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Calcium in PDB 4ayp: Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside

Enzymatic activity of Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside

All present enzymatic activity of Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside:
3.2.1.113;

Protein crystallography data

The structure of Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside, PDB code: 4ayp was solved by A.J.Thompson, J.Dabin, J.Iglesias-Fernandez, A.Iglesias-Fernandez, Z.Dinev, S.J.Williams, A.Siriwardena, C.Moreland, T.C.Hu, D.K.Smith, H.J.Gilbert, C.Rovira, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.16 / 0.85
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 144.135, 144.135, 50.301, 90.00, 90.00, 120.00
R / Rfree (%) 9.646 / 10.555

Other elements in 4ayp:

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

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside (pdb code 4ayp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside, PDB code: 4ayp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4ayp

Go back to Calcium Binding Sites List in 4ayp
Calcium binding site 1 out of 2 in the Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:3.3
occ:1.00
 O A:HOH2694 2.4 4.1 1.0
O12 A:SMD503 2.4 3.6 1.0
O A:HOH2528 2.4 4.8 1.0
O A:HOH2695 2.4 3.9 1.0
O A:HOH2527 2.5 5.5 1.0
O13 A:SMD503 2.5 3.5 1.0
O A:THR451 2.5 3.3 1.0
OG1 A:THR451 2.5 3.3 1.0
C13 A:SMD503 3.4 3.4 1.0
C12 A:SMD503 3.4 3.6 1.0
C A:THR451 3.5 3.0 1.0
CB A:THR451 3.6 3.3 1.0
CA A:THR451 3.8 3.1 1.0
C11 A:SMD503 4.1 3.6 1.0
OE1 A:GLU253 4.2 3.9 1.0
CG2 A:THR451 4.2 3.7 1.0
OD2 A:ASP368 4.2 6.1 1.0
O A:HOH2525 4.4 4.3 1.0
OE1 A:GLU427 4.4 4.2 1.0
O15 A:SMD503 4.4 3.7 1.0
OE2 A:GLU427 4.5 4.8 1.0
O A:HOH2524 4.5 4.4 1.0
OE2 A:GLU365 4.6 5.1 1.0
N A:GLU452 4.7 3.1 1.0
C14 A:SMD503 4.8 3.6 1.0
OE2 A:GLU253 4.8 4.1 1.0
CD A:GLU427 4.9 3.6 1.0
CD A:GLU253 4.9 3.7 1.0
CG A:GLU365 4.9 3.8 1.0

Calcium binding site 2 out of 2 in 4ayp

Go back to Calcium Binding Sites List in 4ayp
Calcium binding site 2 out of 2 in the Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:3.7
occ:1.00
 OE2 A:GLU253 2.3 4.1 1.0
O A:HOH2531 2.3 4.5 1.0
O A:HOH2532 2.3 4.2 1.0
O A:HOH2529 2.3 5.1 1.0
O A:HOH2530 2.4 4.5 1.0
O A:HOH2632 2.4 5.1 1.0
CD A:GLU253 3.4 3.7 1.0
CG A:GLU253 3.9 3.9 1.0
OE1 A:GLN320 4.0 6.3 1.0
O A:HOH2528 4.2 4.8 1.0
OD2 A:ASP257 4.3 4.2 1.0
CB A:GLU253 4.3 3.6 1.0
OD1 A:ASN372 4.4 7.4 1.0
ND2 A:ASN372 4.4 5.1 1.0
OD1 A:ASP257 4.4 4.3 1.0
O A:HOH2774 4.5 5.2 1.0
OE1 A:GLU253 4.5 3.9 1.0
O A:LEU449 4.5 4.0 1.0
O A:HOH2624 4.5 4.4 1.0
OD1 A:ASP368 4.6 4.1 1.0
NE2 A:GLN320 4.7 8.0 1.0
CG A:ASN372 4.7 5.2 1.0
CD A:GLN320 4.7 5.6 1.0
CG A:ASP257 4.8 3.7 1.0
O A:SER450 4.9 3.5 1.0
O A:HOH2799 4.9 5.2 1.0

Reference:

A.J.Thompson, J.Dabin, J.Iglesias-Fernandez, A.Ardevol, Z.Dinev, S.J.Williams, O.Bande, A.Siriwardena, C.Moreland, T.C.Hu, D.K.Smith, H.J.Gilbert, C.Rovira, G.J.Davies. The Reaction Coordinate of A Bacterial GH47 Alpha-Mannosidase: A Combined Quantum Mechanical and Structural Approach. Angew.Chem.Int.Ed.Engl. V. 51 10997 2012.
ISSN: ISSN 1433-7851
PubMed: 23012075
DOI: 10.1002/ANIE.201205338
Page generated: Sat Jul 13 22:26:44 2024

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