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Magnesium in PDB 7ayg: Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp

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

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

Protein crystallography data

The structure of Oxalyl-Coa Decarboxylase From Methylorubrum Extorquens with Bound Tpp and Adp, PDB code: 7ayg 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) 39.30 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 160.176, 181.798, 202.366, 90, 90, 90
R / Rfree (%) 17.7 / 20.8

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 7ayg

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Magnesium binding site 1 out of 8 in the 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 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:21.6
occ:1.00
 O3B A:TPP601 2.0 21.8 1.0
O2A A:TPP601 2.1 20.8 1.0
OD1 A:ASP466 2.1 20.4 1.0
O A:HOH773 2.1 20.6 1.0
OD1 A:ASN493 2.1 21.9 1.0
O A:GLY495 2.1 20.0 1.0
CG A:ASN493 3.0 22.7 1.0
PB A:TPP601 3.2 22.3 1.0
PA A:TPP601 3.2 21.6 1.0
CG A:ASP466 3.3 21.6 1.0
ND2 A:ASN493 3.3 22.1 1.0
C A:GLY495 3.4 23.2 1.0
O3A A:TPP601 3.5 22.8 1.0
O2B A:TPP601 3.7 22.3 1.0
N A:ASP466 3.9 19.3 1.0
OD2 A:ASP466 3.9 21.7 1.0
O7 A:TPP601 4.0 21.6 1.0
N A:GLY495 4.1 21.8 1.0
O A:PHE491 4.2 23.2 1.0
N A:SER467 4.2 19.6 1.0
N A:ILE496 4.3 21.4 1.0
N A:TYR497 4.3 23.2 1.0
CA A:GLY495 4.3 21.1 1.0
CA A:ILE496 4.4 22.9 1.0
CB A:ASN493 4.4 21.2 1.0
O1B A:TPP601 4.5 23.9 1.0
CB A:ASP466 4.5 19.9 1.0
O1A A:TPP601 4.5 20.2 1.0
N A:ASN493 4.6 21.1 1.0
CA A:ASP466 4.6 19.2 1.0
C A:ILE496 4.7 26.8 1.0
C A:GLY465 4.8 19.5 1.0
CA A:GLY465 4.8 19.7 1.0
CB A:SER467 4.9 21.0 1.0
C A:ASP466 4.9 19.9 1.0
CA A:ASN493 4.9 22.9 1.0

Magnesium binding site 2 out of 8 in 7ayg

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Magnesium binding site 2 out of 8 in the 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 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:19.1
occ:1.00
 OD1 B:ASP466 2.0 20.0 1.0
O B:GLY495 2.1 21.8 1.0
OD1 B:ASN493 2.1 21.3 1.0
O3B B:TPP601 2.1 21.0 1.0
O2A B:TPP601 2.1 22.1 1.0
O B:HOH806 2.1 21.3 1.0
CG B:ASN493 3.0 22.2 1.0
CG B:ASP466 3.1 22.0 1.0
PA B:TPP601 3.3 21.9 1.0
PB B:TPP601 3.3 22.8 1.0
C B:GLY495 3.3 23.2 1.0
ND2 B:ASN493 3.4 20.9 1.0
O3A B:TPP601 3.6 22.9 1.0
OD2 B:ASP466 3.8 22.0 1.0
N B:ASP466 3.8 19.9 1.0
O2B B:TPP601 3.8 22.2 1.0
N B:GLY495 4.1 21.4 1.0
O7 B:TPP601 4.1 23.2 1.0
N B:SER467 4.1 18.9 1.0
O B:PHE491 4.2 22.5 1.0
N B:ILE496 4.2 21.3 1.0
CA B:GLY495 4.3 22.0 1.0
CB B:ASP466 4.3 19.0 1.0
N B:TYR497 4.3 24.2 1.0
CA B:ILE496 4.4 24.4 1.0
CB B:ASN493 4.4 21.1 1.0
O1A B:TPP601 4.5 20.8 1.0
CA B:ASP466 4.5 19.4 1.0
N B:ASN493 4.6 21.6 1.0
O1B B:TPP601 4.6 21.9 1.0
C B:GLY465 4.7 20.9 1.0
CA B:GLY465 4.8 19.0 1.0
C B:ASP466 4.8 19.2 1.0
C B:ILE496 4.8 25.4 1.0
CB B:SER467 4.9 21.5 1.0
CA B:ASN493 4.9 21.9 1.0
C B:ASN493 5.0 21.8 1.0

