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

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

All present enzymatic activity of Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Noeuromycin:
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 Noeuromycin, PDB code: 4ayr 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) 46.60 / 1.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 143.919, 143.919, 50.186, 90.00, 90.00, 120.00
R / Rfree (%) 8.264 / 10.208

Other elements in 4ayr:

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

Calcium binding site 1 out of 2 in 4ayr

Go back to Calcium Binding Sites List in 4ayr
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 Noeuromycin


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 Noeuromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:3.6
occ:1.00
 O A:HOH2450 2.4 5.2 1.0
O A:HOH2609 2.4 4.4 1.0
O A:THR451 2.5 4.0 1.0
O A:HOH2449 2.5 5.4 1.0
O3 A:IFL503 2.5 3.7 1.0
O A:HOH2608 2.5 4.3 1.0
OG1 A:THR451 2.5 3.8 1.0
O2 A:IFL503 2.5 4.0 1.0
C2 A:IFL503 3.4 3.7 1.0
C3 A:IFL503 3.4 3.9 1.0
C A:THR451 3.4 3.4 1.0
CB A:THR451 3.6 3.8 1.0
CA A:THR451 3.8 3.6 1.0
N A:IFL503 3.9 4.0 1.0
OE1 A:GLU253 4.1 4.6 1.0
CG2 A:THR451 4.2 4.1 1.0
OD2 A:ASP368 4.2 5.6 1.0
OE1 A:GLU427 4.4 4.5 1.0
O A:HOH2447 4.4 4.9 1.0
OE2 A:GLU427 4.4 4.7 1.0
N A:GLU452 4.7 3.5 1.0
OE2 A:GLU365 4.7 5.1 1.0
O A:HOH2446 4.7 4.8 1.0
OE2 A:GLU253 4.8 5.3 1.0
C4 A:IFL503 4.8 3.7 1.0
CD A:GLU427 4.8 3.9 1.0
CD A:GLU253 4.8 4.8 1.0

Calcium binding site 2 out of 2 in 4ayr

Go back to Calcium Binding Sites List in 4ayr
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 Noeuromycin


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 Noeuromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:4.7
occ:1.00
 OE2 A:GLU253 2.3 5.3 1.0
O A:HOH2454 2.3 5.6 1.0
O A:HOH2452 2.3 5.6 1.0
O A:HOH2453 2.4 6.0 1.0
O A:HOH2451 2.4 5.9 1.0
O A:HOH2546 2.4 6.1 1.0
CD A:GLU253 3.4 4.8 1.0
CG A:GLU253 3.9 4.6 1.0
OE1 A:GLN320 4.0 7.0 1.0
O A:HOH2450 4.2 5.2 1.0
OD2 A:ASP257 4.3 4.9 1.0
CB A:GLU253 4.3 4.6 1.0
OD1 A:ASN372 4.4 8.5 1.0
ND2 A:ASN372 4.4 5.7 1.0
OD1 A:ASP257 4.4 4.9 1.0
O A:HOH2683 4.5 5.8 1.0
O A:LEU449 4.5 4.6 1.0
OE1 A:GLU253 4.5 4.6 1.0
O A:HOH2539 4.5 5.0 1.0
OD1 A:ASP368 4.6 4.4 1.0
CG A:ASN372 4.7 5.6 1.0
NE2 A:GLN320 4.7 8.7 1.0
CD A:GLN320 4.7 6.7 1.0
CG A:ASP257 4.8 4.6 1.0
O A:HOH2707 4.9 6.2 1.0
O A:SER450 4.9 3.7 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: Tue Jul 8 18:47:55 2025

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