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Manganese in PDB 4l6d: Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic Acid

Protein crystallography data

The structure of Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic Acid, PDB code: 4l6d 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) 37.22 / 1.45
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.592, 96.917, 97.029, 109.71, 90.53, 111.89
R / Rfree (%) 14.6 / 16.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic Acid (pdb code 4l6d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic Acid, PDB code: 4l6d:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 4l6d

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Manganese binding site 1 out of 9 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic 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 Vanillic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:5.7
occ:1.00
 O3 A:VNL402 2.0 11.9 1.0
OD1 A:ASP296 2.1 7.5 1.0
OE2 A:GLU7 2.2 6.3 1.0
O A:HOH791 2.2 6.2 1.0
NE2 A:HIS173 2.2 6.9 1.0
CG A:ASP296 3.0 8.5 1.0
CE1 A:HIS173 3.2 6.5 1.0
CZ A:VNL402 3.2 10.4 1.0
CD2 A:HIS173 3.2 6.1 1.0
CD A:GLU7 3.3 4.9 1.0
OD2 A:ASP296 3.3 8.7 1.0
CM1 A:VNL402 3.7 12.3 1.0
CG A:GLU7 3.7 5.0 1.0
O A:HOH525 3.8 8.6 1.0
O H:HOH900 4.1 18.1 1.0
O A:GLU7 4.2 5.4 1.0
O A:HOH572 4.3 8.8 1.0
ND1 A:HIS173 4.3 5.7 1.0
CG A:HIS173 4.3 4.0 1.0
OE1 A:GLU7 4.4 5.1 1.0
CM2 A:VNL402 4.4 10.8 1.0
CB A:ASP296 4.4 6.9 1.0
NE2 A:HIS226 4.4 6.3 1.0
OM A:VNL402 4.6 11.7 1.0
CE1 A:HIS226 4.7 5.2 1.0
CD2 A:TYR299 4.7 11.0 1.0
CA A:ASP296 4.7 6.8 1.0
CB A:GLU7 4.8 3.8 1.0

Manganese binding site 2 out of 9 in 4l6d

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Manganese binding site 2 out of 9 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic 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 Vanillic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:11.1
occ:0.19
 O A:HOH943 1.8 30.5 1.0
O A:HOH941 1.9 21.9 1.0
O A:HOH940 2.1 17.5 1.0
O A:ARG136 2.4 9.2 1.0
O A:HOH910 2.6 37.2 1.0
O A:HOH537 2.6 9.0 1.0
O A:HOH870 3.1 28.0 1.0
C A:ARG136 3.6 8.4 1.0
CB A:ARG136 4.1 12.9 1.0
O A:HOH586 4.1 10.5 1.0
O A:HOH569 4.2 10.7 1.0
O A:HOH792 4.2 11.3 1.0
ND2 A:ASN138 4.2 8.3 1.0
O A:HOH884 4.3 25.9 1.0
O A:HOH847 4.4 33.7 1.0
CA A:ARG136 4.5 8.5 1.0
C A:LEU137 4.5 7.2 1.0
OD1 A:ASN138 4.5 7.0 1.0
CG A:ASN138 4.6 8.4 1.0
O A:LEU137 4.6 8.7 1.0
N A:LEU137 4.6 7.5 1.0
O A:HOH695 4.6 22.9 1.0
CA A:LEU137 4.7 6.3 1.0
O A:ARG332 4.7 11.3 1.0
O A:HOH618 4.9 13.2 1.0
N A:ASN138 4.9 6.2 1.0

Manganese binding site 3 out of 9 in 4l6d

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Manganese binding site 3 out of 9 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic 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 Vanillic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:5.9
occ:1.00
 O3 B:VNL402 2.0 8.9 1.0
OD1 B:ASP296 2.1 6.5 1.0
OE2 B:GLU7 2.2 6.3 1.0
NE2 B:HIS173 2.2 6.1 1.0
O B:HOH950 2.2 7.5 1.0
CG B:ASP296 3.0 7.9 1.0
CZ B:VNL402 3.1 7.6 1.0
CE1 B:HIS173 3.1 7.1 1.0
CD2 B:HIS173 3.2 6.6 1.0
CD B:GLU7 3.2 5.5 1.0
OD2 B:ASP296 3.3 7.8 1.0
CM1 B:VNL402 3.6 11.6 1.0
CG B:GLU7 3.7 4.4 1.0
O B:HOH513 3.8 7.4 1.0
O G:HOH682 4.1 16.4 1.0
O B:HOH571 4.2 9.3 1.0
O B:GLU7 4.3 6.6 1.0
ND1 B:HIS173 4.3 6.7 1.0
CG B:HIS173 4.3 6.4 1.0
OE1 B:GLU7 4.3 6.0 1.0
CM2 B:VNL402 4.4 10.3 1.0
NE2 B:HIS226 4.4 7.9 1.0
CB B:ASP296 4.4 6.4 1.0
OM B:VNL402 4.6 10.1 1.0
CE1 B:HIS226 4.6 5.8 1.0
CD2 B:TYR299 4.7 8.8 1.0
CB B:GLU7 4.8 6.4 1.0
CA B:ASP296 4.8 6.0 1.0

Manganese binding site 4 out of 9 in 4l6d

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Manganese binding site 4 out of 9 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic 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 Vanillic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:7.3
occ:1.00
 O3 C:VNL402 2.0 12.1 1.0
OD1 C:ASP296 2.1 9.1 1.0
O C:HOH897 2.1 9.4 1.0
OE2 C:GLU7 2.2 8.2 1.0
NE2 C:HIS173 2.2 8.2 1.0
CG C:ASP296 3.0 9.5 1.0
CD2 C:HIS173 3.1 8.1 1.0
CE1 C:HIS173 3.2 8.4 1.0
CZ C:VNL402 3.2 11.5 1.0
CD C:GLU7 3.2 6.6 1.0
OD2 C:ASP296 3.3 12.0 1.0
CM1 C:VNL402 3.7 13.1 1.0
CG C:GLU7 3.7 6.0 1.0
O C:HOH515 3.8 9.8 1.0
O F:HOH615 4.1 16.4 1.0
O C:GLU7 4.2 8.5 1.0
O C:HOH564 4.2 12.2 1.0
ND1 C:HIS173 4.3 9.3 1.0
CG C:HIS173 4.3 7.6 1.0
OE1 C:GLU7 4.3 6.7 1.0
CB C:ASP296 4.4 7.2 1.0
CM2 C:VNL402 4.4 12.6 1.0
NE2 C:HIS226 4.4 7.0 1.0
OM C:VNL402 4.6 13.9 1.0
CE1 C:HIS226 4.7 6.2 1.0
CA C:ASP296 4.7 8.2 1.0
CB C:GLU7 4.8 5.7 1.0
CD2 C:TYR299 4.8 10.7 1.0

Manganese binding site 5 out of 9 in 4l6d

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Manganese binding site 5 out of 9 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic 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 Vanillic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:6.0
occ:1.00
 OD1 D:ASP296 2.1 6.5 1.0
O3 D:VNL402 2.1 9.2 1.0
OE2 D:GLU7 2.2 7.0 1.0
O D:HOH908 2.2 6.6 1.0
NE2 D:HIS173 2.2 7.8 1.0
CG D:ASP296 3.0 8.5 1.0
CZ D:VNL402 3.2 9.2 1.0
CD2 D:HIS173 3.2 6.0 1.0
CE1 D:HIS173 3.2 6.3 1.0
CD D:GLU7 3.2 3.8 1.0
OD2 D:ASP296 3.2 7.4 1.0
CM1 D:VNL402 3.6 10.2 1.0
CG D:GLU7 3.7 3.7 1.0
O D:HOH533 3.8 7.9 1.0
O E:HOH595 4.0 15.6 1.0
O D:GLU7 4.2 6.2 1.0
O D:HOH583 4.2 8.6 1.0
ND1 D:HIS173 4.3 7.0 1.0
CG D:HIS173 4.3 6.8 1.0
OE1 D:GLU7 4.3 6.0 1.0
CB D:ASP296 4.4 6.4 1.0
CM2 D:VNL402 4.4 11.6 1.0
NE2 D:HIS226 4.4 6.9 1.0
CE1 D:HIS226 4.6 6.7 1.0
OM D:VNL402 4.6 11.1 1.0
CA D:ASP296 4.7 5.2 1.0
CD2 D:TYR299 4.8 7.2 1.0
CB D:GLU7 4.8 4.8 1.0

