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: Sun Jul 11 15:42:23 2021
|
