Magnesium in PDB 8ffu: Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound
Protein crystallography data
The structure of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound, PDB code: 8ffu
was solved by
P.Y.-T.Chen,
B.S.Moore,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.80 /
2.04
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.062,
158.489,
73.6,
90,
90.02,
90
|
R / Rfree (%)
|
17.6 /
20.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound
(pdb code 8ffu). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound, PDB code: 8ffu:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8ffu
Go back to
Magnesium Binding Sites List in 8ffu
Magnesium binding site 1 out
of 4 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:27.2
occ:1.00
|
O
|
A:HOH537
|
2.0
|
29.6
|
1.0
|
O
|
A:VAL72
|
2.1
|
28.5
|
1.0
|
O
|
A:ALA66
|
2.3
|
30.3
|
1.0
|
O
|
A:ASP69
|
2.5
|
31.1
|
1.0
|
O
|
A:HOH533
|
2.6
|
33.7
|
1.0
|
O
|
A:HOH534
|
2.7
|
28.7
|
1.0
|
C
|
A:ALA66
|
3.2
|
28.4
|
1.0
|
C
|
A:VAL72
|
3.4
|
28.7
|
1.0
|
C
|
A:ASP69
|
3.6
|
31.4
|
1.0
|
CB
|
A:ALA66
|
4.0
|
28.9
|
1.0
|
CA
|
A:ALA66
|
4.0
|
27.8
|
1.0
|
N
|
A:SER67
|
4.0
|
28.0
|
1.0
|
CA
|
A:LYS70
|
4.1
|
30.6
|
1.0
|
N
|
A:VAL72
|
4.1
|
30.4
|
1.0
|
CA
|
A:SER67
|
4.2
|
28.2
|
1.0
|
O
|
A:LYS70
|
4.2
|
32.4
|
1.0
|
CA
|
A:VAL72
|
4.2
|
28.9
|
1.0
|
C
|
A:LYS70
|
4.2
|
29.3
|
1.0
|
N
|
A:LYS70
|
4.3
|
31.0
|
1.0
|
N
|
A:SER73
|
4.4
|
27.8
|
1.0
|
CB
|
A:VAL72
|
4.5
|
28.1
|
1.0
|
N
|
A:ASP69
|
4.6
|
29.8
|
1.0
|
C
|
A:SER67
|
4.6
|
28.5
|
1.0
|
CA
|
A:SER73
|
4.6
|
27.1
|
1.0
|
NZ
|
A:LYS70
|
4.7
|
35.7
|
1.0
|
CA
|
A:ASP69
|
4.7
|
29.7
|
1.0
|
O
|
A:SER67
|
4.9
|
31.8
|
1.0
|
N
|
A:SER71
|
5.0
|
29.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8ffu
Go back to
Magnesium Binding Sites List in 8ffu
Magnesium binding site 2 out
of 4 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:29.1
occ:1.00
|
O
|
B:VAL72
|
2.2
|
30.2
|
1.0
|
O
|
B:HOH525
|
2.2
|
27.9
|
1.0
|
O
|
B:ALA66
|
2.5
|
30.1
|
1.0
|
O
|
B:ASP69
|
2.6
|
33.4
|
1.0
|
O
|
B:HOH535
|
2.8
|
29.4
|
1.0
|
C
|
B:ALA66
|
3.4
|
30.3
|
1.0
|
C
|
B:VAL72
|
3.4
|
30.9
|
1.0
|
C
|
B:ASP69
|
3.7
|
34.5
|
1.0
|
CB
|
B:ALA66
|
4.0
|
29.1
|
1.0
|
N
|
B:VAL72
|
4.0
|
31.9
|
1.0
|
CA
|
B:LYS70
|
4.1
|
32.7
|
1.0
|
O
|
B:LYS70
|
4.1
|
32.9
|
1.0
|
CA
|
B:ALA66
|
4.1
|
29.1
|
1.0
|
C
|
B:LYS70
|
4.1
|
32.1
|
1.0
|
CA
|
B:VAL72
|
4.2
|
31.2
|
1.0
|
N
|
B:SER67
|
4.2
|
30.3
|
1.0
|
CA
|
B:SER67
|
4.3
|
29.9
|
1.0
|
N
|
B:LYS70
|
4.3
|
33.9
|
1.0
|
N
|
B:SER73
|
4.4
|
29.3
|
1.0
|
CB
|
B:VAL72
|
4.5
|
31.8
|
1.0
|
CA
|
B:SER73
|
4.6
|
29.4
|
1.0
|
N
|
B:ASP69
|
4.7