Manganese binding site 6 out of 9 in 4l6d

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Manganese binding site 6 out of 9 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic 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 Vanillic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn401

b:7.3
occ:1.00
 O3 E:VNL402 2.0 12.8 1.0
OD1 E:ASP296 2.1 8.3 1.0
O E:HOH915 2.1 9.0 1.0
OE2 E:GLU7 2.2 9.4 1.0
NE2 E:HIS173 2.2 7.9 1.0
CG E:ASP296 3.0 7.4 1.0
CZ E:VNL402 3.1 10.4 1.0
CD2 E:HIS173 3.2 7.1 1.0
CE1 E:HIS173 3.2 7.1 1.0
OD2 E:ASP296 3.3 11.1 1.0
CD E:GLU7 3.3 6.8 1.0
CM1 E:VNL402 3.7 13.1 1.0
CG E:GLU7 3.7 5.6 1.0
O E:HOH543 3.7 9.5 1.0
O D:HOH912 4.1 17.6 1.0
O E:HOH604 4.2 12.0 1.0
O E:GLU7 4.3 7.4 1.0
ND1 E:HIS173 4.3 6.4 1.0
CG E:HIS173 4.3 6.4 1.0
CM2 E:VNL402 4.4 10.9 1.0
OE1 E:GLU7 4.4 7.1 1.0
CB E:ASP296 4.4 7.4 1.0
NE2 E:HIS226 4.4 8.2 1.0
OM E:VNL402 4.6 13.0 1.0
CE1 E:HIS226 4.7 7.3 1.0
CA E:ASP296 4.7 6.1 1.0
CB E:GLU7 4.8 6.3 1.0
CD2 E:TYR299 4.8 10.1 1.0

Manganese binding site 7 out of 9 in 4l6d

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Manganese binding site 7 out of 9 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic 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 Vanillic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn401

b:6.7
occ:1.00
 O3 F:VNL402 2.0 11.3 1.0
OD1 F:ASP296 2.1 7.4 1.0
O F:HOH909 2.1 7.5 1.0
OE2 F:GLU7 2.2 7.8 1.0
NE2 F:HIS173 2.2 7.6 1.0
CG F:ASP296 3.0 8.9 1.0
CD2 F:HIS173 3.2 7.4 1.0
CZ F:VNL402 3.2 12.6 1.0
CE1 F:HIS173 3.2 7.7 1.0
CD F:GLU7 3.3 7.2 1.0
OD2 F:ASP296 3.3 9.2 1.0
CM1 F:VNL402 3.7 12.6 1.0
CG F:GLU7 3.7 7.1 1.0
O F:HOH517 3.8 8.1 1.0
O C:HOH899 4.1 18.1 1.0
O F:HOH595 4.2 9.0 1.0
O F:GLU7 4.2 7.3 1.0
CG F:HIS173 4.3 7.6 1.0
ND1 F:HIS173 4.3 8.0 1.0
OE1 F:GLU7 4.4 6.3 1.0
CM2 F:VNL402 4.4 10.2 1.0
CB F:ASP296 4.4 6.4 1.0
NE2 F:HIS226 4.5 8.3 1.0
OM F:VNL402 4.6 11.7 1.0
CE1 F:HIS226 4.7 7.7 1.0
CA F:ASP296 4.7 5.4 1.0
CB F:GLU7 4.8 6.0 1.0
CD2 F:TYR299 4.8 9.3 1.0

Manganese binding site 8 out of 9 in 4l6d

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Manganese binding site 8 out of 9 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic 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 Vanillic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn401

b:6.1
occ:1.00
 O3 G:VNL402 2.0 10.7 1.0
OD1 G:ASP296 2.1 6.2 1.0
O G:HOH938 2.1 6.1 1.0
OE2 G:GLU7 2.2 6.6 1.0
NE2 G:HIS173 2.2 5.6 1.0
CG G:ASP296 3.0 6.3 1.0
CZ G:VNL402 3.2 9.6 1.0
CE1 G:HIS173 3.2 6.9 1.0
CD2 G:HIS173 3.2 5.5 1.0
CD G:GLU7 3.2 5.4 1.0
OD2 G:ASP296 3.3 9.2 1.0
CM1 G:VNL402 3.7 10.3 1.0
CG G:GLU7 3.7 4.5 1.0
O G:HOH517 3.7 7.1 1.0
O B:HOH956 4.0 20.8 1.0
O G:HOH595 4.2 9.8 1.0
O G:GLU7 4.2 7.1 1.0
ND1 G:HIS173 4.3 5.5 1.0
CG G:HIS173 4.3 7.2 1.0
OE1 G:GLU7 4.4 6.0 1.0
CM2 G:VNL402 4.4 10.2 1.0
CB G:ASP296 4.4 5.6 1.0
NE2 G:HIS226 4.4 7.5 1.0
OM G:VNL402 4.6 9.3 1.0
CE1 G:HIS226 4.7 6.8 1.0
CD2 G:TYR299 4.7 8.3 1.0
CB G:GLU7 4.8 6.2 1.0
CA G:ASP296 4.8 5.0 1.0

Manganese binding site 9 out of 9 in 4l6d

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Manganese binding site 9 out of 9 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase From Sphingomonas Paucimobilis Complexed with Vanillic 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 From Sphingomonas Paucimobilis Complexed with Vanillic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn401

b:6.3
occ:1.00
 O3 H:VNL402 2.0 11.5 1.0
OD1 H:ASP296 2.1 7.1 1.0
O H:HOH898 2.1 7.2 1.0
NE2 H:HIS173 2.2 8.2 1.0
OE2 H:GLU7 2.2 6.7 1.0
CG H:ASP296 3.0 5.7 1.0
CE1 H:HIS173 3.2 7.2 1.0
CZ H:VNL402 3.2 10.2 1.0
CD2 H:HIS173 3.2 6.3 1.0
CD H:GLU7 3.3 7.1 1.0
OD2 H:ASP296 3.3 8.5 1.0
CG H:GLU7 3.7 5.6 1.0
CM1 H:VNL402 3.7 11.6 1.0
O H:HOH508 3.8 7.8 1.0
O A:HOH926 4.0 16.8 1.0
O H:HOH583 4.2 10.1 1.0
O H:GLU7 4.3 6.2 1.0
ND1 H:HIS173 4.3 6.7 1.0
CG H:HIS173 4.3 5.7 1.0
OE1 H:GLU7 4.4 5.6 1.0
CM2 H:VNL402 4.4 8.8 1.0
CB H:ASP296 4.4 5.8 1.0
NE2 H:HIS226 4.4 6.5 1.0
OM H:VNL402 4.6 11.7 1.0
CE1 H:HIS226 4.7 6.2 1.0
CA H:ASP296 4.7 5.7 1.0
CD2 H:TYR299 4.8 7.6 1.0
CB H:GLU7 4.8 4.5 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 Vanillic Acid To Be Published.
Page generated: Sat Oct 5 20:06:03 2024

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