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

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

The structure of Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31, PDB code: 4ayo 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)	46.57 / 0.85
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	143.770, 143.770, 50.155, 90.00, 90.00, 120.00
R / Rfree (%)	9.464 / 10.478

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

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 (pdb code 4ayo). 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, PDB code: 4ayo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:2.6 occ:1.00 O A:HOH2728 2.4 3.1 1.0 O3 A:BTB503 2.4 4.9 0.5 O A:HOH2559 2.4 4.1 1.0 O A:HOH2558 2.4 4.0 1.0 O A:HOH2727 2.5 3.6 1.0 O1 A:BTB503 2.5 2.2 0.5 O A:THR451 2.5 2.8 1.0 O1 A:BTB503 2.5 4.3 0.5 OG1 A:THR451 2.5 2.8 1.0 O3 A:BTB503 2.6 2.7 0.5 C1 A:BTB503 3.4 3.0 0.5 C A:THR451 3.5 2.5 1.0 C1 A:BTB503 3.5 4.5 0.5 CB A:THR451 3.6 2.8 1.0 C3 A:BTB503 3.6 4.9 0.5 CA A:THR451 3.8 2.6 1.0 C3 A:BTB503 3.9 3.2 0.5 C2 A:BTB503 4.0 4.5 0.5 C2 A:BTB503 4.1 2.8 0.5 OE1 A:GLU253 4.1 3.0 1.0 N A:BTB503 4.1 4.6 0.5 CG2 A:THR451 4.2 3.2 1.0 OD2 A:ASP368 4.3 4.0 1.0 N A:BTB503 4.3 3.5 0.5 OE1 A:GLU427 4.3 3.5 1.0 O A:HOH2556 4.3 4.3 1.0 OE2 A:GLU427 4.5 3.9 1.0 N A:GLU452 4.7 2.6 1.0 OE2 A:GLU365 4.7 4.9 1.0 O A:HOH2555 4.7 4.7 1.0 C8 A:BTB503 4.7 7.3 0.5 CD A:GLU427 4.8 3.0 1.0 OE2 A:GLU253 4.8 3.2 1.0 CD A:GLU253 4.9 2.8 1.0

Calcium binding site 2 out of 2 in the Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:2.9 occ:1.00 O A:HOH2561 2.3 3.6 1.0 OE2 A:GLU253 2.3 3.2 1.0 O A:HOH2560 2.3 3.5 1.0 O A:HOH2563 2.4 4.0 1.0 O A:HOH2661 2.4 4.2 1.0 O A:HOH2562 2.4 3.7 1.0 CD A:GLU253 3.4 2.8 1.0 CG A:GLU253 3.9 2.9 1.0 OE1 A:GLN320 4.0 5.1 1.0 CB A:GLU253 4.3 2.8 1.0 O A:HOH2558 4.3 4.0 1.0 OD2 A:ASP257 4.3 3.5 1.0 OD1 A:ASN372 4.4 6.1 1.0 ND2 A:ASN372 4.4 4.1 1.0 OD1 A:ASP257 4.4 3.5 1.0 O A:LEU449 4.4 3.3 1.0 O A:HOH2812 4.5 4.0 1.0 OE1 A:GLU253 4.5 3.0 1.0 O A:HOH2655 4.5 3.6 1.0 OD1 A:ASP368 4.6 3.1 1.0 CG A:ASN372 4.7 4.2 1.0 NE2 A:GLN320 4.7 6.5 1.0 CD A:GLN320 4.7 4.5 1.0 CG A:ASP257 4.8 3.1 1.0 O A:SER450 4.8 2.9 1.0 O A:HOH2834 4.9 4.4 1.0

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