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Magnesium in PDB 7b2e: Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp

Enzymatic activity of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp

All present enzymatic activity of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp:
4.1.1.8;

Protein crystallography data

The structure of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp, PDB code: 7b2e was solved by P.Pfister, S.Burgener, M.Nattermann, J.Zarzycki, T.J.Erb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 161.094, 180.337, 202.008, 90, 90, 90
R / Rfree (%) 20.2 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp (pdb code 7b2e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp, PDB code: 7b2e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7b2e

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Magnesium binding site 1 out of 8 in the Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:26.0
occ:1.00
 OD1 A:ASN493 2.0 27.4 1.0
O A:HOH785 2.1 29.6 1.0
OD1 A:ASP466 2.2 32.2 1.0
O1A A:TPP601 2.2 27.6 1.0
O3B A:TPP601 2.2 34.9 1.0
O A:GLY495 2.3 29.6 1.0
CG A:ASN493 2.9 28.6 1.0
ND2 A:ASN493 3.1 28.3 1.0
CG A:ASP466 3.3 28.6 1.0
PB A:TPP601 3.3 32.5 1.0
PA A:TPP601 3.4 30.1 1.0
C A:GLY495 3.5 30.8 1.0
O3A A:TPP601 3.6 27.9 1.0
OD2 A:ASP466 3.8 28.1 1.0
O1B A:TPP601 3.9 30.6 1.0
N A:ASP466 4.0 25.4 1.0
O A:PHE491 4.2 26.7 1.0
N A:GLY495 4.2 31.8 1.0
O7 A:TPP601 4.2 31.4 1.0
CB A:ASN493 4.3 29.8 1.0
N A:SER467 4.3 22.7 1.0
N A:PHE497 4.4 31.7 1.0
N A:ILE496 4.4 33.8 1.0
CA A:GLY495 4.4 32.5 1.0
CA A:ILE496 4.5 34.6 1.0
CB A:ASP466 4.5 26.4 1.0
N A:ASN493 4.5 27.2 1.0
O2A A:TPP601 4.5 26.5 1.0
O2B A:TPP601 4.6 26.1 1.0
CA A:ASP466 4.7 29.2 1.0
C A:ILE496 4.8 34.2 1.0
CA A:ASN493 4.8 32.3 1.0
CA A:GLY465 4.9 22.8 1.0
C A:GLY465 4.9 24.2 1.0
C A:ASN493 4.9 31.4 1.0
O A:PHE497 4.9 39.2 1.0
CB A:SER467 4.9 30.2 1.0
C A:PHE497 5.0 39.1 1.0

Magnesium binding site 2 out of 8 in 7b2e

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Magnesium binding site 2 out of 8 in the Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:28.3
occ:1.00
 O3B B:TPP601 2.0 33.0 1.0
OD1 B:ASP466 2.1 34.2 1.0
O1A B:TPP601 2.1 28.3 1.0
O B:HOH742 2.1 27.0 1.0
O B:GLY495 2.2 33.7 1.0
OD1 B:ASN493 2.2 28.0 1.0
CG B:ASN493 3.1 27.5 1.0
PB B:TPP601 3.2 28.3 1.0
CG B:ASP466 3.2 34.7 1.0
PA B:TPP601 3.3 34.5 1.0
C B:GLY495 3.3 30.8 1.0
ND2 B:ASN493 3.4 30.5 1.0
O3A B:TPP601 3.5 32.1 1.0
OD2 B:ASP466 3.7 33.6 1.0
O1B B:TPP601 3.8 30.1 1.0
N B:ASP466 3.9 29.8 1.0
O7 B:TPP601 4.0 35.0 1.0
O B:PHE491 4.2 25.3 1.0
N B:GLY495 4.2 30.5 1.0
N B:SER467 4.2 30.8 1.0
N B:ILE496 4.2 29.9 1.0
N B:PHE497 4.3 34.4 1.0
CA B:ILE496 4.3 32.8 1.0
CA B:GLY495 4.3 29.7 1.0
O2B B:TPP601 4.4 30.8 1.0
O2A B:TPP601 4.4 26.1 1.0
CB B:ASP466 4.5 28.0 1.0
CB B:ASN493 4.5 28.3 1.0
N B:ASN493 4.6 28.1 1.0
CA B:ASP466 4.6 25.6 1.0
C B:ILE496 4.6 36.2 1.0
CA B:GLY465 4.7 20.9 1.0
C B:GLY465 4.7 24.0 1.0
CB B:SER467 4.8 33.8 1.0
C B:ASP466 4.9 29.5 1.0
CA B:ASN493 4.9 30.0 1.0
C B:ASN493 5.0 32.6 1.0

Magnesium binding site 3 out of 8 in 7b2e

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Magnesium binding site 3 out of 8 in the Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:24.6
occ:1.00
 OD1 C:ASN493 2.1 24.9 1.0
O3B C:TPP601 2.1 31.6 1.0
OD1 C:ASP466 2.1 28.6 1.0
O C:HOH750 2.1 27.5 1.0
O2A C:TPP601 2.1 27.7 1.0
O C:GLY495 2.3 30.0 1.0
CG C:ASN493 2.9 27.0 1.0
ND2 C:ASN493 3.1 28.8 1.0
PB C:TPP601 3.2 29.9 1.0
CG C:ASP466 3.2 27.1 1.0
PA C:TPP601 3.3 32.4 1.0
C C:GLY495 3.5 31.0 1.0
O3A C:TPP601 3.5 32.0 1.0
O2B C:TPP601 3.6 30.1 1.0
OD2 C:ASP466 3.6 30.2 1.0
N C:ASP466 4.0 25.8 1.0
O7 C:TPP601 4.0 31.1 1.0
O C:PHE491 4.2 23.8 1.0
N C:SER467 4.3 23.8 1.0
N C:GLY495 4.3 28.5 1.0
CB C:ASN493 4.3 27.5 1.0
N C:PHE497 4.3 32.7 1.0
N C:ILE496 4.4 32.2 1.0
CA C:ILE496 4.4 34.8 1.0
O1B C:TPP601 4.5 32.0 1.0
CB C:ASP466 4.5 22.9 1.0
CA C:GLY495 4.5 30.0 1.0
O1A C:TPP601 4.5 24.2 1.0
N C:ASN493 4.6 24.5 1.0
CA C:ASP466 4.7 24.6 1.0
C C:ILE496 4.7 36.6 1.0
CA C:GLY465 4.8 23.3 1.0
C C:GLY465 4.8 23.6 1.0
CB C:SER467 4.8 28.6 1.0
CA C:ASN493 4.9 29.6 1.0
C C:ASP466 5.0 23.7 1.0

Magnesium binding site 4 out of 8 in 7b2e

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Magnesium binding site 4 out of 8 in the Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:25.6
occ:1.00
 O D:HOH734 2.0 29.0 1.0
OD1 D:ASN493 2.0 29.2 1.0
O3B D:TPP601 2.1 35.5 1.0
O2A D:TPP601 2.1 29.5 1.0
OD1 D:ASP466 2.3 30.2 1.0
O D:GLY495 2.4 32.3 1.0
CG D:ASN493 2.9 28.2 1.0
PB D:TPP601 3.1 30.7 1.0
ND2 D:ASN493 3.2 30.8 1.0
PA D:TPP601 3.3 34.4 1.0
CG D:ASP466 3.4 30.4 1.0
O3A D:TPP601 3.5 34.1 1.0
O2B D:TPP601 3.5 29.3 1.0
C D:GLY495 3.6 31.4 1.0
N D:ASP466 3.9 32.4 1.0
OD2 D:ASP466 3.9 30.0 1.0
O D:PHE491 4.0 26.4 1.0
O7 D:TPP601 4.1 35.4 1.0
N D:SER467 4.3 26.7 1.0
CB D:ASN493 4.4 30.8 1.0
N D:GLY495 4.4 32.5 1.0
N D:PHE497 4.4 33.0 1.0
N D:ASN493 4.5 29.7 1.0
O1A D:TPP601 4.5 27.1 1.0
O1B D:TPP601 4.5 29.3 1.0
CB D:ASP466 4.5 29.0 1.0
CA D:GLY465 4.5 21.9 1.0
N D:ILE496 4.5 31.6 1.0
C D:GLY465 4.6 26.2 1.0
CA D:ILE496 4.6 33.0 1.0
CA D:GLY495 4.6 33.4 1.0
CA D:ASP466 4.6 29.1 1.0
CA D:ASN493 4.8 30.4 1.0
C D:ILE496 4.9 32.6 1.0
CB D:SER467 5.0 33.3 1.0
C D:ASN493 5.0 31.7 1.0
C D:ASP466 5.0 27.7 1.0

