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Manganese in PDB 4ng3: Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid

Protein crystallography data

The structure of Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid, PDB code: 4ng3 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) 48.71 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.544, 100.399, 100.024, 66.64, 67.96, 88.24
R / Rfree (%) 15.2 / 18.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid (pdb code 4ng3). 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 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid, PDB code: 4ng3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4ng3

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Manganese binding site 1 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 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 Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:7.8
occ:0.74
 O11 A:1DF402 1.9 17.0 1.0
O3 A:1DF402 2.1 13.9 1.0
OE2 A:GLU7 2.2 12.0 1.0
O A:HOH726 2.2 16.8 1.0
NE2 A:HIS173 2.2 13.3 1.0
OD1 A:ASP296 2.3 16.3 1.0
N A:1DF402 2.9 18.7 1.0
CG A:ASP296 3.1 22.6 1.0
CZ A:1DF402 3.2 15.2 1.0
CD2 A:HIS173 3.2 16.3 1.0
CE1 A:HIS173 3.2 11.4 1.0
OD2 A:ASP296 3.3 28.3 1.0
CD A:GLU7 3.3 13.0 1.0
CM1 A:1DF402 3.4 8.9 1.0
CG A:GLU7 3.8 7.7 1.0
O A:HOH512 3.9 10.1 1.0
O22 A:1DF402 4.0 22.3 1.0
O A:HOH758 4.3 19.5 1.0
NE2 A:HIS226 4.3 13.7 1.0
ND1 A:HIS173 4.3 10.6 1.0
CG A:HIS173 4.3 15.0 1.0
CM2 A:1DF402 4.4 13.4 1.0
OE1 A:GLU7 4.4 10.8 1.0
CD2 A:TYR299 4.5 10.2 1.0
CB A:ASP296 4.5 7.8 1.0
CE1 A:HIS226 4.6 18.7 1.0
O A:GLU7 4.6 10.4 1.0
OM A:1DF402 4.7 14.7 1.0
CO1 A:1DF402 4.8 9.8 1.0
CA A:ASP296 4.9 6.5 1.0
CE2 A:TYR299 5.0 11.2 1.0
CB A:GLU7 5.0 9.1 1.0

Manganese binding site 2 out of 8 in 4ng3

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Manganese binding site 2 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 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 Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:8.6
occ:0.82
 O11 B:1DF402 1.9 22.0 1.0
O3 B:1DF402 2.1 17.2 1.0
OE2 B:GLU7 2.2 12.3 1.0
NE2 B:HIS173 2.2 11.5 1.0
OD1 B:ASP296 2.3 14.1 1.0
O B:HOH740 2.3 12.3 1.0
N B:1DF402 2.9 23.1 1.0
CG B:ASP296 3.1 21.3 1.0
CD2 B:HIS173 3.1 12.4 1.0
CZ B:1DF402 3.1 18.9 1.0
OD2 B:ASP296 3.2 24.7 1.0
CE1 B:HIS173 3.2 9.2 1.0
CD B:GLU7 3.3 10.5 1.0
CM1 B:1DF402 3.4 16.4 1.0
O B:HOH566 3.8 8.1 1.0
CG B:GLU7 3.9 5.8 1.0
O22 B:1DF402 4.0 19.8 1.0
CG B:HIS173 4.3 9.8 1.0
ND1 B:HIS173 4.3 11.7 1.0
NE2 B:HIS226 4.3 13.1 1.0
OE1 B:GLU7 4.3 11.4 1.0
CM2 B:1DF402 4.4 17.6 1.0
O B:HOH770 4.4 20.6 1.0
CB B:ASP296 4.5 10.3 1.0
CE1 B:HIS226 4.6 14.3 1.0
O B:GLU7 4.6 10.6 1.0
CD2 B:TYR299 4.6 13.9 1.0
CO1 B:1DF402 4.8 11.8 1.0
OM B:1DF402 4.8 18.9 1.0
CA B:ASP296 4.9 6.2 1.0
CB B:GLU7 5.0 5.9 1.0

