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Magnesium in PDB 4q3b: Pyld Cocrystallized with L-Lysine-Ne-D-Lysine and Nad+

Protein crystallography data

The structure of Pyld Cocrystallized with L-Lysine-Ne-D-Lysine and Nad+, PDB code: 4q3b 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 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.640, 261.170, 48.740, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.2

Other elements in 4q3b:

The structure of Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-Lysine-Ne-D-Lysine and Nad+ (pdb code 4q3b). 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-Lysine-Ne-D-Lysine and Nad+, PDB code: 4q3b:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4q3b

Go back to Magnesium Binding Sites List in 4q3b
Magnesium binding site 1 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-Lysine-Ne-D-Lysine and Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:25.5
occ:1.00
O7N A:NAI901 2.6 19.5 1.0
OE1 A:GLU245 2.8 22.3 1.0
OH A:TYR129 2.9 17.1 1.0
N A:GLY250 3.1 16.2 1.0
O A:GLU245 3.2 20.2 1.0
N A:ILE249 3.3 16.6 1.0
C7N A:NAI901 3.4 19.9 1.0
N7N A:NAI901 3.4 19.7 1.0
N A:LEU247 3.4 18.8 1.0
C A:LEU247 3.5 17.8 1.0
CE1 A:TYR129 3.5 16.9 1.0
CB A:ILE249 3.6 16.4 1.0
CZ A:TYR129 3.7 17.0 1.0
CA A:LEU247 3.7 18.1 1.0
N A:GLY248 3.7 17.4 1.0
O A:LEU247 3.7 17.7 1.0
CA A:ILE249 3.8 16.4 1.0
C A:ILE249 3.9 16.2 1.0
C A:GLU245 3.9 20.7 1.0
O A:HOH1004 4.0 14.8 1.0
CD A:GLU245 4.0 21.9 1.0
C A:PRO246 4.0 19.4 1.0
CA A:GLY250 4.0 16.1 1.0
C A:GLY248 4.2 16.8 1.0
CA A:GLY248 4.5 17.1 1.0
N A:PRO246 4.5 20.3 1.0
O A:PRO246 4.6 19.8 1.0
OE2 A:GLU245 4.6 22.3 1.0
CG1 A:ILE249 4.6 16.5 1.0
CG2 A:ILE249 4.6 16.4 1.0
CA A:PRO246 4.6 20.0 1.0
CB A:GLU245 4.7 21.5 1.0
C3N A:NAI901 4.8 20.2 1.0
CD1 A:TYR129 4.8 16.9 1.0
CA A:GLU245 4.9 21.3 1.0

Magnesium binding site 2 out of 4 in 4q3b

Go back to Magnesium Binding Sites List in 4q3b
Magnesium binding site 2 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-Lysine-Ne-D-Lysine and Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:25.2
occ:1.00
O7N B:NAI901 2.7 20.8 1.0
OE1 B:GLU245 2.9 23.5 1.0
N B:GLY250 3.0 16.1 1.0
OH B:TYR129 3.1 18.1 1.0
N B:ILE249 3.3 16.3 1.0
O B:GLU245 3.3 20.5 1.0
C7N B:NAI901 3.4 21.2 1.0
N7N B:NAI901 3.4 21.1 1.0
N B:LEU247 3.5 18.3 1.0
CE1 B:TYR129 3.5 18.0 1.0
C B:LEU247 3.5 17.3 1.0
CB B:ILE249 3.6 16.3 1.0
CA B:ILE249 3.7 16.2 1.0
CZ B:TYR129 3.7 18.1 1.0
CA B:LEU247 3.7 17.7 1.0
O B:LEU247 3.8 17.1 1.0
N B:GLY248 3.8 17.0 1.0
C B:ILE249 3.8 16.1 1.0
O B:HOH1002 3.9 21.1 1.0
CA B:GLY250 4.0 16.1 1.0
CD B:GLU245 4.1 22.9 1.0
C B:GLU245 4.1 20.8 1.0
C B:PRO246 4.1 19.0 1.0
C B:GLY248 4.2 16.5 1.0
CG1 B:ILE249 4.4 16.4 1.0
CA B:GLY248 4.5 16.7 1.0
O B:PRO246 4.7 18.9 1.0
N B:PRO246 4.7 20.1 1.0
CG2 B:ILE249 4.7 16.3 1.0
CB B:GLU245 4.7 22.3 1.0
CD1 B:TYR129 4.7 18.0 1.0
C3N B:NAI901 4.8 21.6 1.0
CA B:PRO246 4.8 19.6 1.0
OE2 B:GLU245 4.8 23.2 1.0
CG2 B:THR125 4.9 17.9 1.0
CA B:GLU245 5.0 21.9 1.0

