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Sodium 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:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine and Nad+, PDB code: 4q3b:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4q3b

Go back to Sodium Binding Sites List in 4q3b
Sodium 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 Sodium with other atoms in the Na 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:Na902

b:35.2
occ:1.00
 O A:PRO227 2.7 29.6 1.0
O A:CYS206 2.7 29.8 1.0
O A:HOH1061 2.9 30.2 1.0
O A:THR204 2.9 24.9 1.0
OE1 A:GLU202 3.0 22.7 1.0
OE2 A:GLU202 3.2 22.6 1.0
CD A:GLU202 3.4 22.7 1.0
N A:CYS206 3.7 29.8 1.0
C A:CYS206 3.8 30.7 1.0
C A:THR204 3.8 25.5 1.0
N A:ALA229 3.8 29.1 1.0
C A:GLY225 3.8 25.9 1.0
CA A:ALA229 3.9 29.3 1.0
CA A:GLY225 3.9 25.0 1.0
CB A:ALA229 3.9 29.1 1.0
CG2 A:THR204 3.9 26.7 1.0
C A:PRO227 4.0 30.1 1.0
N A:ILE226 4.0 27.1 1.0
C A:CYS228 4.1 30.5 1.0
O A:GLY225 4.1 25.5 1.0
CB A:THR204 4.3 26.3 1.0
CA A:CYS206 4.4 31.3 1.0
N A:THR204 4.4 23.8 1.0
CA A:THR204 4.4 25.2 1.0
C A:ILE226 4.4 29.4 1.0
C A:PRO205 4.5 28.7 1.0
O A:CYS228 4.5 29.4 1.0
CA A:ILE226 4.6 28.6 1.0
N A:PRO227 4.6 30.4 1.0
N A:PRO205 4.6 26.5 1.0
OG1 A:THR223 4.6 22.4 1.0
O A:ILE226 4.7 28.4 1.0
CA A:PRO205 4.7 27.2 1.0
CA A:CYS228 4.7 30.7 1.0
OG1 A:THR209 4.7 29.7 1.0
N A:ALA207 4.8 31.1 1.0
N A:CYS228 4.8 30.7 1.0
CG A:GLU202 4.9 22.4 1.0
CA A:PRO227 4.9 30.4 1.0
N A:GLY225 5.0 24.1 1.0

Sodium binding site 2 out of 4 in 4q3b

Go back to Sodium Binding Sites List in 4q3b
Sodium 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 Sodium with other atoms in the Na 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:Na902

b:38.5
occ:1.00
 O B:PRO227 2.7 28.8 1.0
O B:CYS206 2.8 32.4 1.0
OE1 B:GLU202 2.8 26.4 1.0
O B:THR204 3.0 25.5 1.0
O B:HOH1009 3.0 25.6 1.0
OE2 B:GLU202 3.2 25.4 1.0
CD B:GLU202 3.3 25.4 1.0
OG1 B:THR204 3.3 26.6 1.0
N B:ALA229 3.7 31.6 1.0
C B:CYS206 3.7 34.3 1.0
N B:CYS206 3.8 32.2 1.0
C B:GLY225 3.8 26.3 1.0
C B:THR204 3.8 26.2 1.0
CA B:ALA229 3.9 32.4 1.0
CA B:GLY225 3.9 25.3 1.0
C B:PRO227 4.0 29.9 1.0
CB B:ALA229 4.0 31.5 1.0
N B:ILE226 4.0 27.3 1.0
C B:CYS228 4.1 31.9 1.0
O B:GLY225 4.2 26.6 1.0
CA B:CYS206 4.3 34.3 1.0
O B:CYS228 4.4 31.6 1.0
N B:THR204 4.4 25.1 1.0
C B:ILE226 4.5 28.7 1.0
C B:PRO205 4.5 30.2 1.0
CB B:THR204 4.5 26.3 1.0
CA B:THR204 4.5 25.7 1.0
N B:PRO227 4.6 29.6 1.0
OG1 B:THR223 4.6 23.4 1.0
N B:PRO205 4.7 27.5 1.0
CA B:ILE226 4.7 28.2 1.0
CA B:CYS228 4.7 31.8 1.0
OG1 B:THR209 4.7 33.7 1.0
CA B:PRO205 4.7 28.3 1.0
O B:ILE226 4.7 28.0 1.0
N B:ALA207 4.7 34.6 1.0
CG B:GLU202 4.8 25.3 1.0
N B:CYS228 4.8 31.2 1.0
CA B:PRO227 4.9 29.7 1.0

Sodium binding site 3 out of 4 in 4q3b

Go back to Sodium Binding Sites List in 4q3b
Sodium 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 Sodium with other atoms in the Na 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:Na902

b:47.6
occ:1.00
 O C:PRO227 2.4 39.6 1.0
O C:CYS206 2.6 42.0 1.0
O C:HOH1017 2.9 38.2 1.0
O C:THR204 3.0 38.5 1.0
OE1 C:GLU202 3.2 40.3 1.0
OE2 C:GLU202 3.3 41.2 1.0
CD C:GLU202 3.6 41.0 1.0
C C:CYS206 3.6 41.9 1.0
C C:PRO227 3.6 40.7 1.0
N C:ALA229 3.7 43.3 1.0
CA C:ALA229 3.7 43.4 1.0
N C:CYS206 3.8 40.6 1.0
C C:GLY225 3.8 36.9 1.0
CB C:ALA229 3.9 43.0 1.0
C C:THR204 3.9 39.7 1.0
C C:CYS228 4.0 43.7 1.0
N C:ILE226 4.0 38.2 1.0
CA C:GLY225 4.0 36.1 1.0
O C:GLY225 4.0 38.1 1.0
CA C:CYS206 4.3 42.5 1.0
C C:ILE226 4.3 40.2 1.0
N C:PRO227 4.4 40.5 1.0
O C:CYS228 4.4 43.0 1.0
CG2 C:THR204 4.4 41.2 1.0
CA C:CYS228 4.5 42.9 1.0
C C:PRO205 4.5 40.3 1.0
N C:CYS228 4.5 42.0 1.0
CA C:ILE226 4.5 38.9 1.0
N C:ALA207 4.6 42.2 1.0
CB C:THR204 4.6 40.4 1.0
CA C:PRO227 4.6 41.0 1.0
O C:ILE226 4.6 41.4 1.0
CA C:THR204 4.7 39.6 1.0
N C:THR204 4.7 38.0 1.0
OG1 C:THR223 4.7 36.4 1.0
CA C:PRO205 4.7 39.9 1.0
N C:PRO205 4.7 40.4 1.0
CA C:ALA207 4.8 43.0 1.0
OG1 C:THR209 5.0 45.8 1.0

Sodium binding site 4 out of 4 in 4q3b

Go back to Sodium Binding Sites List in 4q3b
Sodium 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 Sodium with other atoms in the Na 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:Na902

b:43.6
occ:1.00
 O D:PRO227 2.6 46.4 1.0
O D:CYS206 2.8 37.1 1.0
OE1 D:GLU202 2.9 39.0 1.0
O D:THR204 3.0 35.4 1.0
O D:HOH1008 3.0 37.6 1.0
OE2 D:GLU202 3.2 37.6 1.0
CD D:GLU202 3.4 38.6 1.0
N D:ALA229 3.7 44.9 1.0
C D:GLY225 3.8 41.5 1.0
N D:CYS206 3.8 37.6 1.0
C D:CYS206 3.8 38.8 1.0
C D:THR204 3.8 36.0 1.0
C D:PRO227 3.8 46.8 1.0
CA D:ALA229 3.9 44.1 1.0
CA D:GLY225 3.9 39.9 1.0
N D:ILE226 4.0 42.0 1.0
CB D:ALA229 4.0 43.9 1.0
C D:CYS228 4.1 46.8 1.0
O D:GLY225 4.2 42.4 1.0
CB D:THR204 4.4 38.9 1.0
CA D:CYS206 4.4 38.8 1.0
C D:ILE226 4.4 42.9 1.0
N D:THR204 4.5 36.2 1.0
CA D:THR204 4.5 36.5 1.0
C D:PRO205 4.5 36.7 1.0
O D:CYS228 4.5 43.8 1.0
N D:PRO227 4.6 45.0 1.0
CA D:ILE226 4.6 43.4 1.0
CG2 D:THR204 4.6 39.2 1.0
CA D:CYS228 4.6 49.0 1.0
OG1 D:THR223 4.6 41.1 1.0
N D:CYS228 4.7 48.2 1.0
N D:PRO205 4.7 36.5 1.0
CA D:PRO205 4.7 36.0 1.0
OG1 D:THR209 4.7 41.3 1.0
O D:ILE226 4.7 40.5 1.0
N D:ALA207 4.8 37.9 1.0
CA D:PRO227 4.8 46.6 1.0
CG D:GLU202 4.9 39.0 1.0
N D:GLY225 5.0 39.0 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: Sun Aug 17 21:20:35 2025

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