Atomistry » Sodium » PDB 4zm0-5ac7 » 5ab3
Atomistry »
  Sodium »
    PDB 4zm0-5ac7 »
      5ab3 »

Sodium in PDB 5ab3: S.Enterica Hisa Mutant D7N, D10G, DUP13-15, Q24L, G102A

Enzymatic activity of S.Enterica Hisa Mutant D7N, D10G, DUP13-15, Q24L, G102A

All present enzymatic activity of S.Enterica Hisa Mutant D7N, D10G, DUP13-15, Q24L, G102A:
5.3.1.16;

Protein crystallography data

The structure of S.Enterica Hisa Mutant D7N, D10G, DUP13-15, Q24L, G102A, PDB code: 5ab3 was solved by X.Guo, A.Soderholm, M.Newton, J.Nasvall, 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) 49.11 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 61.196, 61.196, 391.887, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 20.6

Sodium Binding Sites:

The binding sites of Sodium atom in the S.Enterica Hisa Mutant D7N, D10G, DUP13-15, Q24L, G102A (pdb code 5ab3). 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 D7N, D10G, DUP13-15, Q24L, G102A, PDB code: 5ab3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5ab3

Go back to Sodium Binding Sites List in 5ab3
Sodium binding site 1 out of 4 in the S.Enterica Hisa Mutant D7N, D10G, DUP13-15, Q24L, G102A


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 D7N, D10G, DUP13-15, Q24L, G102A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1246

b:42.9
occ:1.00
O A:HOH2004 3.0 44.5 1.0
N A:ILE2 3.3 36.8 1.0
NE2 A:GLN243 3.3 52.9 1.0
CA A:MET1 3.5 33.6 1.0
CG1 A:ILE239 3.7 39.6 1.0
CB A:MET1 3.9 43.1 1.0
C A:MET1 3.9 37.9 1.0
CG2 A:ILE239 3.9 51.2 1.0
CD1 A:TRP242 4.0 41.4 1.0
CG A:GLN243 4.2 62.5 1.0
CB A:ILE239 4.3 45.3 1.0
CD A:GLN243 4.3 63.7 1.0
CD1 A:ILE239 4.3 44.4 1.0
CB A:ILE2 4.3 38.7 1.0
CG1 A:ILE2 4.3 35.3 1.0
CA A:ILE2 4.4 32.2 1.0
CA A:ILE239 4.5 42.8 1.0
N A:MET1 4.6 39.7 1.0
NE1 A:TRP242 4.7 39.4 1.0
O A:ILE2 4.8 34.9 1.0
OE1 B:GLN243 4.9 72.0 1.0
CG A:TRP242 5.0 43.0 1.0

Sodium binding site 2 out of 4 in 5ab3

Go back to Sodium Binding Sites List in 5ab3
Sodium binding site 2 out of 4 in the S.Enterica Hisa Mutant D7N, D10G, DUP13-15, Q24L, G102A


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 D7N, D10G, DUP13-15, Q24L, G102A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1246

b:32.1
occ:1.00
O B:HOH2001 3.0 31.7 1.0
NE2 B:GLN243 3.3 56.9 1.0
N B:ILE2 3.3 31.6 1.0
CA B:MET1 3.6 34.5 1.0
CG1 B:ILE239 3.7 30.6 1.0
CD1 B:TRP242 3.9 35.9 1.0
CG2 B:ILE239 3.9 38.0 1.0
C B:MET1 3.9 30.6 1.0
CG B:MET1 4.1 52.0 1.0
CG B:GLN243 4.1 67.1 1.0
CB B:MET1 4.2 42.2 1.0
CD B:GLN243 4.2 64.5 1.0
CG1 B:ILE2 4.2 25.3 1.0
CB B:ILE2 4.2 31.7 1.0
CB B:ILE239 4.3 32.9 1.0
CD1 B:ILE239 4.3 32.2 1.0
CA B:ILE2 4.3 30.7 1.0
CA B:ILE239 4.5 34.3 1.0
NE1 B:TRP242 4.6 32.6 1.0
N B:MET1 4.7 32.1 1.0
O B:ILE2 4.7 31.4 1.0
CG B:TRP242 4.9 34.6 1.0

Sodium binding site 3 out of 4 in 5ab3

Go back to Sodium Binding Sites List in 5ab3
Sodium binding site 3 out of 4 in the S.Enterica Hisa Mutant D7N, D10G, DUP13-15, Q24L, G102A


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 D7N, D10G, DUP13-15, Q24L, G102A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1247

b:37.5
occ:1.00
CG B:GLN155 2.7 55.7 1.0
O B:HOH2111 2.8 33.9 1.0
CB B:GLN155 3.6 37.0 1.0
CD B:GLN155 3.8 64.0 1.0
NE2 B:GLN155 4.3 60.7 1.0
OG B:SER152 4.4 40.6 1.0
OE1 B:GLN155 4.7 78.7 1.0
CA B:GLN155 4.7 29.4 1.0

Sodium binding site 4 out of 4 in 5ab3

Go back to Sodium Binding Sites List in 5ab3
Sodium binding site 4 out of 4 in the S.Enterica Hisa Mutant D7N, D10G, DUP13-15, Q24L, G102A


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 D7N, D10G, DUP13-15, Q24L, G102A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1246

b:31.2
occ:1.00
O C:HOH2161 2.9 36.9 1.0
O C:HOH2038 3.0 33.7 1.0
O C:HOH2005 3.2 35.2 1.0
N C:ILE2 3.2 37.9 1.0
CA C:MET1 3.5 32.4 1.0
CG1 C:ILE239 3.8 36.9 1.0
CG C:MET1 3.8 50.1 1.0
C C:MET1 3.9 36.0 1.0
CG2 C:ILE239 3.9 37.3 1.0
CD1 C:TRP242 3.9 35.6 1.0
NE2 C:GLN243 4.1 41.2 1.0
CB C:MET1 4.1 37.1 1.0
CG1 C:ILE2 4.2 38.6 1.0
CB C:ILE2 4.2 39.7 1.0
CB C:ILE239 4.3 42.1 1.0
CA C:ILE2 4.3 36.8 1.0
CD1 C:ILE239 4.3 36.2 1.0
CA C:ILE239 4.5 38.4 1.0
O C:HOH2002 4.6 45.3 1.0
N C:MET1 4.6 32.1 1.0
O C:HOH2160 4.6 47.6 1.0
NE1 C:TRP242 4.7 38.0 1.0
CG C:GLN243 4.7 41.3 1.0
O C:ILE2 4.8 37.4 1.0
CD C:GLN243 4.8 42.1 1.0
O C:HOH2004 4.8 38.6 0.5
CG C:TRP242 4.9 39.7 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 10:18:48 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