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Magnesium in PDB 4q3d: Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+

Protein crystallography data

The structure of Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+, PDB code: 4q3d was solved by F.Quitterer, P.Beck, A.Bacher, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.930, 259.320, 48.820, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 23.7

Other elements in 4q3d:

The structure of Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+ also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+ (pdb code 4q3d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+, PDB code: 4q3d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4q3d

Go back to Magnesium Binding Sites List in 4q3d
Magnesium binding site 1 out of 4 in the Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:30.0
occ:1.00
 O7N A:NAD901 2.6 24.0 1.0
OE2 A:GLU245 2.9 23.7 1.0
OH A:TYR129 3.1 19.9 1.0
N A:GLY250 3.1 17.1 1.0
O A:GLU245 3.1 25.4 1.0
N7N A:NAD901 3.3 21.8 1.0
C7N A:NAD901 3.3 22.3 1.0
N A:LEU247 3.3 19.3 1.0
N A:ILE249 3.3 18.9 1.0
C A:LEU247 3.4 18.6 1.0
O A:LEU247 3.6 16.9 1.0
CA A:LEU247 3.6 19.4 1.0
N A:GLY248 3.7 17.8 1.0
CE2 A:TYR129 3.7 20.3 1.0
O A:HOH1016 3.8 16.1 1.0
CB A:ILE249 3.8 17.6 1.0
C A:PRO246 3.8 19.7 1.0
CA A:ILE249 3.9 18.0 1.0
CZ A:TYR129 3.9 21.0 1.0
C A:GLU245 3.9 22.3 1.0
C A:ILE249 4.0 17.8 1.0
CA A:GLY250 4.0 17.4 1.0
CD A:GLU245 4.0 22.6 1.0
C A:GLY248 4.2 18.9 1.0
O A:PRO246 4.3 23.0 1.0
CA A:GLY248 4.4 19.0 1.0
N A:PRO246 4.5 22.8 1.0
CA A:PRO246 4.5 21.7 1.0
CG1 A:ILE249 4.6 18.4 1.0
OE1 A:GLU245 4.7 24.9 1.0
C3N A:NAD901 4.7 21.8 1.0
CB A:GLU245 4.7 23.2 1.0
CG2 A:ILE249 4.9 17.6 1.0
CA A:GLU245 4.9 22.9 1.0
CD2 A:TYR129 5.0 20.2 1.0
N A:THR251 5.0 18.8 1.0

Magnesium binding site 2 out of 4 in 4q3d

Go back to Magnesium Binding Sites List in 4q3d
Magnesium binding site 2 out of 4 in the Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:31.6
occ:1.00
 OE1 B:GLU245 2.6 22.2 1.0
O7N B:NAD901 2.8 20.2 1.0
OH B:TYR129 2.9 18.5 1.0
O B:GLU245 2.9 20.0 1.0
N B:GLY250 3.1 15.7 1.0
N B:ILE249 3.3 17.1 1.0
N B:LEU247 3.5 22.0 1.0
N7N B:NAD901 3.5 22.0 1.0
C7N B:NAD901 3.5 21.3 1.0
CE1 B:TYR129 3.6 18.9 1.0
C B:LEU247 3.6 17.5 1.0
CB B:ILE249 3.6 17.3 1.0
CZ B:TYR129 3.7 19.8 1.0
CA B:ILE249 3.7 16.8 1.0
CD B:GLU245 3.8 21.9 1.0
CA B:LEU247 3.8 19.8 1.0
O B:LEU247 3.8 16.5 1.0
N B:GLY248 3.8 17.2 1.0
C B:ILE249 3.8 16.4 1.0
C B:GLU245 3.9 20.7 1.0
O B:HOH1009 3.9 19.6 1.0
C B:PRO246 4.0 21.2 1.0
CA B:GLY250 4.0 16.3 1.0
C B:GLY248 4.2 18.0 1.0
O B:PRO246 4.4 25.2 1.0
OE2 B:GLU245 4.4 22.2 1.0
CG1 B:ILE249 4.5 17.6 1.0
N B:PRO246 4.5 21.6 1.0
CG2 B:ILE249 4.5 18.7 1.0
CA B:GLY248 4.6 18.6 1.0
CA B:PRO246 4.7 21.8 1.0
CB B:GLU245 4.7 22.3 1.0
CA B:GLU245 4.8 21.6 1.0
CG B:GLU245 4.8 20.6 1.0
CD1 B:TYR129 4.9 20.4 1.0
C3N B:NAD901 4.9 22.2 1.0

