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Sodium 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:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Structure of the GH47 Processing Alpha-1,2-Mannosidase From Caulobacter Strain K31 in Complex with Thiomannobioside, PDB code: 4ayp:

Sodium binding site 1 out of 1 in 4ayp

Go back to Sodium Binding Sites List in 4ayp
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na502

b:3.5
occ:1.00
 OD1 A:ASN454 2.3 4.0 1.0
O A:GLU84 2.4 4.0 1.0
OD1 A:ASP87 2.4 3.6 1.0
O A:HOH2175 2.5 4.0 1.0
OG A:SER426 2.6 3.9 1.0
CG A:ASP87 3.3 3.4 1.0
C A:GLU84 3.3 3.5 1.0
CG A:ASN454 3.4 3.5 1.0
CB A:SER426 3.4 3.5 1.0
O A:HOH2178 3.5 4.0 1.0
CA A:GLU84 3.8 3.6 1.0
OD2 A:ASP87 3.8 4.0 1.0
NZ A:LYS430 3.9 3.8 1.0
OG A:SER132 4.0 3.7 1.0
ND2 A:ASN454 4.0 3.8 1.0
CA A:SER426 4.1 3.4 1.0
O A:VAL83 4.2 4.1 1.0
N A:ASP87 4.3 3.5 1.0
CA A:GLY129 4.3 3.5 1.0
CB A:ASP87 4.4 3.6 1.0
N A:ALA85 4.5 3.5 1.0
CB A:ASN454 4.6 3.4 1.0
CA A:ASN454 4.6 3.4 1.0
N A:LEU86 4.7 3.6 1.0
CB A:GLU84 4.7 3.9 1.0
C A:ALA85 4.8 3.6 1.0
OG1 A:THR88 4.8 4.1 1.0
CA A:ASP87 4.8 3.6 1.0
N A:GLU84 4.9 3.6 1.0
C A:VAL83 5.0 3.6 1.0
CA A:ALA85 5.0 3.6 1.0
N A:THR88 5.0 3.7 1.0
N A:ASN454 5.0 3.2 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: Mon Oct 7 14:25:37 2024

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