Magnesium binding site 3 out of 8 in 7ayg

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Magnesium binding site 3 out of 8 in the 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 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:22.1
occ:1.00
 O1A C:TPP601 2.0 20.9 1.0
OD1 C:ASP466 2.1 22.1 1.0
O C:GLY495 2.1 24.3 1.0
O3B C:TPP601 2.1 22.3 1.0
OD1 C:ASN493 2.2 22.4 1.0
O C:HOH715 2.3 20.5 1.0
CG C:ASN493 3.2 24.3 1.0
PA C:TPP601 3.2 21.1 1.0
PB C:TPP601 3.2 22.6 1.0
CG C:ASP466 3.2 22.4 1.0
C C:GLY495 3.3 23.9 1.0
ND2 C:ASN493 3.5 21.6 1.0
O3A C:TPP601 3.5 22.5 1.0
O1B C:TPP601 3.7 22.7 1.0
N C:ASP466 3.8 20.7 1.0
OD2 C:ASP466 3.9 23.2 1.0
O7 C:TPP601 4.0 23.3 1.0
N C:SER467 4.1 20.0 1.0
N C:GLY495 4.1 23.7 1.0
O C:PHE491 4.1 22.6 1.0
N C:ILE496 4.3 24.0 1.0
N C:TYR497 4.3 24.4 1.0
CA C:GLY495 4.3 22.2 1.0
O2A C:TPP601 4.4 21.6 1.0
CB C:ASP466 4.4 20.2 1.0
CA C:ILE496 4.4 25.0 1.0
CA C:ASP466 4.5 21.0 1.0
O2B C:TPP601 4.5 22.5 1.0
CB C:ASN493 4.6 23.1 1.0
N C:ASN493 4.6 20.6 1.0
C C:GLY465 4.6 21.0 1.0
CA C:GLY465 4.7 22.2 1.0
C C:ILE496 4.8 25.9 1.0
C C:ASP466 4.8 21.0 1.0
CB C:SER467 4.8 19.6 1.0
CA C:ASN493 5.0 24.2 1.0

Magnesium binding site 4 out of 8 in 7ayg

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Magnesium binding site 4 out of 8 in the 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 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:21.8
occ:1.00
 O1B D:TPP601 2.0 21.9 1.0
O1A D:TPP601 2.0 20.9 1.0
OD1 D:ASP466 2.1 20.2 1.0
OD1 D:ASN493 2.1 20.7 1.0
O D:GLY495 2.1 21.5 1.0
O D:HOH782 2.2 20.2 1.0
CG D:ASN493 3.1 22.3 1.0
PB D:TPP601 3.2 21.3 1.0
PA D:TPP601 3.2 20.9 1.0
CG D:ASP466 3.3 20.4 1.0
C D:GLY495 3.4 21.9 1.0
ND2 D:ASN493 3.4 20.7 1.0
O3A D:TPP601 3.5 22.2 1.0
O3B D:TPP601 3.8 21.4 1.0
N D:ASP466 3.8 20.1 1.0
OD2 D:ASP466 3.9 21.9 1.0
O7 D:TPP601 4.0 22.4 1.0
N D:GLY495 4.1 20.5 1.0
N D:SER467 4.2 20.0 1.0
O D:PHE491 4.2 21.1 1.0
CA D:GLY495 4.3 20.2 1.0
N D:ILE496 4.3 22.6 1.0
N D:TYR497 4.3 23.2 1.0
O2A D:TPP601 4.4 20.3 1.0
CB D:ASP466 4.4 20.2 1.0
O2B D:TPP601 4.4 22.2 1.0
CB D:ASN493 4.5 20.4 1.0
CA D:ILE496 4.5 22.9 1.0
CA D:ASP466 4.5 20.1 1.0
N D:ASN493 4.5 20.5 1.0
C D:GLY465 4.7 20.1 1.0
CA D:GLY465 4.7 20.6 1.0
C D:ILE496 4.8 23.7 1.0
CB D:SER467 4.9 20.9 1.0
C D:ASP466 4.9 20.2 1.0
CA D:ASN493 4.9 22.5 1.0

