU7 3.7 5.6 1.0 CM1 A:1WB402 3.8 19.9 1.0 O A:HOH563 4.1 12.2 1.0 O A:HOH615 4.2 15.6 1.0 O22 A:1WB402 4.3 15.3 1.0 NE2 A:HIS226 4.3 9.2 1.0 OE1 A:GLU7 4.3 9.5 1.0 CG A:HIS173 4.3 8.6 1.0 ND1 A:HIS173 4.3 7.6 1.0 O A:GLU7 4.4 9.7 1.0 CB A:ASP296 4.5 6.7 1.0 CE1 A:HIS226 4.5 10.4 1.0 CM2 A:1WB402 4.7 19.8 1.0 CD2 A:TYR299 4.7 18.8 1.0 CB A:GLU7 4.8 6.1 1.0 CA A:ASP296 4.8 6.0 1.0

Manganese binding site 2 out of 16 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid


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 Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:5.7 occ:0.15 MN A:MN401 0.0 5.7 0.1 NE2 A:HIS226 1.8 9.2 1.0 OD2 A:ASP296 1.9 13.7 1.0 O11 A:1WB402 1.9 14.4 1.0 OE2 A:GLU7 2.0 9.2 1.0 CE1 A:HIS226 2.5 10.4 1.0 MN A:MN401 2.6 8.4 0.8 CG A:ASP296 2.7 12.3 1.0 CCC A:1WB402 2.8 21.7 1.0 OD1 A:ASP296 2.9 10.1 1.0 CD2 A:HIS226 3.0 5.4 1.0 O22 A:1WB402 3.0 15.3 1.0 CD A:GLU7 3.1 8.0 1.0 OE1 A:GLU7 3.5 9.5 1.0 ND1 A:HIS226 3.7 9.6 1.0 OG A:SER271 3.9 9.6 1.0 CG A:HIS226 3.9 5.3 1.0 NE2 A:HIS173 3.9 11.0 1.0 O A:HOH558 3.9 14.1 1.0 CB A:ASP296 4.1 6.7 1.0 CB A:SER271 4.1 8.0 1.0 CM1 A:1WB402 4.1 19.9 1.0 O A:HOH827 4.3 22.0 0.8 CG A:GLU7 4.3 5.6 1.0 NH2 H:ARG237 4.5 7.8 1.0 CD2 A:HIS173 4.5 9.6 1.0 CZ A:1WB402 4.6 16.5 1.0 O A:HOH727 4.7 15.6 1.0 CE1 A:HIS173 4.7 9.2 1.0 NH1 H:ARG237 4.9 9.2 1.0 CD A:PRO174 4.9 7.0 1.0

Manganese binding site 3 out of 16 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid


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 Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:8.7 occ:0.85 MN B:MN401 0.0 8.7 0.8 O B:HOH834 2.1 23.7 0.7 OE2 B:GLU7 2.1 10.3 1.0 OD1 B:ASP296 2.2 10.8 1.0 O11 B:1WB402 2.2 21.6 1.0 NE2 B:HIS173 2.2 9.6 1.0 O B:HOH737 2.3 16.9 1.0 MN B:MN401 2.7 5.8 0.1 CG B:ASP296 3.0 10.8 1.0 CD2 B:HIS173 3.2 8.1 1.0 CE1 B:HIS173 3.3 12.2 1.0 CD B:GLU7 3.3 9.5 1.0 OD2 B:ASP296 3.3 9.6 1.0 CCC B:1WB402 3.3 23.0 1.0 CZ B:1WB402 3.6 15.7 1.0 CG B:GLU7 3.8 6.8 1.0 CM1 B:1WB402 3.8 22.0 1.0 O B:HOH612 4.1 16.1 1.0 NE2 B:HIS226 4.3 10.4 1.0 O22 B:1WB402 4.3 11.9 1.0 OE1 B:GLU7 4.3 8.9 1.0 CG B:HIS173 4.3 9.9 1.0 ND1 B:HIS173 4.3 8.9 1.0 O B:HOH587 4.3 16.0 1.0 O B:GLU7 4.4 10.9 1.0 CB B:ASP296 4.5 6.5 1.0 CE1 B:HIS226 4.5 9.7 1.0 CD2 B:TYR299 4.7 14.8 1.0 CM2 B:1WB402 4.8 17.3 1.0 CB B:GLU7 4.8 6.2 1.0 CA B:ASP296 4.8 8.1 1.0

