Atomistry » Sodium » PDB 5g3g-5gwa » 5g4e
Atomistry »
  Sodium »
    PDB 5g3g-5gwa »
      5g4e »

Sodium in PDB 5g4e: S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L

Enzymatic activity of S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L

All present enzymatic activity of S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L:
5.3.1.16;

Protein crystallography data

The structure of S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L, PDB code: 5g4e was solved by A.Soderholm, X.Guo, M.Newton, J.Nasvall, F.Duarte, D.Andersson, W.Patrick, M.Selmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.10 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.817, 88.830, 117.785, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 29.9

Sodium Binding Sites:

The binding sites of Sodium atom in the S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L (pdb code 5g4e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L, PDB code: 5g4e:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5g4e

Go back to Sodium Binding Sites List in 5g4e
Sodium binding site 1 out of 4 in the S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1246

b:37.8
occ:1.00
O A:VAL72 2.3 36.0 1.0
O A:VAL69 2.3 23.9 1.0
O A:HOH2007 2.4 25.5 1.0
CA A:ALA70 3.2 33.2 1.0
C A:VAL69 3.3 26.8 1.0
C A:ALA70 3.5 35.2 1.0
C A:VAL72 3.5 32.8 1.0
O A:ALA70 3.6 39.6 1.0
N A:ALA70 3.7 26.6 1.0
N A:VAL72 4.1 31.8 1.0
CG1 A:VAL69 4.3 31.8 1.0
N A:GLY71 4.3 31.3 1.0
OD1 A:ASN73 4.4 39.0 1.0
CA A:VAL72 4.4 32.4 1.0
N A:ASN73 4.5 30.6 1.0
CA A:ASN73 4.5 36.9 1.0
CB A:ALA70 4.5 27.7 1.0
CA A:VAL69 4.6 30.6 1.0
CG2 A:VAL72 4.8 29.7 1.0
C A:GLY71 5.0 39.7 1.0

Sodium binding site 2 out of 4 in 5g4e

Go back to Sodium Binding Sites List in 5g4e
Sodium binding site 2 out of 4 in the S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1247

b:28.4
occ:1.00
N A:ILE2 3.2 35.9 1.0
NE2 A:GLN243 3.5 61.0 1.0
CA A:MET1 3.7 36.5 1.0
CG1 A:ILE239 3.7 29.1 1.0
CB A:MET1 3.7 44.4 1.0
CG2 A:ILE239 3.7 27.3 1.0
C A:MET1 3.9 39.1 1.0
CB A:ILE2 4.0 30.3 1.0
CD1 A:ILE239 4.1 29.0 1.0
CG1 A:ILE2 4.1 35.2 1.0
CA A:ILE2 4.1 34.4 1.0
CB A:ILE239 4.2 28.3 1.0
CD1 A:TRP242 4.2 35.4 1.0
CD A:GLN243 4.4 57.0 1.0
CA A:ILE239 4.6 36.0 1.0
CG A:GLN243 4.6 51.5 1.0
O A:ILE2 4.6 29.8 1.0
C A:ILE2 4.9 33.9 1.0
NE1 A:TRP242 4.9 36.9 1.0
CG A:MET1 4.9 43.0 1.0

Sodium binding site 3 out of 4 in 5g4e

Go back to Sodium Binding Sites List in 5g4e
Sodium binding site 3 out of 4 in the S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1248

b:43.7
occ:1.00
O B:HOH2002 2.4 32.2 1.0
O B:VAL69 2.5 31.4 1.0
O B:VAL72 2.7 38.5 1.0
C B:VAL69 3.4 31.3 1.0
CA B:ALA70 3.7 30.9 1.0
CG1 B:VAL69 3.8 30.5 1.0
N B:ALA70 3.9 29.7 1.0
C B:VAL72 3.9 34.4 1.0
C B:ALA70 4.2 34.4 1.0
O B:ALA70 4.4 34.8 1.0
CA B:VAL69 4.5 33.0 1.0
CA B:ASN73 4.6 32.0 1.0
N B:VAL72 4.7 28.4 1.0
N B:ASN73 4.7 31.8 1.0
CB B:VAL69 4.8 35.0 1.0
OD1 B:ASN73 4.9 51.8 1.0
CA B:VAL72 4.9 31.1 1.0
O B:VAL74 4.9 28.1 1.0
N B:GLY71 5.0 30.4 1.0
CB B:ALA70 5.0 19.9 1.0

Sodium binding site 4 out of 4 in 5g4e

Go back to Sodium Binding Sites List in 5g4e
Sodium binding site 4 out of 4 in the S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of S. Enterica Hisa Mutant D10G, DUP13-15, Q24L, G102A, V106L within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1249

b:34.4
occ:1.00
NE2 B:GLN243 2.9 56.4 1.0
N B:ILE2 3.1 31.6 1.0
CA B:MET1 3.7 40.2 1.0
CG B:MET1 3.9 38.0 1.0
CG1 B:ILE239 3.9 37.8 1.0
C B:MET1 3.9 37.8 1.0
CB B:ILE2 4.0 30.3 1.0
CD B:GLN243 4.0 54.6 1.0
CA B:ILE2 4.1 30.3 1.0
CG2 B:ILE239 4.1 35.7 1.0
CG1 B:ILE2 4.2 34.5 1.0
CB B:MET1 4.2 39.9 1.0
CD1 B:TRP242 4.3 44.4 1.0
CG B:GLN243 4.4 49.5 1.0
CD1 B:ILE239 4.4 30.9 1.0
O B:ILE2 4.4 28.7 1.0
CB B:ILE239 4.5 34.6 1.0
C B:ILE2 4.8 29.9 1.0
CA B:ILE239 4.8 36.1 1.0
NE1 B:TRP242 4.9 47.3 1.0
N B:MET1 4.9 36.1 1.0

Reference:

M.S.Newton, X.Guo, A.Soderholm, J.Nasvall, P.Lundstrom, D.I.Andersson, M.Selmer, W.M.Patrick. Structural and Functional Innovations in the Real-Time Evolution of New ( Beta Alpha )8 Barrel Enzymes. Proc. Natl. Acad. Sci. V. 114 4727 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28416687
DOI: 10.1073/PNAS.1618552114
Page generated: Mon Oct 7 21:10:13 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy