Atomistry » Magnesium » PDB 7aom-7b19 » 7ayg
Atomistry »
  Magnesium »
    PDB 7aom-7b19 »
      7ayg »

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

Go back to Magnesium Binding Sites List in 7ayg
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

Go back to Magnesium Binding Sites List in 7ayg
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

Go back to Magnesium Binding Sites List in 7ayg
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

Go back to Magnesium Binding Sites List in 7ayg
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

Go back to Magnesium Binding Sites List in 7ayg
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

Go back to Magnesium Binding Sites List in 7ayg
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

Go back to Magnesium Binding Sites List in 7ayg
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

Go back to Magnesium Binding Sites List in 7ayg
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

Last articles

Na in 6D9B
Na in 6D99
Na in 6D9A
Na in 6D5L
Na in 6D55
Na in 6D5J
Na in 6D5E
Na in 6D56
Na in 6D64
Na in 6D59
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy