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Manganese in PDB 4icm: Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis

Protein crystallography data

The structure of Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis, PDB code: 4icm 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) 38.51 / 1.82
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.817, 96.897, 97.004, 109.58, 90.48, 111.66
R / Rfree (%) 16.3 / 20.5

Manganese Binding Sites:

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

Manganese binding site 1 out of 8 in 4icm

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Manganese binding site 1 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:13.7
occ:1.00
 OD1 A:ASP296 2.2 15.3 1.0
O A:HOH748 2.2 17.6 1.0
OE2 A:GLU7 2.2 11.5 1.0
NE2 A:HIS173 2.2 16.6 1.0
O A:HOH557 2.3 15.6 1.0
O A:HOH519 2.4 8.9 1.0
CG A:ASP296 3.1 18.5 1.0
CE1 A:HIS173 3.1 12.6 1.0
CD2 A:HIS173 3.2 10.2 1.0
CD A:GLU7 3.3 11.5 1.0
OD2 A:ASP296 3.3 14.0 1.0
CG A:GLU7 3.7 9.0 1.0
O A:HOH757 4.0 21.6 1.0
O A:HOH578 4.2 17.3 1.0
ND1 A:HIS173 4.2 11.6 1.0
CG A:HIS173 4.3 11.6 1.0
NE2 A:HIS226 4.3 11.8 1.0
O A:GLU7 4.3 10.6 1.0
O H:HOH648 4.3 21.7 1.0
OE1 A:GLU7 4.4 10.9 1.0
CB A:ASP296 4.4 10.4 1.0
CE1 A:HIS226 4.6 11.8 1.0
CB A:GLU7 4.8 11.2 1.0
CA A:ASP296 4.8 8.2 1.0
CD2 A:TYR299 4.8 26.8 1.0

Manganese binding site 2 out of 8 in 4icm

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Manganese binding site 2 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:10.8
occ:1.00
 O B:HOH791 2.1 6.9 1.0
OE2 B:GLU7 2.2 9.9 1.0
OD1 B:ASP296 2.2 17.9 1.0
NE2 B:HIS173 2.2 14.5 1.0
O B:HOH700 2.2 14.0 1.0
O B:HOH544 2.2 17.5 1.0
CG B:ASP296 3.1 15.4 1.0
CD2 B:HIS173 3.1 9.8 1.0
CE1 B:HIS173 3.2 8.4 1.0
CD B:GLU7 3.2 12.8 1.0
OD2 B:ASP296 3.3 20.0 1.0
CG B:GLU7 3.6 7.7 1.0
O B:HOH707 4.0 21.5 1.0
O B:HOH664 4.0 19.8 1.0
ND1 B:HIS173 4.3 13.6 1.0
NE2 B:HIS226 4.3 14.6 1.0
CG B:HIS173 4.3 9.3 1.0
O B:HOH647 4.3 17.4 1.0
O G:HOH564 4.3 23.1 1.0
OE1 B:GLU7 4.3 10.8 1.0
O B:GLU7 4.3 12.0 1.0
CB B:ASP296 4.4 7.8 1.0
CE1 B:HIS226 4.5 10.4 1.0
CA B:ASP296 4.7 8.1 1.0
CD2 B:TYR299 4.8 29.7 1.0
CB B:GLU7 4.8 7.7 1.0

Manganese binding site 3 out of 8 in 4icm

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Manganese binding site 3 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:13.2
occ:1.00
 OE2 C:GLU7 2.1 15.9 1.0
O C:HOH746 2.2 25.8 1.0
O C:HOH741 2.2 9.6 1.0
OD1 C:ASP296 2.2 13.8 1.0
NE2 C:HIS173 2.2 12.8 1.0
O C:HOH515 2.2 14.5 1.0
CG C:ASP296 3.1 16.8 1.0
CD2 C:HIS173 3.1 12.2 1.0
CD C:GLU7 3.2 14.9 1.0
CE1 C:HIS173 3.2 12.1 1.0
OD2 C:ASP296 3.3 14.9 1.0
CG C:GLU7 3.7 10.4 1.0
O C:HOH575 4.1 20.9 1.0
O C:HOH645 4.2 21.6 1.0
OE1 C:GLU7 4.3 13.5 1.0
CG C:HIS173 4.3 11.8 1.0
ND1 C:HIS173 4.3 13.3 1.0
O C:GLU7 4.3 11.1 1.0
NE2 C:HIS226 4.3 13.8 1.0
O F:HOH684 4.4 25.1 1.0
CB C:ASP296 4.4 13.7 1.0
CE1 C:HIS226 4.5 12.3 1.0
CB C:GLU7 4.7 10.0 1.0
CA C:ASP296 4.8 15.4 1.0