Manganese binding site 4 out of 16 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid


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 Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:5.8 occ:0.15 MN B:MN401 0.0 5.8 0.1 OD2 B:ASP296 1.7 9.6 1.0 NE2 B:HIS226 1.8 10.4 1.0 O11 B:1WB402 2.0 21.6 1.0 OE2 B:GLU7 2.1 10.3 1.0 CG B:ASP296 2.6 10.8 1.0 CE1 B:HIS226 2.6 9.7 1.0 MN B:MN401 2.7 8.7 0.8 CCC B:1WB402 2.8 23.0 1.0 OD1 B:ASP296 2.9 10.8 1.0 CD2 B:HIS226 2.9 6.8 1.0 O22 B:1WB402 3.1 11.9 1.0 CD B:GLU7 3.1 9.5 1.0 OE1 B:GLU7 3.5 8.9 1.0 ND1 B:HIS226 3.7 10.4 1.0 OG B:SER271 3.8 7.0 1.0 O B:HOH513 3.8 14.5 1.0 CB B:ASP296 3.9 6.5 1.0 CG B:HIS226 3.9 7.8 1.0 CB B:SER271 3.9 6.9 1.0 NE2 B:HIS173 4.0 9.6 1.0 CM1 B:1WB402 4.2 22.0 1.0 O B:HOH834 4.3 23.7 0.7 CG B:GLU7 4.4 6.8 1.0 NH2 G:ARG237 4.6 8.6 1.0 CD2 B:HIS173 4.6 8.1 1.0 O B:HOH737 4.8 16.9 1.0 CZ B:1WB402 4.8 15.7 1.0 NH1 G:ARG237 4.8 7.8 1.0 CE1 B:HIS173 4.9 12.2 1.0 C B:SER271 4.9 6.4 1.0 O B:SER271 4.9 7.1 1.0 CA B:ASP296 5.0 8.1 1.0

Manganese binding site 5 out of 16 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid


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 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:10.7 occ:0.85 MN C:MN401 0.0 10.7 0.8 OE2 C:GLU7 2.1 10.0 1.0 OD1 C:ASP296 2.2 12.6 1.0 NE2 C:HIS173 2.2 12.2 1.0 O C:HOH822 2.2 20.5 0.8 O C:HOH811 2.2 17.2 1.0 O22 C:1WB402 2.2 17.0 1.0 MN C:MN401 2.6 6.5 0.1 CG C:ASP296 3.1 15.2 1.0 CD2 C:HIS173 3.1 11.0 1.0 CE1 C:HIS173 3.2 9.7 1.0 CD C:GLU7 3.2 8.2 1.0 CCC C:1WB402 3.3 21.5 1.0 OD2 C:ASP296 3.3 15.6 1.0 CZ C:1WB402 3.6 17.7 1.0 CG C:GLU7 3.7 6.6 1.0 CM1 C:1WB402 3.8 19.3 1.0 O C:HOH545 4.1 15.8 1.0 OE1 C:GLU7 4.3 9.9 1.0 ND1 C:HIS173 4.3 10.3 1.0 CG C:HIS173 4.3 11.4 1.0 O11 C:1WB402 4.3 14.5 1.0 NE2 C:HIS226 4.3 14.1 1.0 O C:HOH683 4.3 19.1 1.0 O C:GLU7 4.4 9.5 1.0 CB C:ASP296 4.5 9.6 1.0 CE1 C:HIS226 4.6 13.6 1.0 CD2 C:TYR299 4.7 22.3 1.0 CM2 C:1WB402 4.8 16.5 1.0 CA C:ASP296 4.8 7.4 1.0 CB C:GLU7 4.8 9.9 1.0

Manganese binding site 6 out of 16 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid


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 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:6.5 occ:0.15 MN C:MN401 0.0 6.5 0.1 NE2 C:HIS226 1.8 14.1 1.0 OD2 C:ASP296 1.8 15.6 1.0 OE2 C:GLU7 2.0 10.0 1.0 O22 C:1WB402 2.0 17.0 1.0 CE1 C:HIS226 2.6 13.6 1.0 MN C:MN401 2.6 10.7 0.8 CG C:ASP296 2.6 15.2 1.0 CCC C:1WB402 2.8 21.5 1.0 OD1 C:ASP296 2.9 12.6 1.0 CD2 C:HIS226 3.0 10.8 1.0 CD C:GLU7 3.0 8.2 1.0 O11 C:1WB402 3.1 14.5 1.0 OE1 C:GLU7 3.4 9.9 1.0 ND1 C:HIS226 3.8 10.2 1.0 OG C:SER271 3.8 6.8 1.0 O C:HOH583 3.9 18.6 1.0 NE2 C:HIS173 4.0 12.2 1.0 CG C:HIS226 4.0 9.0 1.0 CB C:ASP296 4.0 9.6 1.0 CB C:SER271 4.0 6.2 1.0 CM1 C:1WB402 4.2 19.3 1.0 CG C:GLU7 4.3 6.6 1.0 O C:HOH822 4.4 20.5 0.8 CD2 C:HIS173 4.5 11.0 1.0 O C:HOH811 4.6 17.2 1.0 NH2 F:ARG237 4.6 10.1 1.0 CZ C:1WB402 4.7 17.7 1.0 CE1 C:HIS173 4.7 9.7 1.0 NH1 F:ARG237 4.9 9.6 1.0 CD C:PRO174 5.0 10.6 1.0

Manganese binding site 7 out of 16 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid


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 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:7.5 occ:0.82 MN D:MN401 0.0 7.5 0.8 OE2 D:GLU7 2.1 9.4 1.0 O D:HOH747 2.1 16.6 1.0 OD1 D:ASP296 2.1 11.0 1.0 NE2 D:HIS173 2.2 8.7 1.0 O22 D:1WB402 2.3 15.2 1.0 MN D:MN401 2.6 5.3 0.2 CG D:ASP296 3.0 13.8 1.0 CD2 D:HIS173 3.2 6.5 1.0 CD D:GLU7 3.2 6.9 1.0 OD2 D:ASP296 3.2 12.9 1.0 CE1 D:HIS173 3.3 10.1 1.0 CCC D:1WB402 3.3 17.1 1.0 CZ D:1WB402 3.5 16.0 1.0 CG D:GLU7 3.7 6.0 1.0 CM1 D:1WB402 3.8 16.8 1.0 O D:HOH544 4.1 12.4 1.0 NE2 D:HIS226 4.2 10.9 1.0 OE1 D:GLU7 4.3 7.7 1.0 O11 D:1WB402 4.3 10.8 1.0 O D:HOH690 4.3 21.7 1.0 CG D:HIS173 4.3 9.0 1.0 ND1 D:HIS173 4.3 8.6 1.0 CB D:ASP296 4.4 7.5 1.0 O D:GLU7 4.4 9.4 1.0 CE1 D:HIS226 4.5 8.3 1.0 CD2 D:TYR299 4.7 17.6 1.0 CM2 D:1WB402 4.7 14.1 1.0 CA D:ASP296 4.8 7.9 1.0 CB D:GLU7 4.8 7.5 1.0

Manganese binding site 8 out of 16 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid


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 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:5.3 occ:0.18 MN D:MN401 0.0 5.3 0.2 OD2 D:ASP296 1.8 12.9 1.0 NE2 D:HIS226 1.8 10.9 1.0 O22 D:1WB402 1.9 15.2 1.0 OE2 D:GLU7 2.0 9.4 1.0 MN D:MN401 2.6 7.5 0.8 CE1 D:HIS226 2.6 8.3 1.0 CG D:ASP296 2.6 13.8 1.0 CCC D:1WB402 2.9 17.1 1.0 OD1 D:ASP296 2.9 11.0 1.0 CD2 D:HIS226 3.0 6.6 1.0 CD D:GLU7 3.0 6.9 1.0 O11 D:1WB402 3.2 10.8 1.0 OE1 D:GLU7 3.4 7.7 1.0 OG D:SER271 3.8 7.5 1.0 ND1 D:HIS226 3.8 5.7 1.0 O D:HOH581 3.8 15.9 1.0 NE2 D:HIS173 3.9 8.7 1.0 CB D:ASP296 4.0 7.5 1.0 CG D:HIS226 4.0 6.1 1.0 CB D:SER271 4.0 8.2 1.0 CM1 D:1WB402 4.2 16.8 1.0 CG D:GLU7 4.3 6.0 1.0 CD2 D:HIS173 4.5 6.5 1.0 O D:HOH747 4.5 16.6 1.0 NH2 E:ARG237 4.5 8.5 1.0 CZ D:1WB402 4.7 16.0 1.0 CE1 D:HIS173 4.8 10.1 1.0 NH1 E:ARG237 4.9 8.6 1.0 CA D:ASP296 5.0 7.9 1.0

Manganese binding site 9 out of 16 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn401 b:8.0 occ:0.83 MN E:MN401 0.0 8.0 0.8 OE2 E:GLU7 2.1 10.2 1.0 O11 E:1WB402 2.2 15.6 1.0 O E:HOH846 2.2 20.8 0.8 OD1 E:ASP296 2.2 12.0 1.0 O E:HOH834 2.2 15.7 1.0 NE2 E:HIS173 2.2 11.3 1.0 MN E:MN401 2.6 5.4 0.2 CG E:ASP296 3.0 12.3 1.0 CD2 E:HIS173 3.1 6.5 1.0 CD E:GLU7 3.2 8.5 1.0 CCC E:1WB402 3.3 20.1 1.0 OD2 E:ASP296 3.3 13.4 1.0 CE1 E:HIS173 3.3 11.9 1.0 CZ E:1WB402 3.5 14.1 1.0 CG E:GLU7 3.7 6.7 1.0 CM1 E:1WB402 3.8 15.7 1.0 O E:HOH603 4.1 14.4 1.0 NE2 E:HIS226 4.3 8.7 1.0 OE1 E:GLU7 4.3 7.7 1.0 O E:HOH693 4.3 18.0 1.0 O22 E:1WB402 4.3 15.7 1.0 CG E:HIS173 4.3 7.2 1.0 ND1 E:HIS173 4.4 10.9 1.0 O E:GLU7 4.4 10.5 1.0 CB E:ASP296 4.4 8.2 1.0 CE1 E:HIS226 4.5 9.1 1.0 CM2 E:1WB402 4.7 14.8 1.0 CD2 E:TYR299 4.8 15.1 1.0 CA E:ASP296 4.8 7.7 1.0 CB E:GLU7 4.8 5.6 1.0

Manganese binding site 10 out of 16 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn401 b:5.4 occ:0.17 MN E:MN401 0.0 5.4 0.2 NE2 E:HIS226 1.8 8.7 1.0 OD2 E:ASP296 1.9 13.4 1.0 O11 E:1WB402 1.9 15.6 1.0 OE2 E:GLU7 2.0 10.2 1.0 CE1 E:HIS226 2.5 9.1 1.0 MN E:MN401 2.6 8.0 0.8 CG E:ASP296 2.7 12.3 1.0 CCC E:1WB402 2.8 20.1 1.0 CD2 E:HIS226 2.9 6.6 1.0 OD1 E:ASP296 3.0 12.0 1.0 CD E:GLU7 3.1 8.5 1.0 O22 E:1WB402 3.1 15.7 1.0 OE1 E:GLU7 3.5 7.7 1.0 ND1 E:HIS226 3.7 9.7 1.0 OG E:SER271 3.8 7.8 1.0 CG E:HIS226 3.9 7.1 1.0 NE2 E:HIS173 3.9 11.3 1.0 O E:HOH583 3.9 17.1 1.0 CB E:SER271 4.0 8.5 1.0 CB E:ASP296 4.1 8.2 1.0 CM1 E:1WB402 4.2 15.7 1.0 CG E:GLU7 4.3 6.7 1.0 O E:HOH846 4.4 20.8 0.8 CD2 E:HIS173 4.4 6.5 1.0 NH2 D:ARG237 4.5 7.5 1.0 CZ E:1WB402 4.7 14.1 1.0 O E:HOH834 4.7 15.7 1.0 CE1 E:HIS173 4.8 11.9 1.0 NH1 D:ARG237 4.8 7.5 1.0 CD E:PRO174 4.9 8.5 1.0

A.A.Fedorov, E.V.Fedorov, A.Vladimirova, F.M.Raushel, S.C.Almo. Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis Complexed with Mn and 5-Methoxyisophtalic Acid To Be Published.