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Manganese in PDB 5vg3: Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6

Enzymatic activity of Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6

All present enzymatic activity of Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6:
4.1.1.2;

Protein crystallography data

The structure of Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6, PDB code: 5vg3 was solved by A.Angerhofer, M.J.Burg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.21 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.484, 156.657, 79.574, 90.00, 119.28, 90.00
R / Rfree (%) 15.4 / 17.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6 (pdb code 5vg3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6, PDB code: 5vg3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5vg3

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Manganese binding site 1 out of 6 in the Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn410

b:9.9
occ:1.00
 OE1 A:GLU280 2.1 13.7 1.0
NE2 A:HIS275 2.2 10.8 1.0
NE2 A:HIS273 2.2 9.9 1.0
O A:HOH577 2.2 11.8 1.0
NE2 A:HIS319 2.3 8.4 1.0
O A:HOH571 2.4 15.7 1.0
CD A:GLU280 3.1 13.3 1.0
CE1 A:HIS273 3.1 9.3 1.0
CE1 A:HIS275 3.1 8.6 1.0
CD2 A:HIS275 3.2 7.5 1.0
CE1 A:HIS319 3.2 8.4 1.0
CD2 A:HIS273 3.2 9.4 1.0
CD2 A:HIS319 3.3 8.1 1.0
OE2 A:GLU280 3.4 13.4 1.0
OE2 A:GLU333 3.8 15.1 1.0
ND1 A:HIS273 4.2 9.8 1.0
ND1 A:HIS275 4.2 8.8 1.0
CG A:HIS275 4.3 6.4 1.0
ND1 A:HIS319 4.3 8.8 1.0
CG A:HIS273 4.3 9.9 1.0
CG A:HIS319 4.4 8.1 1.0
CG A:GLU280 4.4 11.3 1.0
CD A:GLU333 4.5 18.7 1.0
CZ A:PHE335 4.6 10.1 1.0
CB A:GLU280 4.7 8.1 1.0
CE2 A:PHE335 4.8 8.4 1.0
NH2 A:ARG270 4.9 16.6 1.0
OH A:TYR340 4.9 14.2 1.0
CG A:GLU333 5.0 15.5 1.0

Manganese binding site 2 out of 6 in 5vg3

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Manganese binding site 2 out of 6 in the Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn411

b:11.3
occ:1.00
 NE2 A:HIS97 1.9 10.2 0.4
OE1 A:GLU101 2.0 14.7 1.0
O A:HOH523 2.1 16.4 1.0
NE2 A:HIS140 2.2 9.2 1.0
NE2 A:HIS95 2.2 8.4 1.0
OXT A:ACT401 2.4 17.1 0.8
NE2 A:HIS97 2.4 6.8 0.6
CE1 A:HIS97 2.9 10.0 0.4
CD2 A:HIS97 2.9 7.6 0.4
CD A:GLU101 3.0 14.6 1.0
CE1 A:HIS95 3.2 9.5 1.0
CD2 A:HIS140 3.2 8.2 1.0
CE1 A:HIS140 3.2 9.0 1.0
CD2 A:HIS95 3.3 8.4 1.0
CD2 A:HIS97 3.3 7.7 0.6
C A:ACT401 3.3 16.7 0.8
OE2 A:GLU101 3.4 15.8 1.0
O A:ACT401 3.4 17.4 0.8
CE1 A:HIS97 3.5 7.2 0.6
ND1 A:HIS97 4.0 8.3 0.4
CG A:HIS97 4.1 8.9 0.4
ND1 A:HIS95 4.3 8.3 1.0
CE1 A:PHE155 4.3 9.9 1.0
CG A:HIS140 4.3 7.9 1.0
ND1 A:HIS140 4.3 9.1 1.0
CG A:HIS95 4.4 6.9 1.0
CG A:GLU101 4.4 14.8 1.0
CG A:HIS97 4.5 8.9 0.6
ND1 A:HIS97 4.5 8.4 0.6
CB A:GLU101 4.7 10.8 1.0
CZ A:PHE155 4.7 11.3 1.0
CH3 A:ACT401 4.7 6.2 0.8
H1 A:ACT401 4.9 7.4 0.8

Manganese binding site 3 out of 6 in 5vg3

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Manganese binding site 3 out of 6 in the Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn407

b:9.3
occ:1.00
 OE1 B:GLU280 2.1 13.3 1.0
NE2 B:HIS275 2.2 10.4 1.0
NE2 B:HIS273 2.2 8.0 1.0
O B:HOH568 2.3 11.5 1.0
NE2 B:HIS319 2.3 9.4 1.0
O B:HOH558 2.4 15.1 1.0
CD B:GLU280 3.1 12.6 1.0
CE1 B:HIS275 3.1 8.6 1.0
CE1 B:HIS273 3.1 9.6 1.0
CE1 B:HIS319 3.2 8.6 1.0
CD2 B:HIS275 3.2 7.6 1.0
CD2 B:HIS273 3.3 9.1 1.0
CD2 B:HIS319 3.3 9.2 1.0
OE2 B:GLU280 3.4 12.4 1.0
OE2 B:GLU333 3.8 16.0 1.0
ND1 B:HIS275 4.2 7.3 1.0
ND1 B:HIS273 4.3 9.1 1.0
CG B:HIS275 4.3 5.7 1.0
ND1 B:HIS319 4.3 8.2 1.0
CG B:HIS273 4.4 8.5 1.0
CG B:GLU280 4.4 11.2 1.0
CG B:HIS319 4.4 7.1 1.0
CD B:GLU333 4.5 17.6 1.0
CZ B:PHE335 4.6 11.2 1.0
CB B:GLU280 4.7 9.1 1.0
CE2 B:PHE335 4.8 10.0 1.0
OH B:TYR340 4.9 12.8 1.0
NH2 B:ARG270 5.0 14.5 1.0
CG B:GLU333 5.0 14.4 1.0

Manganese binding site 4 out of 6 in 5vg3

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Manganese binding site 4 out of 6 in the Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn408

b:11.5
occ:1.00
 NE2 B:HIS97 1.8 10.2 0.5
O B:HOH545 2.1 16.4 1.0
OE1 B:GLU101 2.1 15.0 1.0
NE2 B:HIS95 2.2 9.3 1.0
NE2 B:HIS140 2.2 8.7 1.0
NE2 B:HIS97 2.5 9.0 0.5
O B:ACT401 2.5 18.2 0.7
CE1 B:HIS97 2.8 11.2 0.5
CD2 B:HIS97 2.8 8.6 0.5
CE1 B:HIS95 3.1 9.3 1.0
CD B:GLU101 3.1 14.6 1.0
CD2 B:HIS140 3.1 9.2 1.0
CE1 B:HIS140 3.2 7.5 1.0
CD2 B:HIS95 3.2 8.0 1.0
C B:ACT401 3.4 16.9 0.7
OXT B:ACT401 3.4 17.1 0.7
OE2 B:GLU101 3.4 18.1 1.0
CD2 B:HIS97 3.4 9.9 0.5
CE1 B:HIS97 3.4 8.6 0.5
ND1 B:HIS97 3.9 9.6 0.5
CG B:HIS97 4.0 7.6 0.5
ND1 B:HIS95 4.2 9.7 1.0
CG B:HIS140 4.3 9.2 1.0
ND1 B:HIS140 4.3 8.6 1.0
CG B:HIS95 4.3 7.4 1.0
CE1 B:PHE155 4.4 8.5 1.0
CG B:GLU101 4.4 12.3 1.0
ND1 B:HIS97 4.6 5.7 0.5
CG B:HIS97 4.6 6.9 0.5
CB B:GLU101 4.7 10.8 1.0
CH3 B:ACT401 4.7 6.5 0.7
CZ B:PHE155 4.7 11.0 1.0
H1 B:ACT401 4.9 7.8 0.7

