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Sodium in PDB 4c90: Evidence That GH115 Alpha-Glucuronidase Activity Is Dependent on Conformational Flexibility

Protein crystallography data

The structure of Evidence That GH115 Alpha-Glucuronidase Activity Is Dependent on Conformational Flexibility, PDB code: 4c90 was solved by A.Rogowski, A.Basle, C.S.Farinas, A.Solovyova, J.C.Mortimer, P.Dupree, H.J.Gilbert, D.N.Bolam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.60 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.390, 131.680, 199.400, 90.00, 90.00, 90.00
R / Rfree (%) 20.335 / 26.591

Sodium Binding Sites:

The binding sites of Sodium atom in the Evidence That GH115 Alpha-Glucuronidase Activity Is Dependent on Conformational Flexibility (pdb code 4c90). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Evidence That GH115 Alpha-Glucuronidase Activity Is Dependent on Conformational Flexibility, PDB code: 4c90:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4c90

Go back to Sodium Binding Sites List in 4c90
Sodium binding site 1 out of 2 in the Evidence That GH115 Alpha-Glucuronidase Activity Is Dependent on Conformational Flexibility


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Evidence That GH115 Alpha-Glucuronidase Activity Is Dependent on Conformational Flexibility within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1855

b:28.1
occ:1.00
O A:LYS433 2.1 31.0 1.0
OD1 A:ASP465 2.4 26.3 1.0
C A:LYS433 3.3 28.7 1.0
CG A:ASP465 3.4 24.2 1.0
NE2 A:GLN642 3.6 30.1 1.0
OD2 A:ASP465 3.9 24.0 1.0
CA A:LYS433 4.1 28.2 1.0
CB A:LYS433 4.1 26.0 1.0
SG A:CYS210 4.1 29.7 1.0
N A:TRP434 4.3 28.0 1.0
OD2 A:ASP424 4.4 32.3 1.0
O A:TRP434 4.5 26.8 1.0
CB A:ASP465 4.5 24.1 1.0
CA A:TRP434 4.5 26.6 1.0
CB A:GLN642 4.6 28.8 1.0
CD A:GLN642 4.6 29.2 1.0
CB A:CYS210 4.6 28.8 1.0
CG A:GLN642 4.7 28.2 1.0
O A:ASP206 4.8 30.9 1.0
N A:ASP465 4.9 24.0 1.0
C A:TRP434 4.9 26.1 1.0
OD1 A:ASP424 5.0 33.1 1.0

Sodium binding site 2 out of 2 in 4c90

Go back to Sodium Binding Sites List in 4c90
Sodium binding site 2 out of 2 in the Evidence That GH115 Alpha-Glucuronidase Activity Is Dependent on Conformational Flexibility


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Evidence That GH115 Alpha-Glucuronidase Activity Is Dependent on Conformational Flexibility within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1854

b:23.3
occ:1.00
O B:LYS433 2.1 31.2 1.0
OD2 B:ASP465 2.2 20.9 1.0
C B:LYS433 3.3 27.5 1.0
CG B:ASP465 3.4 19.9 1.0
OD1 B:ASP465 4.0 20.7 1.0
CA B:LYS433 4.1 27.2 1.0
CB B:LYS433 4.2 26.7 1.0
OD2 B:ASP424 4.3 25.3 1.0
N B:TRP434 4.4 27.4 1.0
O B:TRP434 4.4 27.0 1.0
CB B:ASP465 4.4 20.1 1.0
CB B:GLN642 4.5 27.9 1.0
OE1 B:GLN642 4.5 33.8 1.0
CA B:TRP434 4.6 25.1 1.0
CG B:GLN642 4.6 30.2 1.0
OD1 B:ASP424 4.7 26.2 1.0
N B:ASP465 4.7 20.7 1.0
SG B:CYS210 4.7 25.2 1.0
O B:ASP206 4.7 27.7 1.0
CB B:CYS210 4.8 27.2 1.0
C B:TRP434 4.8 25.2 1.0
CG B:ASP424 4.9 24.6 1.0

Reference:

A.Rogowski, A.Basle, C.S.Farinas, A.Solovyova, J.C.Mortimer, P.Dupree, H.J.Gilbert, D.N.Bolam. Evidence That GH115 Alpha-Glucuronidase Activity Is Dependent on Conformational Flexibility J.Biol.Chem. V. 289 53 2014.
ISSN: ISSN 0021-9258
PubMed: 24214982
DOI: 10.1074/JBC.M113.525295
Page generated: Tue Dec 15 06:35:27 2020

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