Magnesium binding site 5 out of 8 in 7b2e

Go back to Magnesium Binding Sites List in 7b2e
Magnesium binding site 5 out of 8 in the Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:36.0
occ:1.00
 O3B E:TPP601 2.0 33.8 0.9
OD1 E:ASN493 2.0 36.5 1.0
O1A E:TPP601 2.1 31.9 0.9
OD1 E:ASP466 2.1 35.3 1.0
O E:HOH704 2.2 33.5 1.0
O E:GLY495 2.4 39.6 1.0
CG E:ASN493 3.0 39.0 1.0
PB E:TPP601 3.2 28.2 0.9
CG E:ASP466 3.3 32.8 1.0
PA E:TPP601 3.3 31.4 0.9
ND2 E:ASN493 3.3 35.3 1.0
O3A E:TPP601 3.5 34.6 0.9
C E:GLY495 3.6 36.2 1.0
OD2 E:ASP466 3.7 34.5 1.0
O1B E:TPP601 3.8 35.4 0.9
O E:PHE491 3.9 28.3 1.0
N E:ASP466 3.9 27.6 1.0
O7 E:TPP601 4.1 33.8 0.9
N E:GLY495 4.3 38.1 1.0
CB E:ASN493 4.4 37.3 1.0
N E:SER467 4.4 28.3 1.0
O2B E:TPP601 4.4 33.1 0.9
N E:ASN493 4.4 30.0 1.0
O2A E:TPP601 4.4 26.2 0.9
N E:PHE497 4.5 43.9 1.0
N E:ILE496 4.5 39.6 1.0
CB E:ASP466 4.5 26.6 1.0
CA E:GLY495 4.6 34.9 1.0
CA E:ILE496 4.6 37.8 1.0
CA E:GLY465 4.7 27.2 1.0
CA E:ASP466 4.7 27.4 1.0
C E:GLY465 4.7 29.6 1.0
CA E:ASN493 4.8 32.0 1.0
C E:ILE496 4.9 42.0 1.0
C E:ASN493 5.0 34.6 1.0

Magnesium binding site 6 out of 8 in 7b2e

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Magnesium binding site 6 out of 8 in the Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg603

b:31.4
occ:1.00
 O2A F:TPP601 2.1 32.6 0.9
OD1 F:ASN493 2.1 37.9 1.0
OD1 F:ASP466 2.1 31.9 1.0
O3B F:TPP601 2.2 32.1 0.9
O F:GLY495 2.3 41.7 1.0
O F:HOH711 2.4 38.1 1.0
CG F:ASN493 3.0 34.9 1.0
CG F:ASP466 3.2 32.4 1.0
PA F:TPP601 3.3 34.8 0.9
PB F:TPP601 3.3 30.4 0.9
ND2 F:ASN493 3.3 31.7 1.0
C F:GLY495 3.5 40.9 1.0
O3A F:TPP601 3.5 39.4 0.9
OD2 F:ASP466 3.6 29.9 1.0
N F:ASP466 3.9 27.5 1.0
O2B F:TPP601 4.0 38.1 0.9
O F:PHE491 4.0 25.6 1.0
O7 F:TPP601 4.0 34.5 0.9
N F:GLY495 4.2 38.3 1.0
N F:SER467 4.3 25.8 1.0
N F:ILE496 4.4 39.2 1.0
CA F:GLY495 4.4 37.9 1.0
CB F:ASN493 4.4 34.8 1.0
O1A F:TPP601 4.4 27.7 0.9
N F:PHE497 4.5 42.8 1.0
CB F:ASP466 4.5 28.8 1.0
N F:ASN493 4.5 30.5 1.0
CA F:ILE496 4.5 40.8 1.0
O1B F:TPP601 4.6 34.6 0.9
CA F:ASP466 4.7 28.9 1.0
CA F:GLY465 4.7 29.4 1.0
C F:GLY465 4.7 32.6 1.0
CB F:SER467 4.8 29.5 1.0
C F:ILE496 4.8 45.7 1.0
CA F:ASN493 4.8 31.3 1.0
C F:ASN493 4.9 34.1 1.0
C F:ASP466 5.0 27.4 1.0
N F:ASN494 5.0 34.9 1.0