Magnesium binding site 3 out of 4 in 4q3d

Go back to Magnesium Binding Sites List in 4q3d
Magnesium binding site 3 out of 4 in the Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg903

b:82.9
occ:1.00
 O C:GLU245 2.5 64.8 1.0
OE1 C:GLU245 2.8 79.8 1.0
O7N C:NAD901 2.9 90.6 1.0
N C:LEU247 3.0 55.9 1.0
OH C:TYR129 3.1 60.7 1.0
N7N C:NAD901 3.2 74.2 1.0
C C:LEU247 3.3 51.6 1.0
N C:GLY250 3.3 64.7 1.0
N C:ILE249 3.4 63.4 1.0
CA C:LEU247 3.4 51.7 1.0
C7N C:NAD901 3.4 80.4 1.0
C C:GLU245 3.5 67.7 1.0
O C:LEU247 3.6 57.0 1.0
N C:GLY248 3.7 46.5 1.0
C C:PRO246 3.7 63.2 1.0
CB C:ILE249 3.8 61.1 1.0
CE1 C:TYR129 3.8 55.2 1.0
CA C:ILE249 3.9 63.6 1.0
CZ C:TYR129 3.9 58.3 1.0
CD C:GLU245 3.9 80.0 1.0
C C:ILE249 4.1 62.0 1.0
N C:PRO246 4.1 66.7 1.0
CA C:GLY250 4.2 61.2 1.0
C C:GLY248 4.3 60.2 1.0
CA C:PRO246 4.3 63.5 1.0
CB C:GLU245 4.3 74.3 1.0
O C:PRO246 4.4 67.8 1.0
CA C:GLU245 4.4 67.0 1.0
CA C:GLY248 4.5 61.6 1.0
CG1 C:ILE249 4.6 61.2 1.0
OE2 C:GLU245 4.8 89.9 1.0
CG C:GLU245 4.8 77.4 1.0
CG2 C:ILE249 4.9 62.9 1.0
C3N C:NAD901 4.9 71.9 1.0
N C:GLU245 4.9 66.3 1.0
CB C:LEU247 5.0 56.8 1.0

Magnesium binding site 4 out of 4 in 4q3d

Go back to Magnesium Binding Sites List in 4q3d
Magnesium binding site 4 out of 4 in the Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:76.2
occ:1.00
 O D:GLU245 2.4 60.8 1.0
OE1 D:GLU245 2.7 71.5 1.0
OH D:TYR129 2.9 48.1 1.0
O7N D:NAD901 3.0 69.1 1.0
N D:LEU247 3.1 56.6 1.0
N7N D:NAD901 3.4 63.2 1.0
N D:ILE249 3.4 50.4 1.0
C D:GLU245 3.4 59.6 1.0
C D:LEU247 3.4 56.8 1.0
N D:GLY250 3.5 43.7 1.0
CA D:LEU247 3.6 53.6 1.0
C7N D:NAD901 3.6 68.2 1.0
O D:LEU247 3.6 62.5 1.0
CB D:ILE249 3.7 45.7 1.0
CE1 D:TYR129 3.7 44.1 1.0
CD D:GLU245 3.7 68.1 1.0
C D:PRO246 3.7 59.3 1.0
CZ D:TYR129 3.8 45.4 1.0
N D:GLY248 3.9 55.4 1.0
CA D:ILE249 3.9 47.6 1.0
N D:PRO246 4.2 60.9 1.0
C D:ILE249 4.2 43.2 1.0
CB D:GLU245 4.3 63.4 1.0
CA D:PRO246 4.3 57.8 1.0
C D:GLY248 4.3 50.4 1.0
CA D:GLU245 4.4 59.1 1.0
CG1 D:ILE249 4.4 46.7 1.0
O D:PRO246 4.4 60.7 1.0
CA D:GLY250 4.4 43.4 1.0
OE2 D:GLU245 4.4 74.7 1.0
CA D:GLY248 4.6 53.1 1.0
CG D:GLU245 4.6 66.6 1.0
N D:GLU245 4.8 57.7 1.0
CG2 D:ILE249 4.8 45.5 1.0
CD1 D:ILE249 5.0 45.5 1.0

Reference:

F.Quitterer, P.Beck, A.Bacher, M.Groll. The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed By Pyrrolysine Synthase (Pyld). Angew.Chem.Int.Ed.Engl. V. 53 8150 2014.
ISSN: ISSN 1433-7851
PubMed: 24916332
DOI: 10.1002/ANIE.201402595
Page generated: Tue Aug 20 01:44:42 2024

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