Magnesium binding site 3 out of 4 in 4q3b

Go back to Magnesium Binding Sites List in 4q3b
Magnesium binding site 3 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-Lysine-Ne-D-Lysine and Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg903

b:50.9
occ:1.00
OH C:TYR129 2.8 34.8 1.0
O7N C:NAI901 2.8 40.3 1.0
OE1 C:GLU245 2.8 44.1 1.0
O C:GLU245 2.9 39.1 1.0
N C:GLY250 3.2 34.5 1.0
N7N C:NAI901 3.3 38.8 1.0
N C:ILE249 3.4 36.9 1.0
C7N C:NAI901 3.4 40.1 1.0
CE1 C:TYR129 3.5 33.5 1.0
N C:LEU247 3.5 37.4 1.0
CZ C:TYR129 3.6 34.4 1.0
CB C:ILE249 3.6 36.2 1.0
C C:LEU247 3.7 37.4 1.0
C C:GLU245 3.8 39.8 1.0
CA C:ILE249 3.8 36.4 1.0
CA C:LEU247 3.9 37.6 1.0
N C:GLY248 3.9 37.7 1.0
C C:ILE249 4.0 35.5 1.0
O C:LEU247 4.0 37.1 1.0
CD C:GLU245 4.0 43.5 1.0
C C:PRO246 4.0 37.4 1.0
CA C:GLY250 4.1 34.7 1.0
O C:HOH1008 4.3 30.1 1.0
C C:GLY248 4.3 37.7 1.0
CG1 C:ILE249 4.4 36.8 1.0
CB C:GLU245 4.4 42.0 1.0
N C:PRO246 4.5 39.1 1.0
O C:PRO246 4.5 37.8 1.0
CA C:GLU245 4.6 40.9 1.0
CG2 C:ILE249 4.6 36.6 1.0
CA C:GLY248 4.6 38.0 1.0
CA C:PRO246 4.7 38.3 1.0
CD1 C:TYR129 4.7 33.8 1.0
CD1 C:ILE249 4.8 36.9 1.0
OE2 C:GLU245 4.8 43.6 1.0
C3N C:NAI901 4.8 39.5 1.0
CG C:GLU245 4.8 43.2 1.0
CE2 C:TYR129 4.9 34.8 1.0
N C:GLU245 5.0 41.1 1.0

Magnesium binding site 4 out of 4 in 4q3b

Go back to Magnesium Binding Sites List in 4q3b
Magnesium binding site 4 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-Lysine-Ne-D-Lysine and Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:54.6
occ:1.00
O7N D:NAI901 2.6 43.7 1.0
OE1 D:GLU245 2.9 49.4 1.0
OH D:TYR129 2.9 39.9 1.0
O D:GLU245 3.0 44.7 1.0
N D:GLY250 3.2 39.2 1.0
N D:LEU247 3.2 42.0 1.0
N D:ILE249 3.4 41.2 1.0
C7N D:NAI901 3.4 43.3 1.0
N7N D:NAI901 3.4 44.7 1.0
C D:LEU247 3.4 41.3 1.0
CA D:LEU247 3.6 41.1 1.0
CB D:ILE249 3.6 40.9 1.0
CE2 D:TYR129 3.6 38.6 1.0
N D:GLY248 3.7 41.0 1.0
O D:LEU247 3.7 40.5 1.0
CZ D:TYR129 3.7 38.8 1.0
C D:GLU245 3.8 45.8 1.0
CA D:ILE249 3.8 40.8 1.0
C D:PRO246 3.9 44.1 1.0
O D:HOH1017 4.0 38.5 1.0
C D:ILE249 4.0 39.8 1.0
CD D:GLU245 4.1 50.0 1.0
CA D:GLY250 4.1 39.5 1.0
C D:GLY248 4.3 41.9 1.0
N D:PRO246 4.4 46.0 1.0
O D:PRO246 4.4 45.4 1.0
CG1 D:ILE249 4.5 41.2 1.0
CA D:PRO246 4.5 45.5 1.0
CA D:GLY248 4.6 41.9 1.0
CB D:GLU245 4.6 47.9 1.0
CG2 D:ILE249 4.6 40.6 1.0
CA D:GLU245 4.7 46.4 1.0
C3N D:NAI901 4.8 41.3 1.0
OE2 D:GLU245 4.9 51.2 1.0
CD1 D:ILE249 4.9 41.7 1.0
CD2 D:TYR129 4.9 37.9 1.0
CG D:GLU245 5.0 48.6 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: Mon Dec 14 19:21:29 2020

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