Manganese binding site 5 out of 6 in 5vg3

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Manganese binding site 5 out of 6 in the Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn405

b:10.2
occ:1.00
 OE1 C:GLU280 2.0 14.1 1.0
NE2 C:HIS275 2.2 11.2 1.0
NE2 C:HIS273 2.2 8.3 1.0
O C:HOH586 2.3 12.7 1.0
NE2 C:HIS319 2.3 8.7 1.0
O C:HOH585 2.4 17.4 1.0
CE1 C:HIS275 3.1 10.6 1.0
CD C:GLU280 3.1 12.1 1.0
CE1 C:HIS273 3.1 9.3 1.0
CD2 C:HIS275 3.2 8.1 1.0
CE1 C:HIS319 3.2 8.8 1.0
CD2 C:HIS273 3.3 7.1 1.0
CD2 C:HIS319 3.3 8.2 1.0
OE2 C:GLU280 3.4 14.6 1.0
OE2 C:GLU333 3.9 15.6 1.0
ND1 C:HIS275 4.2 9.3 1.0
ND1 C:HIS273 4.3 9.1 1.0
CG C:HIS275 4.3 8.7 1.0
ND1 C:HIS319 4.4 8.5 1.0
CG C:HIS273 4.4 8.0 1.0
CG C:GLU280 4.4 9.2 1.0
CG C:HIS319 4.4 7.8 1.0
CD C:GLU333 4.4 18.4 1.0
CZ C:PHE335 4.5 10.1 1.0
CB C:GLU280 4.7 9.4 1.0
CE2 C:PHE335 4.8 9.7 1.0
OH C:TYR340 4.9 13.4 1.0
NH2 C:ARG270 4.9 15.5 1.0
CG C:GLU333 4.9 17.6 1.0

Manganese binding site 6 out of 6 in 5vg3

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Manganese binding site 6 out of 6 in the Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn406

b:11.2
occ:1.00
 NE2 C:HIS97 1.9 9.5 0.5
OE1 C:GLU101 2.0 14.7 1.0
O C:HOH523 2.1 16.9 1.0
NE2 C:HIS95 2.2 10.4 1.0
NE2 C:HIS140 2.2 9.0 1.0
O C:ACT401 2.4 20.2 0.8
NE2 C:HIS97 2.5 9.5 0.6
CE1 C:HIS97 2.9 10.2 0.5
CD2 C:HIS97 2.9 7.3 0.5
CD C:GLU101 3.0 17.2 1.0
CE1 C:HIS95 3.1 9.0 1.0
CD2 C:HIS140 3.1 8.0 1.0
CD2 C:HIS95 3.2 9.4 1.0
CE1 C:HIS140 3.2 8.7 1.0
OE2 C:GLU101 3.3 16.7 1.0
CD2 C:HIS97 3.3 8.4 0.6
C C:ACT401 3.4 19.0 0.8
OXT C:ACT401 3.5 18.3 0.8
CE1 C:HIS97 3.5 8.9 0.6
ND1 C:HIS97 4.0 9.9 0.5
CG C:HIS97 4.1 9.1 0.5
ND1 C:HIS95 4.3 9.9 1.0
CG C:HIS140 4.3 7.1 1.0
CG C:HIS95 4.3 9.3 1.0
CE1 C:PHE155 4.3 10.2 1.0
ND1 C:HIS140 4.3 7.9 1.0
CG C:GLU101 4.4 15.0 1.0
CG C:HIS97 4.5 7.6 0.6
ND1 C:HIS97 4.6 7.5 0.6
CZ C:PHE155 4.7 11.2 1.0
CB C:GLU101 4.7 9.6 1.0
CH3 C:ACT401 4.7 6.6 0.8
H2 C:ACT401 4.8 8.0 0.8
CD2 C:PHE134 5.0 11.9 1.0

Reference:

A.Angerhofer, M.J.Burg. Structure of Oxalate Decarboxylase From Bacillus Subtilis at pH 4.6 To Be Published.
Page generated: Sun Oct 6 03:10:51 2024

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