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Sodium in PDB 8b5m: Crystal Structure of GH47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Cyclosulfamidate Inhibitor

Enzymatic activity of Crystal Structure of GH47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Cyclosulfamidate Inhibitor

All present enzymatic activity of Crystal Structure of GH47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Cyclosulfamidate Inhibitor:
3.2.1.113;

Protein crystallography data

The structure of Crystal Structure of GH47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Cyclosulfamidate Inhibitor, PDB code: 8b5m 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) 72.07 / 0.97
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 144.134, 144.134, 50.32, 90, 90, 120
R / Rfree (%) 13.7 / 14.8

Other elements in 8b5m:

The structure of Crystal Structure of GH47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Cyclosulfamidate Inhibitor also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of GH47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Cyclosulfamidate Inhibitor (pdb code 8b5m). 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 GH47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Cyclosulfamidate Inhibitor, PDB code: 8b5m:

Sodium binding site 1 out of 1 in 8b5m

Go back to Sodium Binding Sites List in 8b5m
Sodium binding site 1 out of 1 in the Crystal Structure of GH47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Cyclosulfamidate Inhibitor


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 GH47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Cyclosulfamidate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:4.2
occ:1.00
 OD1 A:ASN454 2.3 4.0 1.0
OD1 A:ASP87 2.3 4.1 1.0
O A:GLU84 2.3 3.9 1.0
O A:HOH792 2.4 4.0 1.0
OG A:SER426 2.5 4.0 1.0
HG A:SER426 2.6 4.0 0.0
HZ2 A:LYS430 3.2 4.4 1.0
CG A:ASP87 3.2 3.8 1.0
HG A:SER132 3.2 4.0 0.0
HB2 A:SER426 3.2 3.9 1.0
HA A:GLU84 3.3 4.0 1.0
C A:GLU84 3.4 3.8 1.0
CB A:SER426 3.4 3.9 1.0
CG A:ASN454 3.4 3.9 1.0
H A:ASP87 3.4 4.2 1.0
HA2 A:GLY129 3.5 3.9 1.0
HA A:SER426 3.5 3.8 1.0
O A:HOH857 3.6 4.4 1.0
HA A:ASN454 3.7 3.8 1.0
OD2 A:ASP87 3.8 4.1 1.0
HD21 A:ASN454 3.8 3.7 1.0
HZ3 A:LYS430 3.8 4.4 1.0
CA A:GLU84 3.8 4.0 1.0
NZ A:LYS430 3.9 4.3 1.0
OG A:SER132 3.9 4.0 1.0
ND2 A:ASN454 4.0 3.7 1.0
CA A:SER426 4.0 3.7 1.0
H A:THR88 4.1 4.3 1.0
O A:VAL83 4.2 4.4 1.0
HZ1 A:LYS430 4.2 4.4 1.0
HB3 A:SER426 4.2 3.9 1.0
N A:ASP87 4.2 4.1 1.0
HA3 A:GLY129 4.3 3.9 1.0
CB A:ASP87 4.3 4.0 1.0
CA A:GLY129 4.3 3.8 1.0
H A:LEU86 4.4 4.0 1.0
HB3 A:GLU84 4.4 4.1 1.0
HB3 A:ASP87 4.4 4.0 1.0
N A:ALA85 4.5 3.9 1.0
CA A:ASN454 4.5 3.7 1.0
CB A:ASN454 4.5 3.9 1.0
N A:LEU86 4.6 4.0 1.0
CB A:GLU84 4.7 4.1 1.0
C A:ALA85 4.8 3.9 1.0
OG1 A:THR88 4.8 4.5 1.0
HA A:ALA85 4.8 4.0 1.0
CA A:ASP87 4.8 4.4 1.0
HB3 A:ASN454 4.8 3.8 1.0
HD22 A:ASN454 4.8 3.7 1.0
N A:THR88 4.9 4.2 1.0
CA A:ALA85 4.9 4.0 1.0
N A:GLU84 4.9 3.8 1.0
HG1 A:THR88 4.9 4.5 0.0
N A:ASN454 5.0 3.7 1.0
O A:GLY129 5.0 4.1 1.0
C A:VAL83 5.0 3.9 1.0
N A:SER426 5.0 3.9 1.0

Reference:

A.Males, G.J.Davies, M.Artola, H.S.Overkleeft. GH47 and Cyclosulfamidate To Be Published.
Page generated: Mon Aug 18 13:12:58 2025

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