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Sodium in PDB 4zk6: Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States

Enzymatic activity of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States

All present enzymatic activity of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States:
2.5.1.72;

Protein crystallography data

The structure of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States, PDB code: 4zk6 was solved by O.A.Esakova, T.L.Grove, A.H.Saunders, N.H.Yennawar, S.J.Booker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.59 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.562, 51.588, 97.541, 90.00, 94.95, 90.00
R / Rfree (%) 18.4 / 23.1

Other elements in 4zk6:

The structure of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States (pdb code 4zk6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States, PDB code: 4zk6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4zk6

Go back to Sodium Binding Sites List in 4zk6
Sodium binding site 1 out of 4 in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:19.6
occ:0.50
 OG1 A:THR125 2.6 15.6 1.0
OD2 A:ASP37 3.1 33.6 1.0
CG A:ASP37 3.2 28.6 1.0
CB A:THR125 3.2 18.7 1.0
O4 A:NTM402 3.3 30.7 1.0
N A:LEU39 3.3 18.7 1.0
OG A:SER38 3.5 31.2 1.0
CB A:ASP37 3.6 16.7 1.0
CB A:LEU39 3.6 23.3 1.0
OD1 A:ASP37 3.6 25.9 1.0
N A:SER38 3.7 16.3 1.0
CB A:ALA127 3.7 19.1 1.0
CG2 A:THR125 3.8 18.3 1.0
CL A:CL403 3.9 31.2 1.0
N A:ALA127 4.0 15.9 1.0
C8 A:NTM402 4.0 31.0 1.0
O3 A:NTM402 4.0 31.8 1.0
CA A:LEU39 4.1 20.0 1.0
C A:SER38 4.2 18.0 1.0
CA A:SER38 4.3 15.8 1.0
C A:ASP37 4.3 16.2 1.0
N A:SER126 4.4 15.8 1.0
CB A:SER38 4.5 27.2 1.0
CA A:ALA127 4.5 16.1 1.0
CA A:THR125 4.5 16.5 1.0
CA A:ASP37 4.5 18.1 1.0
OH A:TYR109 4.6 37.9 1.0
OG A:SER212 4.6 30.6 1.0
C A:THR125 4.7 16.7 1.0
CB A:SER212 4.7 27.2 1.0
NA A:NA405 4.8 29.7 0.5
CG A:LEU39 5.0 28.5 1.0
C A:SER126 5.0 16.8 1.0

Sodium binding site 2 out of 4 in 4zk6

Go back to Sodium Binding Sites List in 4zk6
Sodium binding site 2 out of 4 in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:29.7
occ:0.50
 O3 A:NTM402 2.3 31.8 1.0
CL A:CL403 2.5 31.2 1.0
OG1 A:THR213 2.7 19.5 1.0
C8 A:NTM402 2.9 31.0 1.0
C3 A:NTM402 3.2 29.3 1.0
C4 A:NTM402 3.2 27.9 1.0
NE2 A:HIS21 3.2 13.3 1.0
CG2 A:THR213 3.3 20.3 1.0
CB A:ASP37 3.4 16.7 1.0
CB A:THR213 3.5 19.6 1.0
CE1 A:HIS21 3.6 12.7 1.0
O4 A:NTM402 3.8 30.7 1.0
CA A:ASP37 3.9 18.1 1.0
C2 A:NTM402 4.1 28.4 1.0
OH A:TYR23 4.2 23.4 1.0
C5 A:NTM402 4.2 27.4 1.0
CZ A:TYR23 4.4 16.8 1.0
N A:THR213 4.4 19.1 1.0
CD2 A:HIS21 4.5 13.2 1.0
N A:SER38 4.5 16.3 1.0
CA A:THR213 4.6 18.6 1.0
NE2 A:HIS196 4.6 16.0 1.0
CE1 A:TYR23 4.7 18.5 1.0
ND2 A:ASN22 4.7 19.6 1.0
CG A:ASP37 4.7 28.6 1.0
C A:ASP37 4.8 16.2 1.0
NA A:NA404 4.8 19.6 0.5
CE2 A:TYR23 4.8 16.6 1.0
ND1 A:HIS21 4.8 11.2 1.0
O2 A:NTM402 4.8 32.3 1.0
N1 A:NTM402 4.9 28.5 1.0
C7 A:NTM402 4.9 31.5 1.0
C6 A:NTM402 5.0 27.0 1.0