Manganese binding site 3 out of 8 in 4ng3

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Manganese binding site 3 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 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 Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:9.3
occ:0.85
 O3 C:1DF402 2.0 15.5 1.0
O11 C:1DF402 2.0 18.1 1.0
O C:HOH834 2.0 11.6 1.0
OE2 C:GLU7 2.2 13.7 1.0
NE2 C:HIS173 2.2 15.7 1.0
OD1 C:ASP296 2.2 13.4 1.0
N C:1DF402 3.0 22.6 1.0
CZ C:1DF402 3.0 17.0 1.0
CG C:ASP296 3.1 17.5 1.0
CE1 C:HIS173 3.2 13.3 1.0
CD2 C:HIS173 3.2 11.3 1.0
OD2 C:ASP296 3.2 21.7 1.0
CD C:GLU7 3.3 13.1 1.0
CM1 C:1DF402 3.4 15.7 1.0
CG C:GLU7 3.8 7.0 1.0
O C:HOH515 3.9 7.6 1.0
O22 C:1DF402 4.1 20.8 1.0
CM2 C:1DF402 4.3 17.0 1.0
ND1 C:HIS173 4.3 11.7 1.0
NE2 C:HIS226 4.4 15.3 1.0
CG C:HIS173 4.4 14.5 1.0
OE1 C:GLU7 4.4 11.9 1.0
O C:HOH718 4.4 15.2 1.0
CD2 C:TYR299 4.4 8.4 1.0
CB C:ASP296 4.5 6.4 1.0
O C:GLU7 4.5 14.1 1.0
CE1 C:HIS226 4.6 13.8 1.0
OM C:1DF402 4.7 13.7 1.0
CO1 C:1DF402 4.7 8.6 1.0
CE2 C:TYR299 4.9 11.2 1.0
CA C:ASP296 4.9 6.1 1.0
CB C:GLU7 4.9 8.3 1.0

Manganese binding site 4 out of 8 in 4ng3

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Manganese binding site 4 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 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 Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:9.1
occ:0.80
 O11 D:1DF402 2.0 26.5 1.0
O3 D:1DF402 2.1 18.9 1.0
OE2 D:GLU7 2.2 11.6 1.0
OD1 D:ASP296 2.2 13.7 1.0
O D:HOH759 2.2 12.6 1.0
NE2 D:HIS173 2.3 9.5 1.0
N D:1DF402 3.0 23.1 1.0
CG D:ASP296 3.0 17.1 1.0
CZ D:1DF402 3.1 14.0 1.0
CD2 D:HIS173 3.2 10.5 1.0
OD2 D:ASP296 3.2 24.9 1.0
CD D:GLU7 3.3 11.2 1.0
CE1 D:HIS173 3.3 9.8 1.0
CM1 D:1DF402 3.5 12.8 1.0
CG D:GLU7 3.8 10.3 1.0
O D:HOH521 4.0 10.2 1.0
O22 D:1DF402 4.1 18.9 1.0
O D:HOH771 4.2 15.1 1.0
NE2 D:HIS226 4.3 16.3 1.0
CG D:HIS173 4.3 12.7 1.0
CM2 D:1DF402 4.3 15.7 1.0
OE1 D:GLU7 4.3 10.5 1.0
ND1 D:HIS173 4.4 8.3 1.0
CB D:ASP296 4.4 11.4 1.0
O D:GLU7 4.5 14.9 1.0
CD2 D:TYR299 4.5 10.8 1.0
CE1 D:HIS226 4.6 17.8 1.0
OM D:1DF402 4.7 14.6 1.0
CO1 D:1DF402 4.8 12.8 1.0
CA D:ASP296 4.8 12.4 1.0
CB D:GLU7 4.9 9.6 1.0
CE2 D:TYR299 5.0 7.5 1.0

