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Cobalt in PDB 4met: Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations

Enzymatic activity of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations

All present enzymatic activity of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations:
4.1.1.2;

Protein crystallography data

The structure of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations, PDB code: 4met was solved by P.Campomanes, W.F.Kellett, L.M.Easthon, A.Ozarowski, K.N.Allen, A.Angerhofer, U.Rothlisberger, N.G.J.Richards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.39 / 2.10
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 156.973, 156.973, 330.473, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 22.7

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations (pdb code 4met). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations, PDB code: 4met:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 4met

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Cobalt binding site 1 out of 8 in the Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co500

b:20.7
occ:1.00
OE1 A:GLU101 2.1 13.6 1.0
NE2 A:HIS95 2.1 12.9 1.0
NE2 A:HIS140 2.2 14.6 1.0
O A:HOH691 2.3 17.8 1.0
NE2 A:HIS97 2.5 13.7 1.0
CE1 A:HIS97 2.5 14.6 1.0
O A:HOH619 2.5 20.1 1.0
CD2 A:HIS140 3.0 14.9 1.0
CE1 A:HIS95 3.1 14.6 1.0
CD A:GLU101 3.1 15.6 1.0
CD2 A:HIS95 3.2 15.0 1.0
CE1 A:HIS140 3.2 15.2 1.0
OE2 A:GLU101 3.4 17.3 1.0
ND1 A:HIS97 3.8 16.3 1.0
CD2 A:HIS97 3.8 14.8 1.0
ND1 A:HIS95 4.2 13.0 1.0
CG A:HIS140 4.2 14.1 1.0
CG A:HIS95 4.3 12.4 1.0
ND1 A:HIS140 4.3 13.7 1.0
CE2 A:PHE155 4.4 16.3 1.0
CG A:HIS97 4.4 15.7 1.0
CG A:GLU101 4.4 14.5 1.0
OE1 A:GLU162 4.5 23.8 1.0
CZ A:PHE155 4.7 15.2 1.0
CB A:GLU101 4.8 12.3 1.0
CD2 A:PHE134 4.8 15.8 1.0

Cobalt binding site 2 out of 8 in 4met

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Cobalt binding site 2 out of 8 in the Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co501

b:19.4
occ:1.00
NE2 A:HIS275 2.0 13.2 1.0
OE1 A:GLU280 2.1 16.9 1.0
NE2 A:HIS273 2.2 14.1 1.0
O A:HOH685 2.3 16.4 1.0
NE2 A:HIS319 2.3 13.3 1.0
O A:HOH667 2.4 19.9 1.0
CE1 A:HIS275 2.9 13.3 1.0
CD2 A:HIS275 3.0 12.3 1.0
CD A:GLU280 3.1 15.4 1.0
CE1 A:HIS273 3.2 14.0 1.0
CD2 A:HIS273 3.2 14.8 1.0
CE1 A:HIS319 3.2 12.0 1.0
CD2 A:HIS319 3.3 13.0 1.0
OE2 A:GLU280 3.5 13.7 1.0
OE2 A:GLU333 3.8 15.6 1.0
ND1 A:HIS275 4.0 14.7 1.0
CG A:HIS275 4.1 14.6 1.0
ND1 A:HIS273 4.3 14.1 1.0
CG A:HIS273 4.3 15.2 1.0
ND1 A:HIS319 4.3 13.5 1.0
CD A:GLU333 4.4 16.4 1.0
CG A:GLU280 4.4 12.8 1.0
CG A:HIS319 4.4 11.5 1.0
CZ A:PHE335 4.5 15.4 1.0
CB A:GLU280 4.8 14.1 1.0
CE1 A:PHE335 4.8 14.6 1.0
OH A:TYR340 4.8 25.5 1.0
OE1 A:GLU333 4.9 21.7 1.0
NH2 A:ARG270 5.0 18.0 1.0
CG A:GLU333 5.0 14.7 1.0

Cobalt binding site 3 out of 8 in 4met

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Cobalt binding site 3 out of 8 in the Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co500

b:17.2
occ:1.00
OE1 B:GLU101 2.1 12.6 1.0
NE2 B:HIS95 2.2 12.5 1.0
NE2 B:HIS140 2.2 10.8 1.0
O B:HOH696 2.3 13.3 1.0
CE1 B:HIS97 2.4 12.6 1.0
NE2 B:HIS97 2.4 13.0 1.0
O B:HOH705 2.5 16.9 1.0
CD B:GLU101 3.0 11.0 1.0
CD2 B:HIS140 3.0 9.9 1.0
CE1 B:HIS95 3.1 12.3 1.0
CD2 B:HIS95 3.2 12.8 1.0
CE1 B:HIS140 3.3 13.2 1.0
OE2 B:GLU101 3.3 10.5 1.0
ND1 B:HIS97 3.7 13.5 1.0
CD2 B:HIS97 3.8 12.3 1.0
ND1 B:HIS95 4.2 11.3 1.0
CG B:HIS140 4.2 11.8 1.0
CG B:HIS95 4.3 11.2 1.0
ND1 B:HIS140 4.3 10.8 1.0
CG B:HIS97 4.4 15.4 1.0
CE2 B:PHE155 4.4 13.1 1.0
CG B:GLU101 4.4 15.3 1.0
OE2 B:GLU162 4.5 24.8 1.0
CZ B:PHE155 4.7 12.2 1.0
CB B:GLU101 4.8 9.7 1.0
CD2 B:PHE134 4.8 9.5 1.0

