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Sodium 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:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Pyld Cocrystallized with L-Ornithine-Nd-D-Ornithine and Nad+, PDB code: 4q3d:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4q3d

Go back to Sodium Binding Sites List in 4q3d
Sodium 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 Sodium with other atoms in the Na 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:Na902

b:35.5
occ:1.00
 O A:CYS206 2.6 29.4 1.0
O A:PRO227 2.6 37.7 1.0
O A:THR204 3.0 26.4 1.0
OE1 A:GLU202 3.0 29.3 1.0
OE2 A:GLU202 3.4 27.3 1.0
OG1 A:THR204 3.4 27.9 1.0
CD A:GLU202 3.6 27.7 1.0
C A:CYS206 3.6 32.9 1.0
N A:ALA229 3.7 34.4 1.0
N A:CYS206 3.8 32.0 1.0
C A:PRO227 3.8 36.3 1.0
C A:THR204 3.8 26.1 1.0
CA A:ALA229 3.9 30.4 1.0
C A:GLY225 3.9 28.0 1.0
CB A:ALA229 4.0 30.9 1.0
CA A:GLY225 4.0 27.5 1.0
N A:ILE226 4.1 29.4 1.0
C A:CYS228 4.1 35.8 1.0
O A:GLY225 4.3 29.4 1.0
CA A:CYS206 4.3 32.7 1.0
C A:PRO205 4.5 30.9 1.0
CA A:CYS228 4.5 33.7 1.0
C A:ILE226 4.5 31.3 1.0
N A:PRO227 4.5 33.5 1.0
CA A:THR204 4.5 26.6 1.0
N A:THR204 4.6 24.9 1.0
CB A:THR204 4.6 27.0 1.0
N A:CYS228 4.6 36.5 1.0
OG1 A:THR223 4.6 27.2 1.0
N A:PRO205 4.6 26.7 1.0
N A:ALA207 4.7 35.1 1.0
CA A:ILE226 4.7 31.1 1.0
O A:CYS228 4.7 40.0 1.0
OG1 A:THR209 4.7 25.2 1.0
CA A:PRO205 4.7 28.0 1.0
CA A:PRO227 4.8 33.8 1.0
O A:ILE226 4.9 37.3 1.0
CA A:ALA207 4.9 35.1 1.0
CD A:PRO227 5.0 33.6 1.0

Sodium binding site 2 out of 4 in 4q3d

Go back to Sodium Binding Sites List in 4q3d
Sodium 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 Sodium with other atoms in the Na 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:Na902

b:42.2
occ:1.00
 O B:CYS206 2.7 38.6 1.0
O B:PRO227 2.7 39.7 1.0
O B:THR204 2.8 27.9 1.0
O B:HOH1165 3.0 41.9 1.0
OE1 B:GLU202 3.2 27.9 1.0
OE2 B:GLU202 3.4 22.9 1.0
OG1 B:THR204 3.5 29.3 1.0
CD B:GLU202 3.7 26.9 1.0
C B:CYS206 3.7 37.1 1.0
N B:CYS206 3.7 34.6 1.0
C B:THR204 3.7 29.1 1.0
C B:GLY225 3.8 27.3 1.0
N B:ILE226 3.9 31.6 1.0
C B:PRO227 3.9 36.6 1.0
CA B:GLY225 3.9 25.7 1.0
N B:ALA229 4.0 33.5 1.0
CB B:ALA229 4.1 33.0 1.0
CA B:ALA229 4.1 33.8 1.0
O B:GLY225 4.2 30.0 1.0
C B:CYS228 4.2 32.0 1.0
CA B:CYS206 4.3 36.5 1.0
C B:ILE226 4.3 34.1 1.0
C B:PRO205 4.4 32.2 1.0
N B:THR204 4.5 27.5 1.0
CA B:THR204 4.5 29.9 1.0
N B:PRO227 4.5 34.8 1.0
CA B:ILE226 4.5 32.3 1.0
N B:PRO205 4.5 30.7 1.0
CA B:PRO205 4.6 31.6 1.0
OG1 B:THR223 4.6 29.1 1.0
CB B:THR204 4.6 30.8 1.0
O B:CYS228 4.6 31.4 1.0
O B:ILE226 4.6 40.9 1.0
CA B:CYS228 4.7 32.7 1.0
N B:ALA207 4.7 40.5 1.0
N B:CYS228 4.7 35.7 1.0
CA B:PRO227 4.8 34.2 1.0
OG1 B:THR209 4.9 31.0 1.0
N B:GLY225 5.0 26.1 1.0
CD B:PRO227 5.0 36.2 1.0

Sodium binding site 3 out of 4 in 4q3d

Go back to Sodium Binding Sites List in 4q3d
Sodium 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 Sodium with other atoms in the Na 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:Na902

b:59.4
occ:1.00
 O C:PRO227 2.6 61.2 1.0
O C:CYS206 2.8 45.2 1.0
O C:THR204 3.0 47.7 1.0
OE1 C:GLU202 3.2 45.6 1.0
OE2 C:GLU202 3.3 44.4 1.0
CD C:GLU202 3.6 44.8 1.0
N C:ALA229 3.7 51.8 1.0
C C:CYS206 3.8 42.0 1.0
C C:GLY225 3.8 50.0 1.0
C C:PRO227 3.8 53.6 1.0
N C:CYS206 3.9 44.2 1.0
C C:THR204 3.9 44.5 1.0
CA C:ALA229 3.9 47.2 1.0
O C:GLY225 4.0 57.8 1.0
CA C:GLY225 4.0 47.9 1.0
C C:CYS228 4.1 50.1 1.0
CB C:ALA229 4.1 45.4 1.0
N C:ILE226 4.1 51.6 1.0
CB C:THR204 4.4 45.3 1.0
C C:ILE226 4.4 53.2 1.0
CA C:CYS206 4.4 41.5 1.0
N C:PRO227 4.5 51.3 1.0
OG1 C:THR223 4.5 48.2 1.0
CA C:CYS228 4.5 55.8 1.0
O C:CYS228 4.5 47.5 1.0
CA C:THR204 4.6 44.1 1.0
C C:PRO205 4.6 42.3 1.0
N C:CYS228 4.6 53.7 1.0
O C:ILE226 4.6 60.2 1.0
CA C:ILE226 4.6 53.1 1.0
N C:THR204 4.6 40.9 1.0
N C:ALA207 4.8 41.5 1.0
N C:PRO205 4.8 42.2 1.0
CA C:PRO227 4.8 49.7 1.0
CA C:PRO205 4.9 40.9 1.0
OG1 C:THR209 4.9 40.5 1.0
CD C:PRO227 5.0 49.0 1.0
CG2 C:THR204 5.0 44.0 1.0
N C:GLY225 5.0 48.4 1.0

Sodium binding site 4 out of 4 in 4q3d

Go back to Sodium Binding Sites List in 4q3d
Sodium 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 Sodium with other atoms in the Na 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:Na902

b:66.9
occ:1.00
 O D:PRO227 2.5 61.1 1.0
O D:THR204 2.7 47.0 1.0
O D:CYS206 2.9 40.0 1.0
O D:HOH1006 3.0 42.3 1.0
OE1 D:GLU202 3.2 46.7 1.0
OE2 D:GLU202 3.4 48.9 1.0
C D:GLY225 3.7 45.8 1.0
C D:THR204 3.7 44.4 1.0
CD D:GLU202 3.7 43.8 1.0
C D:PRO227 3.7 59.1 1.0
N D:CYS206 3.7 44.5 1.0
N D:ALA229 3.8 50.2 1.0
O D:GLY225 3.8 44.9 1.0
C D:CYS206 3.8 41.7 1.0
N D:ILE226 3.9 49.3 1.0
CA D:GLY225 3.9 44.7 1.0
CA D:ALA229 4.0 44.9 1.0
CB D:ALA229 4.0 41.9 1.0
C D:CYS228 4.0 51.4 1.0
C D:ILE226 4.3 54.0 1.0
C D:PRO205 4.3 42.9 1.0
N D:PRO227 4.4 55.5 1.0
CA D:CYS206 4.4 44.3 1.0
CA D:ILE226 4.5 50.9 1.0
CA D:CYS228 4.5 54.8 1.0
O D:CYS228 4.5 48.7 1.0
N D:PRO205 4.5 43.4 1.0
CA D:PRO205 4.5 42.2 1.0
N D:CYS228 4.5 56.3 1.0
CA D:THR204 4.6 43.1 1.0
N D:THR204 4.6 41.3 1.0
OG1 D:THR223 4.6 38.5 1.0
CG2 D:THR204 4.6 41.0 1.0
O D:ILE226 4.7 59.6 1.0
CA D:PRO227 4.7 55.4 1.0
CB D:THR204 4.7 43.5 1.0
N D:ALA207 4.8 44.0 1.0
CD D:PRO227 4.9 54.1 1.0
N D:GLY225 5.0 45.2 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 Oct 7 17:55:53 2024

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