Manganese binding site 5 out of 8 in 4ng3

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Manganese binding site 5 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 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 5 of Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn401

b:8.8
occ:0.82
 O11 E:1DF402 1.9 20.6 1.0
O3 E:1DF402 2.1 15.6 1.0
O E:HOH837 2.1 18.7 1.0
OE2 E:GLU7 2.2 12.3 1.0
NE2 E:HIS173 2.2 10.8 1.0
OD1 E:ASP296 2.2 15.4 1.0
N E:1DF402 3.0 21.0 1.0
CG E:ASP296 3.1 17.6 1.0
CE1 E:HIS173 3.1 11.1 1.0
CZ E:1DF402 3.1 11.7 1.0
CD2 E:HIS173 3.2 10.9 1.0
CD E:GLU7 3.3 11.5 1.0
OD2 E:ASP296 3.3 21.0 1.0
CM1 E:1DF402 3.4 11.4 1.0
CG E:GLU7 3.8 8.2 1.0
O E:HOH510 3.9 8.5 1.0
O22 E:1DF402 4.1 15.2 1.0
ND1 E:HIS173 4.3 10.1 1.0
CM2 E:1DF402 4.3 13.8 1.0
CG E:HIS173 4.3 10.8 1.0
O E:HOH664 4.4 15.3 1.0
OE1 E:GLU7 4.4 14.6 1.0
NE2 E:HIS226 4.4 19.1 1.0
CB E:ASP296 4.5 7.4 1.0
CD2 E:TYR299 4.5 11.6 1.0
O E:GLU7 4.5 13.6 1.0
CE1 E:HIS226 4.7 12.9 1.0
OM E:1DF402 4.7 13.4 1.0
CO1 E:1DF402 4.8 9.0 1.0
CA E:ASP296 4.9 9.6 1.0
CE2 E:TYR299 4.9 10.5 1.0
CB E:GLU7 4.9 5.2 1.0

Manganese binding site 6 out of 8 in 4ng3

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Manganese binding site 6 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 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 6 of Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn401

b:10.2
occ:0.86
 O3 F:1DF402 2.0 18.4 1.0
O11 F:1DF402 2.0 20.7 1.0
O F:HOH830 2.0 11.2 1.0
OE2 F:GLU7 2.2 15.2 1.0
NE2 F:HIS173 2.2 11.2 1.0
OD1 F:ASP296 2.3 13.6 1.0
N F:1DF402 3.0 23.0 1.0
CZ F:1DF402 3.1 15.8 1.0
CG F:ASP296 3.1 21.2 1.0
CE1 F:HIS173 3.2 12.8 1.0
CD2 F:HIS173 3.2 12.6 1.0
OD2 F:ASP296 3.2 26.0 1.0
CD F:GLU7 3.2 12.9 1.0
CM1 F:1DF402 3.4 15.7 1.0
CG F:GLU7 3.8 5.5 1.0
O F:HOH527 3.9 10.6 1.0
O22 F:1DF402 4.1 22.5 1.0
ND1 F:HIS173 4.3 10.9 1.0
CM2 F:1DF402 4.3 15.1 1.0
NE2 F:HIS226 4.3 13.7 1.0
OE1 F:GLU7 4.3 10.4 1.0
CG F:HIS173 4.3 10.8 1.0
O F:HOH643 4.4 19.2 1.0
O F:GLU7 4.5 11.1 1.0
CB F:ASP296 4.5 15.8 1.0
CE1 F:HIS226 4.6 8.8 1.0
CD2 F:TYR299 4.6 11.5 1.0
OM F:1DF402 4.7 14.9 1.0
CO1 F:1DF402 4.8 16.9 1.0
CB F:GLU7 4.9 9.5 1.0
CA F:ASP296 4.9 9.1 1.0