Sodium binding site 3 out of 4 in 4zk6

Go back to Sodium Binding Sites List in 4zk6
Sodium binding site 3 out of 4 in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:20.7
occ:0.50
 CL B:CL407 2.4 33.6 1.0
O3 B:NTM402 2.6 28.3 0.9
OG1 B:THR213 2.9 27.8 1.0
C4 B:NTM402 3.0 29.4 0.9
C8 B:NTM402 3.0 29.2 0.9
C3 B:NTM402 3.0 29.4 0.9
CG2 B:THR213 3.1 23.0 1.0
NE2 B:HIS21 3.5 21.1 1.0
CB B:THR213 3.6 23.3 1.0
OH B:TYR23 3.6 27.5 1.0
CE1 B:HIS21 3.8 21.2 1.0
C5 B:NTM402 3.8 29.3 0.9
CB B:ASP37 3.9 23.1 1.0
NE2 B:HIS196 3.9 28.7 1.0
C2 B:NTM402 3.9 29.0 0.9
CZ B:TYR23 4.0 25.7 1.0
N B:THR213 4.0 21.8 1.0
O4 B:NTM402 4.1 30.5 0.9
NA B:NA406 4.3 23.9 0.5
CE2 B:TYR23 4.4 27.4 1.0
CA B:THR213 4.4 21.3 1.0
CD2 B:HIS196 4.4 20.6 1.0
CE1 B:TYR23 4.5 25.1 1.0
C6 B:NTM402 4.5 29.9 0.9
N1 B:NTM402 4.6 28.2 0.9
CA B:ASP37 4.6 24.3 1.0
CD2 B:HIS21 4.8 19.5 1.0
C7 B:NTM402 4.8 28.7 0.9
O1 B:NTM402 4.8 29.1 0.9
N B:SER38 4.9 33.7 1.0

Sodium binding site 4 out of 4 in 4zk6

Go back to Sodium Binding Sites List in 4zk6
Sodium binding site 4 out of 4 in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:23.9
occ:0.50
 O4 B:NTM402 2.2 30.5 0.9
O B:HOH521 2.2 33.5 1.0
C8 B:NTM402 2.8 29.2 0.9
O3 B:NTM402 2.9 28.3 0.9
CL B:CL407 3.0 33.6 1.0
CB B:THR125 3.3 22.8 1.0
CB B:SER38 3.3 37.0 1.0
OG1 B:THR125 3.3 25.6 1.0
N B:SER38 3.6 33.7 1.0
OG B:SER126 3.7 27.6 1.0
OG B:SER38 3.8 39.6 1.0
N B:SER126 3.8 24.0 1.0
CA B:SER38 3.9 34.0 1.0
N B:LEU39 4.0 33.5 1.0
CB B:ASP37 4.0 23.1 1.0
CG B:ASP37 4.1 31.5 1.0
C3 B:NTM402 4.1 29.4 0.9
CG2 B:THR125 4.2 22.2 1.0
OD2 B:ASP37 4.2 34.1 1.0
CA B:THR125 4.3 22.6 1.0
NA B:NA405 4.3 20.7 0.5
C4 B:NTM402 4.4 29.4 0.9
N B:ALA127 4.4 22.2 1.0
C B:SER38 4.5 28.9 1.0
C B:THR125 4.5 23.9 1.0
C B:ASP37 4.6 23.9 1.0
OD1 B:ASP37 4.6 31.0 1.0
CB B:SER212 4.7 29.0 1.0
CB B:SER126 4.7 24.6 1.0
CA B:SER126 4.7 22.6 1.0
CA B:ASP37 4.9 24.3 1.0
CB B:ALA127 4.9 25.9 1.0
CB B:LEU39 4.9 33.5 1.0

Reference:

O.A.Esakova, A.Silakov, T.L.Grove, A.H.Saunders, M.I.Mclaughlin, N.H.Yennawar, S.J.Booker. Structure of Quinolinate Synthase From Pyrococcus Horikoshii in the Presence of Its Product, Quinolinic Acid. J.Am.Chem.Soc. V. 138 7224 2016.
ISSN: ESSN 1520-5126
PubMed: 27224840
DOI: 10.1021/JACS.6B02708
Page generated: Mon Oct 7 19:43:09 2024

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