|
32.3
|
1.0
|
C
|
B:SER67
|
4.7
|
30.8
|
1.0
|
CA
|
B:ASP69
|
4.8
|
32.3
|
1.0
|
N
|
B:SER71
|
4.9
|
30.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8ffu
Go back to
Magnesium Binding Sites List in 8ffu
Magnesium binding site 3 out
of 4 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg401
b:28.4
occ:1.00
|
O
|
C:HOH533
|
2.1
|
27.2
|
1.0
|
O
|
C:ASP69
|
2.1
|
29.5
|
1.0
|
O
|
C:ALA66
|
2.5
|
29.6
|
1.0
|
O
|
C:VAL72
|
2.7
|
27.4
|
1.0
|
O
|
C:HOH538
|
2.9
|
27.6
|
1.0
|
C
|
C:ASP69
|
3.0
|
31.7
|
1.0
|
CA
|
C:LYS70
|
3.5
|
32.3
|
1.0
|
C
|
C:ALA66
|
3.5
|
27.1
|
1.0
|
N
|
C:LYS70
|
3.6
|
33.3
|
1.0
|
C
|
C:VAL72
|
3.8
|
27.9
|
1.0
|
C
|
C:LYS70
|
3.9
|
30.6
|
1.0
|
N
|
C:ASP69
|
4.1
|
30.9
|
1.0
|
O
|
C:LYS70
|
4.1
|
33.0
|
1.0
|
CA
|
C:ASP69
|
4.1
|
31.2
|
1.0
|
CA
|
C:SER67
|
4.1
|
27.4
|
1.0
|
N
|
C:VAL72
|
4.2
|
31.7
|
1.0
|
N
|
C:SER67
|
4.3
|
28.2
|
1.0
|
C
|
C:SER67
|
4.3
|
29.3
|
1.0
|
CA
|
C:VAL72
|
4.5
|
30.1
|
1.0
|
CA
|
C:ALA66
|
4.5
|
27.0
|
1.0
|
O
|
C:SER67
|
4.5
|
31.9
|
1.0
|
CB
|
C:ALA66
|
4.6
|
28.0
|
1.0
|
N
|
C:SER71
|
4.7
|
27.9
|
1.0
|
CB
|
C:VAL72
|
4.7
|
28.9
|
1.0
|
CB
|
C:LYS70
|
4.8
|
33.3
|
1.0
|
N
|
C:LEU68
|
4.9
|
30.1
|
1.0
|
N
|
C:SER73
|
4.9
|
28.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8ffu
Go back to
Magnesium Binding Sites List in 8ffu
Magnesium binding site 4 out
of 4 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg401
b:35.6
occ:1.00
|
O
|
D:ALA66
|
2.3
|
33.6
|
1.0
|
O
|
D:HOH546
|
2.6
|
36.5
|
1.0
|
O
|
D:ASP69
|
2.6
|
35.1
|
1.0
|
O
|
D:VAL72
|
2.7
|
33.8
|
1.0
|
C
|
D:ALA66
|
3.2
|
32.2
|
1.0
|
C
|
D:ASP69
|
3.5
|
36.5
|
1.0
|
CA
|
D:LYS70
|
3.8
|
38.2
|
1.0
|
CA
|
D:SER67
|
3.8
|
30.6
|
1.0
|
C
|
D:VAL72
|
3.9
|
34.0
|
1.0
|
N
|
D:SER67
|
3.9
|
31.5
|
1.0
|
N
|
D:LYS70
|
4.0
|
38.6
|
1.0
|
C
|
D:LYS70
|
4.2
|
36.0
|
1.0
|
CA
|
D:ALA66
|
4.2
|
29.7
|
1.0
|
CB
|
D:ALA66
|
4.2
|
32.3
|
1.0
|
O
|
D:LYS70
|
4.2
|
36.9
|
1.0
|
C
|
D:SER67
|
4.2
|
32.2
|
1.0
|
N
|
D:ASP69
|
4.4
|
34.5
|
1.0
|
N
|
D:VAL72
|
4.4
|
34.6
|
1.0
|
O
|
D:SER67
|
4.5
|
34.8
|
1.0
|
CA
|
D:VAL72
|
4.6
|
34.4
|
1.0
|
CA
|
D:ASP69
|
4.6
|
35.7
|
1.0
|
CB
|
D:VAL72
|
4.8
|
32.9
|
1.0
|
N
|
D:LEU68
|
4.8
|
33.0
|
1.0
|
N
|
D:SER73
|
4.9
|
32.2
|
1.0
|
N
|
D:SER71
|
5.0
|
35.1
|
1.0
|
|
Reference:
J.L.Cordoza,
P.Y.Chen,
L.R.Blaustein,
S.T.Lima,
M.F.Fiore,
J.R.Chekan,
B.S.Moore,
S.M.K.Mckinnie.
Mechanistic and Structural Insights Into A Divergent Plp-Dependent L-Enduracididine Cyclase From A Toxic Cyanobacterium. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 36993528
DOI: 10.1101/2023.03.21.533663
Page generated: Fri Oct 4 02:30:27 2024
|