Manganese binding site 7 out of 8 in 4ng3

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Manganese binding site 7 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 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 7 of Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn401

b:9.0
occ:0.77
 O11 G:1DF402 1.9 22.2 1.0
O G:HOH834 2.0 14.2 1.0
O3 G:1DF402 2.0 18.2 1.0
NE2 G:HIS173 2.2 12.4 1.0
OE2 G:GLU7 2.2 11.1 1.0
OD1 G:ASP296 2.3 14.2 1.0
N G:1DF402 3.0 24.6 1.0
CZ G:1DF402 3.1 15.4 1.0
CG G:ASP296 3.1 16.5 1.0
CE1 G:HIS173 3.1 15.2 1.0
CD2 G:HIS173 3.2 13.1 1.0
OD2 G:ASP296 3.3 15.6 1.0
CD G:GLU7 3.3 11.5 1.0
CM1 G:1DF402 3.4 13.0 1.0
CG G:GLU7 3.7 8.1 1.0
O G:HOH531 3.8 9.7 1.0
O22 G:1DF402 4.1 22.7 1.0
ND1 G:HIS173 4.2 14.5 1.0
CM2 G:1DF402 4.3 12.4 1.0
CG G:HIS173 4.3 10.5 1.0
O G:HOH665 4.3 20.5 1.0
OE1 G:GLU7 4.4 13.5 1.0
NE2 G:HIS226 4.4 17.2 1.0
CB G:ASP296 4.5 9.4 1.0
O G:GLU7 4.5 11.1 1.0
CD2 G:TYR299 4.6 9.8 1.0
CE1 G:HIS226 4.6 15.2 1.0
OM G:1DF402 4.6 10.0 1.0
CO1 G:1DF402 4.8 12.9 1.0
CA G:ASP296 4.9 10.8 1.0
CB G:GLU7 4.9 9.2 1.0

Manganese binding site 8 out of 8 in 4ng3

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Manganese binding site 8 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 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 8 of Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5- Nitrobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn401

b:8.2
occ:0.77
 O11 H:1DF402 2.0 25.4 1.0
O3 H:1DF402 2.0 18.2 1.0
OE2 H:GLU7 2.2 14.0 1.0
OD1 H:ASP296 2.2 12.4 1.0
O H:HOH821 2.2 17.3 1.0
NE2 H:HIS173 2.2 12.5 1.0
CG H:ASP296 3.0 21.3 1.0
N H:1DF402 3.0 23.9 1.0
CD2 H:HIS173 3.1 12.5 1.0
CZ H:1DF402 3.1 16.4 1.0
OD2 H:ASP296 3.2 28.4 1.0
CD H:GLU7 3.3 9.9 1.0
CE1 H:HIS173 3.3 14.6 1.0
CM1 H:1DF402 3.5 17.1 1.0
CG H:GLU7 3.8 6.8 1.0
O H:HOH524 3.9 13.3 1.0
O22 H:1DF402 4.2 23.8 1.0
CG H:HIS173 4.3 15.8 1.0
NE2 H:HIS226 4.3 19.7 1.0
CM2 H:1DF402 4.3 16.0 1.0
OE1 H:GLU7 4.3 12.7 1.0
ND1 H:HIS173 4.4 11.8 1.0
O H:HOH743 4.4 18.8 1.0
CB H:ASP296 4.5 15.8 1.0
O H:GLU7 4.5 12.5 1.0
CE1 H:HIS226 4.6 17.1 1.0
CD2 H:TYR299 4.6 13.3 1.0
OM H:1DF402 4.7 16.6 1.0
CO1 H:1DF402 4.8 12.1 1.0
CA H:ASP296 4.9 11.5 1.0
CB H:GLU7 4.9 8.1 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, A.Vladimirova, F.M.Raushel, S.C.Almo. Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with 4-Hydroxy-3-Methoxy-5-Nitrobenzoic Acid To Be Published.
Page generated: Sat Oct 5 20:31:55 2024

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