Magnesium binding site 7 out of 8 in 7b2e

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Magnesium binding site 7 out of 8 in the Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:29.3
occ:1.00
 OD1 G:ASP466 2.0 23.4 1.0
O2A G:TPP601 2.1 26.4 1.0
O G:GLY495 2.1 26.2 1.0
OD1 G:ASN493 2.2 28.0 1.0
O3B G:TPP601 2.2 29.4 1.0
O G:HOH712 2.3 19.6 1.0
CG G:ASP466 3.1 23.4 1.0
CG G:ASN493 3.1 26.8 1.0
PA G:TPP601 3.3 22.9 1.0
C G:GLY495 3.3 27.7 1.0
PB G:TPP601 3.4 25.3 1.0
ND2 G:ASN493 3.4 26.0 1.0
OD2 G:ASP466 3.5 24.6 1.0
O3A G:TPP601 3.6 24.7 1.0
N G:ASP466 3.9 19.5 1.0
O7 G:TPP601 4.0 22.2 1.0
O2B G:TPP601 4.0 31.7 1.0
O G:PHE491 4.0 21.0 1.0
N G:GLY495 4.1 24.0 1.0
N G:ILE496 4.2 28.1 1.0
N G:SER467 4.3 24.0 1.0
CA G:GLY495 4.3 27.8 1.0
CA G:ILE496 4.3 30.8 1.0
CB G:ASP466 4.4 22.9 1.0
N G:PHE497 4.4 35.3 1.0
O1A G:TPP601 4.5 23.9 1.0
CB G:ASN493 4.5 28.2 1.0
N G:ASN493 4.5 19.8 1.0
O1B G:TPP601 4.6 23.6 1.0
CA G:ASP466 4.6 19.8 1.0
C G:GLY465 4.7 24.3 1.0
CA G:GLY465 4.7 20.4 1.0
C G:ILE496 4.7 33.5 1.0
CB G:SER467 4.9 20.9 1.0
C G:ASP466 4.9 22.3 1.0
CA G:ASN493 4.9 25.1 1.0
C G:ASN493 5.0 22.6 1.0

Magnesium binding site 8 out of 8 in 7b2e

Go back to Magnesium Binding Sites List in 7b2e
Magnesium binding site 8 out of 8 in the Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Quadruple Mutant of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:26.2
occ:1.00
 O H:GLY495 2.0 28.7 1.0
OD1 H:ASP466 2.0 25.4 1.0
O1A H:TPP601 2.1 24.0 1.0
OD1 H:ASN493 2.1 26.4 1.0
O1B H:TPP601 2.2 28.3 1.0
O H:HOH722 2.2 23.4 1.0
CG H:ASP466 3.1 26.7 1.0
CG H:ASN493 3.1 26.8 1.0
C H:GLY495 3.2 28.3 1.0
PA H:TPP601 3.3 23.2 1.0
ND2 H:ASN493 3.4 25.4 1.0
PB H:TPP601 3.4 25.5 1.0
OD2 H:ASP466 3.4 25.8 1.0
O3A H:TPP601 3.7 28.6 1.0
O7 H:TPP601 4.0 27.0 1.0
N H:GLY495 4.0 23.7 1.0
N H:ASP466 4.0 21.8 1.0
N H:ILE496 4.1 29.6 1.0
O H:PHE491 4.1 22.5 1.0
O3B H:TPP601 4.2 34.5 1.0
CA H:GLY495 4.2 27.1 1.0
N H:SER467 4.2 24.6 1.0
CA H:ILE496 4.3 30.9 1.0
N H:PHE497 4.3 34.3 1.0
CB H:ASP466 4.4 24.3 1.0
CB H:ASN493 4.5 24.3 1.0
O2B H:TPP601 4.5 28.6 1.0
O2A H:TPP601 4.5 21.5 1.0
N H:ASN493 4.5 22.2 1.0
CA H:ASP466 4.6 21.5 1.0
C H:ILE496 4.7 33.3 1.0
CB H:SER467 4.8 24.0 1.0
CA H:ASN493 4.9 23.5 1.0
C H:GLY465 4.9 25.0 1.0
C H:ASN493 4.9 23.2 1.0
C H:ASP466 4.9 21.8 1.0
CA H:GLY465 4.9 20.8 1.0
N H:ASN494 5.0 27.3 1.0

Reference:

M.Nattermann, S.Burgener, P.Pfister, A.Chou, L.Schulz, S.H.Lee, J.Zarzycki, R.Gonzales, T.J.Erb. Enineering A Highly Efficient Carboligase For A New-to-Nature One-Carbon Metabolism To Be Published.
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