Atomistry » Manganese » PDB 4k3v-4lt5 » 4l6d
Atomistry »
  Manganese »
    PDB 4k3v-4lt5 »
      4l6d »

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

Go back to Manganese Binding Sites List in 4l6d
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

Go back to Manganese Binding Sites List in 4l6d
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

Go back to Manganese Binding Sites List in 4l6d
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

Go back to Manganese Binding Sites List in 4l6d
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

Go back to Manganese Binding Sites List in 4l6d
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

Go back to Manganese Binding Sites List in 4l6d
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

Go back to Manganese Binding Sites List in 4l6d
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

Go back to Manganese Binding Sites List in 4l6d
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

Go back to Manganese Binding Sites List in 4l6d
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy