Sodium in PDB 4r3n: Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid

Enzymatic activity of Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid

All present enzymatic activity of Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid:
1.2.1.11;

Protein crystallography data

The structure of Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid, PDB code: 4r3n was solved by A.G.Pavlovsky, R.E.Viola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.536, 97.658, 63.978, 90.00, 102.55, 90.00
R / Rfree (%) 13.1 / 16.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid (pdb code 4r3n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid, PDB code: 4r3n:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4r3n

Go back to Sodium Binding Sites List in 4r3n
Sodium binding site 1 out of 3 in the Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:14.4
occ:1.00
O A:ALA279 2.3 14.7 1.0
O A:ALA274 2.3 16.4 1.0
O A:PHE276 2.3 12.3 1.0
C A:ALA274 3.2 15.0 1.0
C A:PHE276 3.2 11.8 1.0
N A:PHE276 3.3 13.4 1.0
O A:ILE273 3.4 14.1 1.0
C A:ALA279 3.4 13.2 1.0
C A:ALA275 3.7 13.7 1.0
CA A:PHE276 3.8 13.7 1.0
O A:HOH638 3.9 20.9 1.0
N A:ALA279 4.0 11.1 1.0
N A:ALA275 4.0 14.7 1.0
CA A:ALA274 4.0 14.9 1.0
O A:HOH620 4.0 20.3 1.0
N A:PRO277 4.1 13.6 1.0
CA A:ALA279 4.2 11.8 1.0
CA A:ALA275 4.2 14.3 1.0
CA A:PRO277 4.3 12.3 1.0
O A:ALA275 4.3 14.6 1.0
CB A:ALA279 4.4 12.1 1.0
C A:ILE273 4.5 13.5 1.0
N A:VAL280 4.5 11.7 1.0
N A:GLY278 4.6 13.0 1.0
CB A:PHE276 4.6 13.2 1.0
C A:PRO277 4.7 12.5 1.0
CA A:VAL280 4.7 12.8 0.5
CA A:VAL280 4.7 12.9 0.5
N A:ALA274 4.8 13.6 1.0

Sodium binding site 2 out of 3 in 4r3n

Go back to Sodium Binding Sites List in 4r3n
Sodium binding site 2 out of 3 in the Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:14.1
occ:1.00
O A:GLU343 2.3 15.1 1.0
C A:GLU343 3.3 14.5 1.0
N A:ARG344 4.2 14.8 1.0
CA A:GLU343 4.2 15.1 1.0
CA A:ARG344 4.3 15.7 1.0
N A:GLY345 4.4 14.6 1.0
C A:ARG344 4.5 14.6 1.0
O A:HIS342 4.6 13.5 1.0

Sodium binding site 3 out of 3 in 4r3n

Go back to Sodium Binding Sites List in 4r3n
Sodium binding site 3 out of 3 in the Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Ternary Complex of Sp-Asadh with Nadp and 1, 2,3-Benzenetricarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:24.2
occ:1.00
O B:HOH562 2.3 32.6 1.0
O B:HOH628 2.4 31.5 1.0
OD1 B:ASP147 2.4 28.7 1.0
O B:HOH551 2.4 26.1 1.0
O B:SER236 2.5 22.1 1.0
O B:ASP147 2.5 17.1 1.0
C B:ASP147 3.3 14.0 1.0
CA B:ASP147 3.5 16.3 1.0
CG B:ASP147 3.5 27.7 1.0
C B:SER236 3.5 18.8 1.0
NZ B:LYS261 3.9 40.6 1.0
CA B:ILE237 4.0 18.5 1.0
N B:ALA238 4.0 16.2 1.0
CB B:ASP147 4.1 17.7 1.0
N B:ILE237 4.2 18.5 1.0
OG B:SER236 4.3 25.4 1.0
CB B:SER236 4.4 26.8 1.0
OD2 B:ASP147 4.5 38.0 1.0
C B:ILE237 4.5 17.8 1.0
O B:LEU146 4.5 18.8 1.0
CA B:SER236 4.5 22.1 1.0
N B:ARG148 4.6 14.4 1.0
CE B:LYS261 4.7 34.9 1.0
N B:ASP147 4.8 17.0 1.0
CB B:ALA238 4.8 16.3 1.0

Reference:

A.G.Pavlovsky, B.Thangavelu, P.Bhansali, R.E.Viola. A Cautionary Tale of Structure-Guided Inhibitor Development Against An Essential Enzyme in the Aspartate-Biosynthetic Pathway Acta Crystallogr.,Sect.D V. 70 3244 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714023979
Page generated: Tue Dec 15 07:09:16 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy