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Sodium in PDB 3tr9: Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii

Enzymatic activity of Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii

All present enzymatic activity of Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii:
2.5.1.15;

Protein crystallography data

The structure of Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii, PDB code: 3tr9 was solved by J.Cheung, M.C.Franklin, M.Rudolph, M.Cassidy, E.Gary, F.Burshteyn, J.Love, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.44 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.877, 86.883, 158.159, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.2

Other elements in 3tr9:

The structure of Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii (pdb code 3tr9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii, PDB code: 3tr9:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3tr9

Go back to Sodium Binding Sites List in 3tr9
Sodium binding site 1 out of 3 in the Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na316

b:31.3
occ:0.99
 OD1 A:ASP111 2.8 29.8 1.0
O A:HOH427 2.8 38.2 0.9
N A:GLN132 3.0 17.6 1.0
OD1 A:ASP131 3.3 17.1 1.0
O A:THR112 3.4 21.8 1.0
C A:THR112 3.4 22.2 1.0
OG A:SER113 3.4 18.3 1.0
O A:ASN130 3.5 24.6 1.0
N A:THR112 3.5 21.2 1.0
CB A:GLN132 3.6 19.5 1.0
NE2 A:GLN132 3.6 21.7 1.0
CA A:ASP131 3.6 16.1 1.0
CG A:GLN132 3.6 20.0 1.0
CA A:THR112 3.7 19.5 1.0
C A:ASP131 3.8 17.6 1.0
CA A:GLN132 3.9 15.9 1.0
N A:SER113 3.9 17.4 1.0
C A:ASP111 4.0 23.0 1.0
CG A:ASP111 4.0 27.3 1.0
CD A:GLN132 4.0 21.9 1.0
CG A:ASP131 4.3 20.3 1.0
C A:ASN130 4.4 23.6 1.0
O A:ASP111 4.5 22.4 1.0
N A:ARG133 4.5 15.4 1.0
CB A:ASP131 4.5 16.0 1.0
N A:ASP131 4.5 19.9 1.0
CB A:SER113 4.5 16.6 1.0
CA A:SER113 4.5 18.8 1.0
CA A:ASP111 4.6 20.6 1.0
C A:GLN132 4.7 16.4 1.0
OD2 A:ASP111 4.8 31.5 1.0
NH1 A:ARG133 4.8 22.0 1.0
CB A:ASP111 4.9 18.5 1.0

Sodium binding site 2 out of 3 in 3tr9

Go back to Sodium Binding Sites List in 3tr9
Sodium binding site 2 out of 3 in the Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na317

b:34.9
occ:0.91
 O A:HOH361 2.7 26.4 1.0
O A:HOH335 3.1 21.4 0.9
NH1 A:ARG195 3.1 37.8 1.0
N A:SER192 3.1 23.6 1.0
CD A:ARG195 3.4 34.0 1.0
OG A:SER192 3.5 34.9 1.0
CA A:ILE191 3.6 25.4 1.0
O A:GLY190 3.8 23.6 1.0
C A:ILE191 3.8 26.4 1.0
CB A:SER192 4.0 32.4 1.0
CZ A:ARG195 4.1 37.5 1.0
CA A:LYS148 4.1 27.6 1.0
CA A:SER192 4.1 27.9 1.0
CG2 A:ILE191 4.1 21.2 1.0
NE A:ARG195 4.2 36.7 1.0
CB A:ILE191 4.3 23.3 1.0
N A:ILE191 4.5 24.9 1.0
CG A:ARG195 4.6 33.1 1.0
C A:GLY190 4.6 28.6 1.0
C A:LYS148 4.6 30.2 1.0
O A:SER145 4.6 34.6 1.0
CB A:ARG195 4.6 32.9 1.0
CG1 A:ILE191 4.7 21.2 1.0
CB A:LYS148 4.7 35.2 1.0
CG A:LYS148 4.8 41.1 1.0
O A:LYS148 4.9 26.6 1.0
O A:SER192 4.9 26.9 1.0

Sodium binding site 3 out of 3 in 3tr9

Go back to Sodium Binding Sites List in 3tr9
Sodium binding site 3 out of 3 in the Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Dihydropteroate Synthase (Folp) in Complex with Pteroic Acid From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na315

b:26.4
occ:1.00
 O C:HOH326 2.9 24.1 1.0
O C:ALA268 2.9 12.2 1.0
O C:VAL264 2.9 12.4 1.0
CB C:GLN11 3.3 37.0 1.0
C C:GLY267 3.4 14.2 1.0
CA C:GLY267 3.4 14.9 1.0
CG1 C:VAL264 3.6 12.4 1.0
N C:ALA268 3.7 11.5 1.0
CG C:PRO28 3.7 20.4 1.0
C C:VAL264 3.8 10.4 1.0
O C:GLY267 3.8 14.2 1.0
C C:ALA268 3.9 12.8 1.0
CG C:GLN11 3.9 39.4 1.0
CA C:VAL264 3.9 13.5 1.0
NE C:ARG290 3.9 29.4 1.0
N C:GLY267 3.9 14.0 1.0
CD C:ARG290 4.0 29.2 1.0
CB C:VAL264 4.3 13.4 1.0
CA C:ALA268 4.4 11.0 1.0
CZ C:ARG290 4.6 29.2 1.0
CA C:GLN11 4.6 39.7 1.0
NE2 C:GLN11 4.7 30.1 1.0
CD C:PRO28 4.7 20.9 1.0
CD C:GLN11 4.8 40.7 1.0
CG2 C:VAL264 4.8 13.1 1.0
N C:GLN11 4.8 35.4 1.0
CB C:PRO28 4.8 19.6 1.0
OG1 C:THR287 4.8 20.4 1.0
N C:SER269 4.9 8.9 1.0

Reference:

M.C.Franklin, J.Cheung, M.J.Rudolph, F.Burshteyn, M.Cassidy, E.Gary, B.Hillerich, Z.K.Yao, P.R.Carlier, M.Totrov, J.D.Love. Structural Genomics For Drug Design Against the Pathogen Coxiella Burnetii. Proteins V. 83 2124 2015.
ISSN: ISSN 0887-3585
PubMed: 26033498
DOI: 10.1002/PROT.24841
Page generated: Mon Oct 7 13:19:45 2024

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