Cobalt binding site 4 out of 8 in 4met

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Cobalt binding site 4 out of 8 in the Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co501

b:15.3
occ:1.00
NE2 B:HIS275 2.0 10.1 1.0
OE1 B:GLU280 2.1 10.6 1.0
O B:HOH704 2.2 12.8 1.0
NE2 B:HIS273 2.2 9.4 1.0
NE2 B:HIS319 2.3 9.8 1.0
O B:HOH716 2.3 15.0 1.0
CE1 B:HIS275 2.9 11.5 1.0
CD B:GLU280 3.1 12.9 1.0
CE1 B:HIS319 3.1 10.0 1.0
CD2 B:HIS275 3.1 9.7 1.0
CD2 B:HIS273 3.2 11.6 1.0
CE1 B:HIS273 3.2 10.7 1.0
CD2 B:HIS319 3.3 10.2 1.0
OE2 B:GLU280 3.4 12.3 1.0
OE2 B:GLU333 4.0 13.4 1.0
ND1 B:HIS275 4.1 11.1 1.0
CG B:HIS275 4.2 10.2 1.0
ND1 B:HIS319 4.3 9.5 1.0
ND1 B:HIS273 4.3 12.3 1.0
CG B:HIS273 4.3 12.7 1.0
CG B:HIS319 4.4 10.6 1.0
CG B:GLU280 4.4 9.9 1.0
CD B:GLU333 4.4 12.9 1.0
CZ B:PHE335 4.5 11.4 1.0
CB B:GLU280 4.7 9.6 1.0
CE1 B:PHE335 4.8 13.4 1.0
OH B:TYR340 4.9 17.1 1.0
CG B:GLU333 4.9 11.0 1.0
NH2 B:ARG270 5.0 16.3 1.0

Cobalt binding site 5 out of 8 in 4met

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Cobalt binding site 5 out of 8 in the Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co500

b:24.3
occ:1.00
OE1 C:GLU101 2.0 29.3 1.0
NE2 C:HIS97 2.1 24.9 1.0
NE2 C:HIS95 2.1 23.3 1.0
NE2 C:HIS140 2.2 24.9 1.0
O C:HOH666 2.2 23.1 1.0
O C:HOH679 2.7 30.4 1.0
CE1 C:HIS97 2.7 28.8 1.0
CE1 C:HIS95 2.9 26.5 1.0
CD C:GLU101 3.0 27.3 1.0
CD2 C:HIS140 3.0 24.6 1.0
CD2 C:HIS95 3.3 24.2 1.0
CD2 C:HIS97 3.3 25.9 1.0
OE2 C:GLU101 3.3 26.3 1.0
CE1 C:HIS140 3.3 25.3 1.0
ND1 C:HIS97 4.0 30.8 1.0
ND1 C:HIS95 4.1 23.2 1.0
CG C:HIS97 4.2 27.2 1.0
CE2 C:PHE155 4.2 25.2 1.0
CG C:HIS140 4.2 26.2 1.0
CG C:HIS95 4.3 23.0 1.0
ND1 C:HIS140 4.4 22.9 1.0
CG C:GLU101 4.4 21.0 1.0
CZ C:PHE155 4.6 23.3 1.0
CD2 C:PHE134 4.7 25.6 1.0
CB C:GLU101 4.7 23.4 1.0
OE2 C:GLU162 4.9 31.2 1.0
CE2 C:PHE134 5.0 27.9 1.0

Cobalt binding site 6 out of 8 in 4met

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Cobalt binding site 6 out of 8 in the Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co501

b:22.6
occ:1.00
NE2 C:HIS275 2.0 23.4 1.0
OE1 C:GLU280 2.1 23.6 1.0
NE2 C:HIS273 2.2 22.3 1.0
O C:HOH667 2.2 25.2 1.0
NE2 C:HIS319 2.3 20.0 1.0
O C:HOH665 2.3 18.3 1.0
CE1 C:HIS275 3.0 25.8 1.0
CD2 C:HIS275 3.0 22.3 1.0
CD C:GLU280 3.1 23.3 1.0
CE1 C:HIS319 3.1 21.4 1.0
CE1 C:HIS273 3.1 23.4 1.0
CD2 C:HIS273 3.2 24.7 1.0
CD2 C:HIS319 3.3 21.5 1.0
OE2 C:GLU280 3.4 23.1 1.0
OE2 C:GLU333 3.9 26.0 1.0
ND1 C:HIS275 4.1 25.9 1.0
CG C:HIS275 4.1 24.0 1.0
ND1 C:HIS273 4.3 25.5 1.0
ND1 C:HIS319 4.3 22.2 1.0
CG C:HIS273 4.3 24.9 1.0
CG C:HIS319 4.4 19.8 1.0
CG C:GLU280 4.4 21.9 1.0
CD C:GLU333 4.5 24.7 1.0
CZ C:PHE335 4.5 26.0 1.0
CE1 C:PHE335 4.6 25.9 1.0
CB C:GLU280 4.7 21.8 1.0
OH C:TYR340 4.9 29.9 1.0
OE1 C:GLU333 4.9 27.8 1.0

Cobalt binding site 7 out of 8 in 4met

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Cobalt binding site 7 out of 8 in the Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co500

b:20.9
occ:1.00
NE2 D:HIS97 1.9 24.5 1.0
NE2 D:HIS95 2.0 22.2 1.0
OE1 D:GLU101 2.1 17.8 1.0
NE2 D:HIS140 2.2 20.2 1.0
O D:HOH690 2.3 24.2 1.0
O D:HOH685 2.3 17.8 1.0
CE1 D:HIS97 2.7 26.0 1.0
CE1 D:HIS95 3.0 21.5 1.0
CD2 D:HIS140 3.1 19.0 1.0
CD D:GLU101 3.1 20.9 1.0
CD2 D:HIS97 3.1 20.9 1.0
CD2 D:HIS95 3.1 21.0 1.0
CE1 D:HIS140 3.2 19.7 1.0
OE2 D:GLU101 3.4 18.6 1.0
ND1 D:HIS97 3.9 21.5 1.0
CG D:HIS97 4.1 21.9 1.0
ND1 D:HIS95 4.1 17.2 1.0
CG D:HIS95 4.2 22.5 1.0
CE2 D:PHE155 4.2 20.7 1.0
CG D:HIS140 4.2 18.8 1.0
ND1 D:HIS140 4.3 19.7 1.0
CZ D:PHE155 4.4 18.6 1.0
CG D:GLU101 4.4 19.2 1.0
OE2 D:GLU162 4.8 25.1 1.0
CB D:GLU101 4.8 17.3 1.0
CD2 D:PHE134 4.9 18.4 1.0

Cobalt binding site 8 out of 8 in 4met

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Cobalt binding site 8 out of 8 in the Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co501

b:18.3
occ:1.00
NE2 D:HIS275 2.1 16.6 1.0
OE1 D:GLU280 2.2 20.2 1.0
NE2 D:HIS273 2.2 17.2 1.0
NE2 D:HIS319 2.3 20.1 1.0
O D:HOH671 2.3 16.5 1.0
O D:HOH623 2.4 19.0 1.0
CD D:GLU280 3.1 18.8 1.0
CD2 D:HIS275 3.1 17.8 1.0
CE1 D:HIS275 3.1 19.4 1.0
CE1 D:HIS273 3.1 17.8 1.0
CE1 D:HIS319 3.1 19.1 1.0
CD2 D:HIS273 3.2 20.5 1.0
CD2 D:HIS319 3.3 20.1 1.0
OE2 D:GLU280 3.3 19.1 1.0
OE2 D:GLU333 4.0 21.0 1.0
ND1 D:HIS275 4.2 16.8 1.0
CG D:HIS275 4.2 19.4 1.0
ND1 D:HIS273 4.3 18.0 1.0
ND1 D:HIS319 4.3 16.3 1.0
CG D:HIS273 4.3 21.1 1.0
CG D:HIS319 4.4 17.1 1.0
CG D:GLU280 4.4 18.3 1.0
CZ D:PHE335 4.4 18.8 1.0
CD D:GLU333 4.5 20.4 1.0
CE1 D:PHE335 4.6 19.1 1.0
CB D:GLU280 4.7 17.2 1.0
OH D:TYR340 4.9 23.1 1.0

Reference:

P.Campomanes, W.F.Kellett, L.M.Easthon, A.Ozarowski, K.N.Allen, A.Angerhofer, U.Rothlisberger, N.G.Richards. Assigning the Epr Fine Structure Parameters of the Mn(II) Centers in Bacillus Subtilis Oxalate Decarboxylase By Site-Directed Mutagenesis and Dft/Mm Calculations. J.Am.Chem.Soc. V. 136 2313 2014.
ISSN: ISSN 0002-7863
PubMed: 24444454
DOI: 10.1021/JA408138F
Page generated: Sun Dec 13 10:45:14 2020

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