Magnesium binding site 5 out of 8 in 7ayg

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Magnesium binding site 5 out of 8 in the 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 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:22.9
occ:1.00
 OD1 E:ASP466 2.0 20.9 1.0
O3B E:TPP601 2.1 23.4 1.0
O1A E:TPP601 2.1 22.9 1.0
O E:GLY495 2.1 21.7 1.0
OD1 E:ASN493 2.1 21.8 1.0
O E:HOH794 2.2 22.4 1.0
CG E:ASN493 3.0 23.4 1.0
PB E:TPP601 3.2 22.7 1.0
PA E:TPP601 3.2 22.3 1.0
CG E:ASP466 3.2 22.3 1.0
C E:GLY495 3.3 22.4 1.0
ND2 E:ASN493 3.3 23.3 1.0
O3A E:TPP601 3.5 22.6 1.0
O1B E:TPP601 3.8 23.1 1.0
OD2 E:ASP466 3.9 21.6 1.0
N E:ASP466 3.9 21.4 1.0
O7 E:TPP601 4.0 22.8 1.0
N E:GLY495 4.1 21.2 1.0
N E:SER467 4.1 20.3 1.0
O E:PHE491 4.2 22.9 1.0
N E:TYR497 4.2 22.7 1.0
N E:ILE496 4.2 22.0 1.0
CA E:GLY495 4.3 20.8 1.0
CA E:ILE496 4.4 22.9 1.0
CB E:ASP466 4.4 21.1 1.0
CB E:ASN493 4.4 21.9 1.0
O2A E:TPP601 4.5 21.7 1.0
O2B E:TPP601 4.5 23.1 1.0
CA E:ASP466 4.5 21.4 1.0
N E:ASN493 4.6 22.2 1.0
C E:ILE496 4.7 25.4 1.0
C E:GLY465 4.8 21.4 1.0
CA E:GLY465 4.8 20.6 1.0
C E:ASP466 4.8 20.9 1.0
CB E:SER467 4.9 21.1 1.0
CA E:ASN493 4.9 23.8 1.0
C E:TYR497 5.0 25.0 1.0

Magnesium binding site 6 out of 8 in 7ayg

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Magnesium binding site 6 out of 8 in the 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 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:19.7
occ:1.00
 OD1 F:ASP466 2.0 20.7 1.0
O3B F:TPP601 2.1 22.2 1.0
O1A F:TPP601 2.1 21.3 1.0
O F:HOH804 2.1 19.9 1.0
O F:GLY495 2.1 21.7 1.0
OD1 F:ASN493 2.2 23.1 1.0
CG F:ASN493 3.1 23.2 1.0
CG F:ASP466 3.2 22.4 1.0
PB F:TPP601 3.2 23.3 1.0
PA F:TPP601 3.3 21.8 1.0
C F:GLY495 3.3 23.5 1.0
ND2 F:ASN493 3.4 22.2 1.0
O3A F:TPP601 3.6 22.6 1.0
O1B F:TPP601 3.8 22.4 1.0
OD2 F:ASP466 3.8 23.0 1.0
N F:ASP466 3.8 19.6 1.0
O7 F:TPP601 4.0 24.2 1.0
N F:GLY495 4.1 21.9 1.0
N F:SER467 4.1 20.3 1.0
O F:PHE491 4.2 21.2 1.0
CA F:GLY495 4.3 22.1 1.0
N F:ILE496 4.3 22.3 1.0
N F:TYR497 4.4 25.6 1.0
CB F:ASP466 4.4 19.8 1.0
CA F:ILE496 4.4 25.3 1.0
O2A F:TPP601 4.4 20.4 1.0
O2B F:TPP601 4.5 23.6 1.0
CB F:ASN493 4.5 22.6 1.0
CA F:ASP466 4.5 19.7 1.0
N F:ASN493 4.6 21.8 1.0
C F:GLY465 4.7 21.1 1.0
CA F:GLY465 4.7 19.5 1.0
C F:ILE496 4.8 26.8 1.0
C F:ASP466 4.8 20.6 1.0
CB F:SER467 4.8 22.6 1.0
CA F:ASN493 4.9 22.8 1.0

