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Calcium 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:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of GH47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Cyclosulfamidate Inhibitor, PDB code: 8b5m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 8b5m

Go back to Calcium Binding Sites List in 8b5m
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca503

b:3.8
occ:1.00
 H13 A:5OV501 1.8 4.0 0.0
O A:HOH703 2.4 5.0 1.0
O A:HOH723 2.4 4.9 1.0
O7 A:5OV501 2.4 4.0 1.0
O A:HOH641 2.4 4.5 1.0
O6 A:5OV501 2.5 3.8 1.0
O A:THR451 2.5 3.9 1.0
OG1 A:THR451 2.5 3.7 1.0
O A:HOH805 2.6 5.3 1.0
HG1 A:THR451 2.9 3.7 0.0
H11 A:5OV501 3.1 3.8 0.0
C7 A:5OV501 3.4 3.9 1.0
C6 A:5OV501 3.4 3.9 1.0
C A:THR451 3.5 3.3 1.0
H2 A:5OV501 3.6 4.3 1.0
H10 A:5OV501 3.6 3.9 1.0
CB A:THR451 3.6 3.8 1.0
HA A:THR451 3.6 3.5 1.0
CA A:THR451 3.8 3.4 1.0
HG23 A:THR451 3.8 3.8 1.0
C1 A:5OV501 4.0 4.3 1.0
OE1 A:GLU253 4.1 4.2 1.0
OD2 A:ASP368 4.2 5.1 1.0
CG2 A:THR451 4.2 3.8 1.0
H12 A:5OV501 4.2 4.0 1.0
H5 A:5OV501 4.3 4.6 1.0
HG3 A:GLU365 4.3 4.2 1.0
HB A:THR451 4.4 3.7 1.0
OE1 A:GLU427 4.4 4.4 1.0
O A:HOH644 4.4 5.9 1.0
HB3 A:SER250 4.4 4.1 1.0
OE2 A:GLU427 4.5 5.0 1.0
HB3 A:TYR313 4.5 4.9 1.0
HG22 A:THR451 4.5 3.8 1.0
N A:GLU452 4.7 3.3 1.0
HB2 A:TYR313 4.7 4.9 1.0
HA A:GLU452 4.7 3.6 1.0
OE2 A:GLU365 4.7 5.3 1.0
O A:HOH645 4.7 5.1 1.0
OE2 A:GLU253 4.8 4.5 1.0
C5 A:5OV501 4.8 3.9 1.0
N1 A:5OV501 4.8 4.8 1.0
CD A:GLU427 4.8 4.0 1.0
CD A:GLU253 4.9 4.3 1.0

Calcium binding site 2 out of 2 in 8b5m

Go back to Calcium Binding Sites List in 8b5m
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca binding site number 2 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:Ca504

b:4.0
occ:1.00
 OE2 A:GLU253 2.3 4.5 1.0
O A:HOH683 2.3 4.5 1.0
O A:HOH659 2.3 4.6 1.0
O A:HOH806 2.3 5.1 1.0
O A:HOH708 2.4 5.1 1.0
O A:HOH783 2.4 5.6 1.0
CD A:GLU253 3.4 4.3 1.0
HG2 A:GLU253 3.5 4.3 1.0
HB3 A:GLU253 3.7 4.2 1.0
HD21 A:ASN372 3.9 5.4 1.0
CG A:GLU253 3.9 4.3 1.0
OE1 A:GLN320 4.0 6.3 1.0
HE21 A:GLN320 4.2 7.3 1.0
O A:HOH723 4.2 4.9 1.0
OD2 A:ASP257 4.3 4.2 1.0
OD1 A:ASN372 4.3 6.7 1.0
CB A:GLU253 4.3 4.3 1.0
HA A:THR451 4.4 3.5 1.0
ND2 A:ASN372 4.4 5.2 1.0
OD1 A:ASP257 4.4 4.4 1.0
O A:HOH839 4.4 5.2 1.0
O A:LEU449 4.5 4.4 1.0
OE1 A:GLU253 4.5 4.2 1.0
O A:HOH744 4.5 4.8 1.0
OD1 A:ASP368 4.7 4.2 1.0
CG A:ASN372 4.7 5.7 1.0
CD A:GLN320 4.7 6.1 1.0
HG3 A:GLU253 4.8 4.3 1.0
NE2 A:GLN320 4.8 8.0 1.0
CG A:ASP257 4.8 4.4 1.0
HB2 A:LEU449 4.8 5.8 1.0
O A:HOH955 4.9 5.4 1.0
O A:SER450 4.9 3.7 1.0
HD2 A:TYR313 4.9 4.8 1.0
HD13 A:LEU317 5.0 5.4 1.0
HB2 A:GLU253 5.0 4.2 1.0
HD22 A:ASN372 5.0 5.4 1.0

Reference:

A.Males, G.J.Davies, M.Artola, H.S.Overkleeft. GH47 and Cyclosulfamidate To Be Published.
Page generated: Fri Jul 19 07:09:25 2024

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