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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: Tue Dec 15 11:01:29 2020

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