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Sodium in PDB 5ne5: Crystal Structure of Family 47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Kifunensine

Enzymatic activity of Crystal Structure of Family 47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Kifunensine

All present enzymatic activity of Crystal Structure of Family 47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Kifunensine:
3.2.1.113;

Protein crystallography data

The structure of Crystal Structure of Family 47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Kifunensine, PDB code: 5ne5 was solved by A.Males, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.23 / 1.05
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 144.923, 144.923, 50.593, 90.00, 90.00, 120.00
R / Rfree (%) 14.6 / 15.2

Other elements in 5ne5:

The structure of Crystal Structure of Family 47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Kifunensine also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Family 47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Kifunensine (pdb code 5ne5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Family 47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Kifunensine, PDB code: 5ne5:

Sodium binding site 1 out of 1 in 5ne5

Go back to Sodium Binding Sites List in 5ne5
Sodium binding site 1 out of 1 in the Crystal Structure of Family 47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Kifunensine


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 Family 47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Kifunensine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:9.7
occ:1.00
 OD1 A:ASP87 2.5 7.0 1.0
OD1 A:ASN454 2.5 8.2 1.0
O A:GLU84 2.5 9.2 1.0
O A:HOH758 2.7 8.6 1.0
OG A:SER426 2.7 7.4 1.0
CG A:ASP87 3.4 6.5 1.0
C A:GLU84 3.4 7.2 1.0
CB A:SER426 3.5 6.6 1.0
O A:HOH820 3.5 7.0 1.0
CG A:ASN454 3.6 6.4 1.0
CA A:GLU84 3.8 6.6 1.0
OD2 A:ASP87 3.9 7.2 1.0
NZ A:LYS430 4.0 6.4 1.0
OG A:SER132 4.0 7.0 1.0
O A:VAL83 4.1 7.5 1.0
CA A:SER426 4.1 6.5 1.0
ND2 A:ASN454 4.1 6.8 1.0
N A:ASP87 4.4 6.5 1.0
CA A:GLY129 4.4 6.1 1.0
CB A:ASP87 4.5 6.2 1.0
N A:ALA85 4.6 6.7 1.0
CA A:ASN454 4.6 6.3 1.0
N A:LEU86 4.7 6.7 1.0
CB A:ASN454 4.7 6.8 1.0
CB A:GLU84 4.7 6.9 1.0
C A:ALA85 4.9 6.4 1.0
N A:GLU84 4.9 6.3 1.0
OG1 A:THR88 4.9 7.2 1.0
C A:VAL83 4.9 6.7 1.0
CA A:ASP87 4.9 7.0 1.0

Reference:

A.Males, L.Raich, S.J.Williams, C.Rovira, G.J.Davies. Conformational Analysis of the Mannosidase Inhibitor Kifunensine: A Quantum Mechanical and Structural Approach. Chembiochem V. 18 1496 2017.
ISSN: ESSN 1439-7633
PubMed: 28493500
DOI: 10.1002/CBIC.201700166
Page generated: Mon Oct 7 22:55:52 2024

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