Manganese binding site 4 out of 8 in 4icm

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Manganese binding site 4 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:11.0
occ:1.00
 OE2 D:GLU7 2.0 8.3 1.0
OD1 D:ASP296 2.1 11.8 1.0
O D:HOH508 2.2 8.3 1.0
O D:HOH702 2.2 5.3 1.0
NE2 D:HIS173 2.2 14.3 1.0
O D:HOH663 2.3 19.8 1.0
CG D:ASP296 3.0 18.8 1.0
CD2 D:HIS173 3.1 11.0 1.0
CD D:GLU7 3.1 9.9 1.0
CE1 D:HIS173 3.2 11.6 1.0
OD2 D:ASP296 3.2 16.7 1.0
CG D:GLU7 3.7 4.9 1.0
O D:HOH610 4.0 14.2 1.0
OE1 D:GLU7 4.2 7.1 1.0
CG D:HIS173 4.3 14.7 1.0
ND1 D:HIS173 4.3 5.8 1.0
O D:HOH618 4.3 17.9 1.0
O D:GLU7 4.4 12.5 1.0
CB D:ASP296 4.4 17.6 1.0
O E:HOH557 4.4 20.9 1.0
NE2 D:HIS226 4.4 11.6 1.0
CE1 D:HIS226 4.5 10.0 1.0
CD2 D:TYR299 4.7 20.4 1.0
CA D:ASP296 4.7 10.7 1.0
CB D:GLU7 4.8 5.6 1.0

Manganese binding site 5 out of 8 in 4icm

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Manganese binding site 5 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn401

b:11.5
occ:1.00
 O E:HOH777 2.1 15.1 1.0
OE2 E:GLU7 2.1 12.7 1.0
O E:HOH691 2.1 7.6 1.0
OD1 E:ASP296 2.2 14.5 1.0
O E:HOH589 2.2 17.9 1.0
NE2 E:HIS173 2.2 9.7 1.0
CG E:ASP296 3.1 16.4 1.0
CD2 E:HIS173 3.2 10.7 1.0
CD E:GLU7 3.2 11.3 1.0
CE1 E:HIS173 3.3 14.3 1.0
OD2 E:ASP296 3.3 21.6 1.0
CG E:GLU7 3.7 8.6 1.0
O E:HOH780 3.9 28.9 1.0
O E:HOH620 4.1 21.3 1.0
O E:HOH619 4.2 19.1 1.0
NE2 E:HIS226 4.3 15.8 1.0
CG E:HIS173 4.3 10.7 1.0
O E:GLU7 4.3 10.1 1.0
OE1 E:GLU7 4.3 7.7 1.0
ND1 E:HIS173 4.3 10.8 1.0
O D:HOH624 4.4 25.4 1.0
CB E:ASP296 4.5 12.0 1.0
CE1 E:HIS226 4.5 10.6 1.0
CB E:GLU7 4.8 8.8 1.0
CD2 E:TYR299 4.8 27.6 1.0
CA E:ASP296 4.8 9.4 1.0

Manganese binding site 6 out of 8 in 4icm

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Manganese binding site 6 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn401

b:13.3
occ:1.00
 O F:HOH752 2.1 5.6 1.0
NE2 F:HIS173 2.2 16.6 1.0
OE2 F:GLU7 2.2 10.5 1.0
OD1 F:ASP296 2.2 13.2 1.0
O F:HOH675 2.3 19.7 1.0
O F:HOH535 2.3 16.6 1.0
CG F:ASP296 3.1 16.5 1.0
CE1 F:HIS173 3.1 12.0 1.0
CD2 F:HIS173 3.1 12.7 1.0
CD F:GLU7 3.2 9.0 1.0
OD2 F:ASP296 3.3 19.4 1.0
CG F:GLU7 3.7 9.2 1.0
O F:HOH624 4.0 19.1 1.0
O F:HOH603 4.2 20.5 1.0
ND1 F:HIS173 4.2 11.8 1.0
O C:HOH654 4.2 18.2 1.0
CG F:HIS173 4.3 11.1 1.0
O F:GLU7 4.3 9.6 1.0
NE2 F:HIS226 4.3 14.5 1.0
OE1 F:GLU7 4.3 10.1 1.0
CB F:ASP296 4.4 9.0 1.0
CE1 F:HIS226 4.6 13.3 1.0
CB F:GLU7 4.8 10.7 1.0
CA F:ASP296 4.8 9.2 1.0
CD2 F:TYR299 4.9 33.2 1.0

Manganese binding site 7 out of 8 in 4icm

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Manganese binding site 7 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn401

b:10.1
occ:1.00
 O G:HOH781 2.0 19.4 1.0
O G:HOH780 2.1 8.0 1.0
OD1 G:ASP296 2.2 13.0 1.0
NE2 G:HIS173 2.2 7.4 1.0
O G:HOH518 2.2 14.8 1.0
OE2 G:GLU7 2.2 13.9 1.0
CG G:ASP296 3.0 15.0 1.0
CD2 G:HIS173 3.1 7.3 1.0
CE1 G:HIS173 3.2 13.2 1.0
OD2 G:ASP296 3.3 13.4 1.0
CD G:GLU7 3.3 12.5 1.0
CG G:GLU7 3.8 8.9 1.0
O G:HOH791 3.8 26.6 1.0
O G:HOH591 4.0 17.4 1.0
O B:HOH579 4.3 15.9 1.0
CG G:HIS173 4.3 7.5 1.0
ND1 G:HIS173 4.3 8.4 1.0
O G:GLU7 4.3 9.7 1.0
NE2 G:HIS226 4.3 14.4 1.0
O G:HOH568 4.4 11.3 1.0
OE1 G:GLU7 4.4 10.5 1.0
CB G:ASP296 4.4 9.4 1.0
CE1 G:HIS226 4.5 8.9 1.0
CD2 G:TYR299 4.8 20.4 1.0
CA G:ASP296 4.8 8.8 1.0
CB G:GLU7 4.8 6.6 1.0

Manganese binding site 8 out of 8 in 4icm

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Manganese binding site 8 out of 8 in the Crystal Structure of 5-Carboxyvanillate Decarboxylase Ligw From Sphingomonas Paucimobilis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn401

b:10.7
occ:1.00
 OE2 H:GLU7 2.1 6.7 1.0
OD1 H:ASP296 2.2 12.6 1.0
O H:HOH796 2.2 15.8 1.0
O H:HOH707 2.2 6.0 1.0
O H:HOH520 2.2 10.3 1.0
NE2 H:HIS173 2.3 13.2 1.0
CG H:ASP296 3.0 12.6 1.0
CD2 H:HIS173 3.2 11.6 1.0
CD H:GLU7 3.2 6.3 1.0
CE1 H:HIS173 3.2 10.5 1.0
OD2 H:ASP296 3.3 12.4 1.0
CG H:GLU7 3.7 3.9 1.0
O H:HOH799 3.8 27.1 1.0
O H:HOH603 4.0 13.9 1.0
OE1 H:GLU7 4.3 6.7 1.0
NE2 H:HIS226 4.3 12.5 1.0
O H:GLU7 4.3 8.7 1.0
O A:HOH585 4.3 21.7 1.0
ND1 H:HIS173 4.3 10.8 1.0
CG H:HIS173 4.3 11.6 1.0
O H:HOH582 4.4 11.8 1.0
CB H:ASP296 4.4 6.3 1.0
CE1 H:HIS226 4.5 12.0 1.0
CA H:ASP296 4.7 4.0 1.0
CD2 H:TYR299 4.8 27.7 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 Ligw From Sphingomonas Paucimobilis To Be Published.
Page generated: Sat Aug 16 14:15:20 2025

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