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Calcium in PDB 5meh: Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin

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

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

Protein crystallography data

The structure of Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin, PDB code: 5meh 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) 47.14 / 0.95
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 145.371, 145.371, 50.838, 90.00, 90.00, 120.00
R / Rfree (%) 9.1 / 10.3

Other elements in 5meh:

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

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin (pdb code 5meh). 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 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin, PDB code: 5meh:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5meh

Go back to Calcium Binding Sites List in 5meh
Calcium binding site 1 out of 2 in the Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin


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 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:5.5
occ:1.00
 O2 A:DMJ506 2.4 6.2 0.5
O A:HOH731 2.5 7.2 1.0
O A:HOH668 2.5 6.5 1.0
O3 A:DMJ506 2.5 5.7 0.5
O A:HOH621 2.5 9.6 1.0
O2 A:DMJ506 2.5 6.3 0.5
O A:HOH782 2.5 8.3 1.0
O A:THR451 2.5 5.5 1.0
O3 A:DMJ506 2.5 5.5 0.5
OG1 A:THR451 2.5 5.8 1.0
C3 A:DMJ506 3.4 5.7 0.5
C2 A:DMJ506 3.4 7.8 0.5
C3 A:DMJ506 3.5 6.3 0.5
C2 A:DMJ506 3.5 6.0 0.5
C A:THR451 3.5 5.2 1.0
CB A:THR451 3.6 5.6 1.0
CA A:THR451 3.9 5.3 1.0
C1 A:DMJ506 3.9 8.1 0.5
OE1 A:GLU253 4.2 7.2 1.0
CG2 A:THR451 4.2 6.2 1.0
OD2 A:ASP368 4.3 7.9 1.0
C1 A:DMJ506 4.4 5.7 0.5
N5 A:DMJ506 4.4 6.2 0.5
OE1 A:GLU427 4.5 6.0 1.0
O A:HOH788 4.5 7.3 1.0
OE2 A:GLU427 4.5 7.0 1.0
OE2 A:GLU365 4.6 7.0 1.0
O A:HOH627 4.6 7.0 1.0
N A:GLU452 4.7 5.3 1.0
C4 A:DMJ506 4.8 6.0 0.5
C4 A:DMJ506 4.8 6.5 0.5
OE2 A:GLU253 4.9 8.0 1.0
CD A:GLU427 4.9 5.5 1.0
CD A:GLU253 4.9 7.1 1.0

Calcium binding site 2 out of 2 in 5meh

Go back to Calcium Binding Sites List in 5meh
Calcium binding site 2 out of 2 in the Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin


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 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:5.5
occ:0.75
 O A:HOH676 2.3 8.0 1.0
OE2 A:GLU253 2.3 8.0 1.0
O A:HOH646 2.3 7.9 1.0
O A:HOH790 2.3 8.7 1.0
O A:HOH702 2.4 8.5 1.0
O A:HOH734 2.4 8.4 1.0
CD A:GLU253 3.5 7.1 1.0
CG A:GLU253 4.0 6.9 1.0
OE1 A:GLN320 4.1 9.2 1.0
O A:HOH731 4.3 7.2 1.0
OD2 A:ASP257 4.3 6.6 1.0
ND2 A:ASN372 4.4 8.9 1.0
CB A:GLU253 4.4 6.5 1.0
OD1 A:ASN372 4.4 10.1 1.0
OD1 A:ASP257 4.5 6.5 1.0
O A:HOH819 4.5 7.9 1.0
O A:LEU449 4.5 6.3 1.0
OE1 A:GLU253 4.5 7.2 1.0
O A:HOH742 4.5 7.3 1.0
NE2 A:GLN320 4.7 11.4 1.0
OD1 A:ASP368 4.7 6.6 1.0
CG A:ASN372 4.7 8.0 1.0
CD A:GLN320 4.7 8.2 1.0
CG A:ASP257 4.8 6.0 1.0
O A:SER450 4.9 5.4 1.0
O A:HOH904 5.0 8.3 1.0

Reference:

E.R.Van Rijssel, A.P.A.Janssen, A.Males, G.J.Davies, G.A.Van Der Marel, H.S.Overkleeft, J.D.C.Codee. Conformational Behaviour of Azasugars Based on Mannuronic Acid. Chembiochem V. 18 1297 2017.
ISSN: ESSN 1439-7633
PubMed: 28256791
DOI: 10.1002/CBIC.201700080
Page generated: Mon Jul 15 08:02:56 2024

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