Magnesium binding site 7 out of 8 in 7ayg

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Magnesium binding site 7 out of 8 in the 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 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:21.1
occ:1.00
 O2A G:TPP601 2.0 22.1 1.0
OD1 G:ASP466 2.1 21.4 1.0
O3B G:TPP601 2.1 21.6 1.0
O G:GLY495 2.1 23.8 1.0
OD1 G:ASN493 2.2 21.5 1.0
O G:HOH743 2.3 19.8 1.0
CG G:ASN493 3.1 22.8 1.0
PB G:TPP601 3.2 21.1 1.0
CG G:ASP466 3.2 22.2 1.0
PA G:TPP601 3.2 20.2 1.0
C G:GLY495 3.3 23.4 1.0
ND2 G:ASN493 3.5 20.3 1.0
O3A G:TPP601 3.5 22.3 1.0
O2B G:TPP601 3.8 21.5 1.0
N G:ASP466 3.8 20.3 1.0
OD2 G:ASP466 3.8 22.1 1.0
O7 G:TPP601 4.0 21.3 1.0
N G:GLY495 4.1 22.1 1.0
N G:SER467 4.1 19.0 1.0
O G:PHE491 4.1 20.8 1.0
N G:ILE496 4.2 23.1 1.0
CA G:GLY495 4.3 22.2 1.0
N G:TYR497 4.3 24.2 1.0
O1A G:TPP601 4.4 20.4 1.0
CA G:ILE496 4.4 24.2 1.0
CB G:ASP466 4.4 21.0 1.0
O1B G:TPP601 4.5 22.0 1.0
CB G:ASN493 4.5 21.7 1.0
CA G:ASP466 4.5 20.5 1.0
N G:ASN493 4.6 18.9 1.0
C G:GLY465 4.7 19.9 1.0
CA G:GLY465 4.7 20.0 1.0
C G:ILE496 4.8 25.4 1.0
C G:ASP466 4.8 21.0 1.0
CB G:SER467 4.9 19.6 1.0
CA G:ASN493 4.9 21.4 1.0

Magnesium binding site 8 out of 8 in 7ayg

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Magnesium binding site 8 out of 8 in the 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 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:21.1
occ:1.00
 O2A H:TPP601 2.0 21.3 1.0
OD1 H:ASP466 2.0 19.1 1.0
O3B H:TPP601 2.1 22.2 1.0
O H:GLY495 2.1 19.6 1.0
O H:HOH737 2.1 19.0 1.0
OD1 H:ASN493 2.2 19.9 1.0
CG H:ASN493 3.1 21.6 1.0
PB H:TPP601 3.2 22.2 1.0
CG H:ASP466 3.2 20.1 1.0
PA H:TPP601 3.2 19.8 1.0
C H:GLY495 3.4 21.5 1.0
ND2 H:ASN493 3.5 20.7 1.0
O3A H:TPP601 3.5 22.4 1.0
N H:ASP466 3.8 18.3 1.0
O2B H:TPP601 3.8 20.8 1.0
OD2 H:ASP466 3.8 21.1 1.0
O7 H:TPP601 4.0 22.5 1.0
N H:GLY495 4.1 18.7 1.0
O H:PHE491 4.1 21.2 1.0
N H:SER467 4.1 19.4 1.0
CA H:GLY495 4.3 18.9 1.0
N H:ILE496 4.3 22.5 1.0
N H:TYR497 4.3 22.4 1.0
CB H:ASP466 4.4 19.3 1.0
O1A H:TPP601 4.4 20.3 1.0
O1B H:TPP601 4.5 21.9 1.0
CA H:ILE496 4.5 22.8 1.0
CA H:ASP466 4.5 19.4 1.0
CB H:ASN493 4.5 20.4 1.0
N H:ASN493 4.5 18.7 1.0
C H:GLY465 4.6 19.8 1.0
CA H:GLY465 4.6 20.5 1.0
C H:ILE496 4.8 22.4 1.0
C H:ASP466 4.8 19.5 1.0
CB H:SER467 4.9 19.8 1.0
CA H:ASN493 4.9 21.0 1.0

Reference:

M.Nattermann, S.Burgener, P.Pfister, A.Chou, L.Schulz, S.H.Lee, N.Paczia, J.Zarzycki, R.Gonzalez, T.J.Erb. Engineering A Highly Efficient Carboligase For Synthetic One-Carbon Metabolism Acs Catalysis 5396 2021.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.1C01237
Page generated: Wed Oct 2 10:15:18 2024

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