Magnesium in PDB 8fft: Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine

Protein crystallography data

The structure of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, PDB code: 8fft was solved by P.Y.-T.Chen, S.T.Lima, J.R.Chekan, B.S.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.23 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.855, 158.159, 73.231, 90, 90.01, 90
R / Rfree (%) 22 / 24.2

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 (pdb code 8fft). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 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, PDB code: 8fft:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8fft

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Magnesium binding site 1 out of 5 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:22.1
occ:1.00
 O A:ALA66 2.2 21.1 1.0
O A:ASP69 2.2 22.2 1.0
O A:HOH534 2.3 20.5 1.0
O A:HOH515 2.4 25.8 1.0
O A:VAL72 2.4 22.3 1.0
C A:ALA66 3.2 21.6 1.0
C A:ASP69 3.3 25.1 1.0
C A:VAL72 3.6 24.3 1.0
CA A:LYS70 3.8 25.4 1.0
O A:LYS70 4.0 25.3 1.0
N A:LYS70 4.0 24.3 1.0
N A:SER67 4.0 21.5 1.0
C A:LYS70 4.0 24.7 1.0
CA A:ALA66 4.0 22.2 1.0
CB A:ALA66 4.1 21.3 1.0
N A:VAL72 4.1 24.3 1.0
CA A:SER67 4.1 21.7 1.0
CA A:VAL72 4.3 24.9 1.0
N A:ASP69 4.3 24.1 1.0
CA A:ASP69 4.4 25.7 1.0
CB A:VAL72 4.5 24.6 1.0
C A:SER67 4.5 22.6 1.0
N A:SER73 4.6 22.7 1.0
N A:SER71 4.8 24.4 1.0
O A:HOH521 4.8 22.4 1.0
CA A:SER73 4.9 23.6 1.0
O A:SER67 5.0 23.6 1.0
N A:LEU68 5.0 21.5 1.0

Magnesium binding site 2 out of 5 in 8fft

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Magnesium binding site 2 out of 5 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:36.1
occ:1.00
 O A:HOH506 2.1 33.4 1.0
OE2 A:GLU149 2.2 33.1 1.0
O A:HOH523 2.2 33.1 1.0
O A:ASP146 2.3 32.5 1.0
CD A:GLU149 3.4 33.3 1.0
C A:ASP146 3.4 32.9 1.0
NH2 A:ARG96 3.9 33.7 1.0
OE1 A:GLU149 4.0 36.2 1.0
O A:HIS179 4.1 32.1 1.0
O A:THR148 4.1 31.6 1.0
CA A:ASP146 4.3 33.0 1.0
O A:ASN180 4.3 33.1 1.0
N A:ASN147 4.3 32.7 1.0
CA A:ASN147 4.4 31.4 1.0
CG A:GLU149 4.5 31.9 1.0
C A:ASN147 4.6 31.5 1.0
C A:THR148 4.7 30.1 1.0
N A:THR148 4.8 30.6 1.0
CZ A:ARG96 4.8 32.6 1.0
NE A:ARG96 4.8 34.3 1.0
CB A:ASP146 4.9 33.6 1.0
CB A:ASN180 5.0 33.5 1.0
C A:ASN180 5.0 32.3 1.0

Magnesium binding site 3 out of 5 in 8fft

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Magnesium binding site 3 out of 5 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:33.1
occ:1.00
 O B:ALA66 2.2 33.6 1.0
O B:VAL72 2.3 34.7 1.0
O B:ASP69 2.4 37.9 1.0
C B:ALA66 3.1 32.3 1.0
C B:VAL72 3.5 33.9 1.0
C B:ASP69 3.5 38.0 1.0
CA B:ALA66 3.9 30.1 1.0
CB B:ALA66 3.9 29.7 1.0
N B:SER67 4.0 31.1 1.0
CA B:LYS70 4.0 37.9 1.0
N B:VAL72 4.1 35.4 1.0
CA B:SER67 4.1 31.5 1.0
O B:LYS70 4.1 35.4 1.0
C B:LYS70 4.2 35.8 1.0
N B:LYS70 4.2 37.9 1.0
CA B:VAL72 4.2 35.3 1.0
N B:ASP69 4.4 38.9 1.0
CB B:VAL72 4.4 33.3 1.0
N B:SER73 4.5 31.3 1.0
C B:SER67 4.5 32.3 1.0
CA B:ASP69 4.6 38.2 1.0
CA B:SER73 4.8 30.9 1.0
N B:SER71 4.9 35.2 1.0
N B:LEU68 5.0 31.9 1.0
O B:SER67 5.0 35.1 1.0

Magnesium binding site 4 out of 5 in 8fft

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Magnesium binding site 4 out of 5 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:25.0
occ:1.00
 O C:HOH522 2.2 26.1 1.0
O C:ASP69 2.2 24.8 1.0
O C:HOH520 2.2 27.5 1.0
O C:VAL72 2.3 24.5 1.0
O C:ALA66 2.3 23.4 1.0
O C:HOH526 2.5 22.8 1.0
C C:ALA66 3.3 22.4 1.0
C C:ASP69 3.3 26.4 1.0
C C:VAL72 3.5 25.8 1.0
CA C:LYS70 3.8 27.2 1.0
N C:LYS70 4.0 25.7 1.0
C C:LYS70 4.0 27.3 1.0
O C:LYS70 4.0 27.6 1.0
N C:VAL72 4.0 26.8 1.0
N C:SER67 4.1 21.7 1.0
CA C:ALA66 4.1 23.8 1.0
CB C:ALA66 4.1 22.1 1.0
CA C:SER67 4.1 22.9 1.0
CA C:VAL72 4.2 27.4 1.0
N C:ASP69 4.3 24.6 1.0
CA C:ASP69 4.4 25.7 1.0
CB C:VAL72 4.5 26.7 1.0
N C:SER73 4.5 26.1 1.0
C C:SER67 4.6 23.4 1.0
O C:HOH519 4.6 23.0 1.0
CA C:SER73 4.8 24.2 1.0
N C:SER71 4.8 25.3 1.0
O C:SER67 4.9 25.1 1.0

Magnesium binding site 5 out of 5 in 8fft

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Magnesium binding site 5 out of 5 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:35.6
occ:1.00
 O D:VAL72 2.4 34.3 1.0
O D:ALA66 2.4 33.5 1.0
O D:ASP69 2.5 38.9 1.0
C D:ALA66 3.2 32.7 1.0
C D:ASP69 3.6 40.6 1.0
C D:VAL72 3.6 34.8 1.0
N D:SER67 4.0 31.9 1.0
CA D:LYS70 4.0 39.1 1.0
CB D:ALA66 4.0 31.4 1.0
CA D:ALA66 4.1 31.5 1.0
CA D:SER67 4.1 33.2 1.0
O D:LYS70 4.1 38.4 1.0
C D:LYS70 4.2 37.2 1.0
N D:LYS70 4.2 39.1 1.0
N D:VAL72 4.3 36.5 1.0
CA D:VAL72 4.4 36.1 1.0
N D:ASP69 4.5 40.6 1.0
N D:SER73 4.6 32.8 1.0
C D:SER67 4.6 34.5 1.0
CB D:VAL72 4.7 35.0 1.0
CA D:ASP69 4.7 41.1 1.0
CA D:SER73 4.7 32.9 1.0
O D:SER67 5.0 37.9 1.0

Reference:

J.L.Cordoza, P.Y.-T.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 An Unusual Plp-Dependent L-Enduracididine Cyclase From A Toxic Cyanobacterium To Be Published.
Page generated: Tue Apr 25 23:29:12 2023

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