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Calcium 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:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Family 47 Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with Kifunensine, PDB code: 5ne5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5ne5

Go back to Calcium Binding Sites List in 5ne5
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca502

b:6.5
occ:1.00
 O A:HOH667 2.4 7.8 1.0
O A:HOH734 2.4 8.8 1.0
O A:HOH627 2.5 7.8 1.0
O A:THR451 2.5 6.6 1.0
O2 A:KIF501 2.5 6.8 1.0
O3 A:KIF501 2.5 6.4 1.0
OG1 A:THR451 2.5 7.1 1.0
O A:HOH618 2.6 8.7 1.0
C3 A:KIF501 3.4 6.2 1.0
C2 A:KIF501 3.4 6.2 1.0
C A:THR451 3.5 5.9 1.0
CB A:THR451 3.7 7.1 1.0
CA A:THR451 3.8 6.2 1.0
C1 A:KIF501 4.0 6.4 1.0
OE1 A:GLU253 4.1 8.1 0.5
OE1 A:GLU253 4.2 8.2 0.5
CG2 A:THR451 4.2 7.7 1.0
OD2 A:ASP368 4.3 9.8 1.0
O A:HOH625 4.4 10.4 1.0
OE1 A:GLU427 4.5 7.2 1.0
OE2 A:GLU427 4.5 7.5 1.0
OE2 A:GLU253 4.6 9.2 0.5
OE2 A:GLU365 4.7 8.5 1.0
N A:GLU452 4.7 6.3 1.0
O A:HOH644 4.8 7.5 1.0
OE2 A:GLU253 4.8 7.4 0.5
C4 A:KIF501 4.8 6.4 1.0
CD A:GLU253 4.9 8.1 0.5
N9 A:KIF501 4.9 7.1 1.0
CD A:GLU427 4.9 6.2 1.0
CD A:GLU253 4.9 8.1 0.5

Calcium binding site 2 out of 2 in 5ne5

Go back to Calcium Binding Sites List in 5ne5
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca binding site number 2 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:Ca503

b:7.5
occ:0.50
 O A:HOH611 2.3 12.5 1.0
O A:HOH761 2.3 14.7 1.0
OE2 A:GLU253 2.4 7.4 0.5
O A:HOH626 2.4 15.8 1.0
O A:HOH698 2.4 13.3 1.0
O A:HOH602 2.4 13.0 0.8
OE2 A:GLU253 2.5 9.2 0.5
CE1 A:TYR313 2.9 8.6 0.2
CD A:GLU253 3.3 8.1 0.5
CG A:GLU253 3.3 8.7 0.5
CD A:GLU253 3.5 8.1 0.5
OH A:TYR313 3.6 7.4 0.2
CZ A:TYR313 3.7 8.6 0.2
CD1 A:TYR313 3.8 7.9 0.2
CG A:GLU253 4.0 8.6 0.5
OE1 A:GLN320 4.2 13.1 1.0
O A:HOH734 4.2 8.8 1.0
ND2 A:ASN372 4.3 10.9 0.3
OD2 A:ASP257 4.3 7.8 1.0
OE1 A:GLU253 4.4 8.2 0.5
O A:HOH796 4.5 13.2 1.0
OD1 A:ASP257 4.5 7.8 1.0
OD1 A:ASN372 4.5 9.7 0.7
ND2 A:ASN372 4.5 9.2 0.7
OE1 A:GLU253 4.5 8.1 0.5
O A:LEU449 4.6 7.6 1.0
CB A:GLU253 4.6 8.8 0.5
OD1 A:ASP368 4.6 10.5 1.0
O A:HOH777 4.7 9.3 1.0
CB A:GLU253 4.7 8.4 0.5
CG A:ASN372 4.8 8.2 0.7
CG A:ASP257 4.8 7.3 1.0
CD2 A:TYR313 4.8 8.7 0.3
O A:HOH859 4.9 12.3 1.0
CD A:GLN320 4.9 12.6 1.0
CE2 A:TYR313 4.9 9.2 0.2
NE2 A:GLN320 5.0 18.1 1.0
O A:SER450 5.0 6.7 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: Wed Jul 9 08:44:13 2025

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