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Sodium 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:

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 Noeuromycin (pdb code 4ayr). 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 Noeuromycin, PDB code: 4ayr:

Sodium binding site 1 out of 1 in 4ayr

Go back to Sodium Binding Sites List in 4ayr
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 Noeuromycin


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 Noeuromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:4.8
occ:1.00
 OD1 A:ASN454 2.4 4.9 1.0
O A:GLU84 2.4 5.0 1.0
OD1 A:ASP87 2.4 4.3 1.0
O A:HOH2153 2.5 4.9 1.0
OG A:SER426 2.6 4.7 1.0
CG A:ASP87 3.3 4.2 1.0
C A:GLU84 3.4 4.3 1.0
CB A:SER426 3.4 4.1 1.0
CG A:ASN454 3.4 4.1 1.0
O A:HOH2155 3.5 4.7 1.0
OD2 A:ASP87 3.8 4.6 1.0
CA A:GLU84 3.8 4.2 1.0
NZ A:LYS430 3.9 4.4 1.0
OG A:SER132 4.0 4.5 1.0
ND2 A:ASN454 4.0 4.3 1.0
CA A:SER426 4.1 4.1 1.0
O A:VAL83 4.1 4.8 1.0
N A:ASP87 4.3 4.1 1.0
CA A:GLY129 4.4 4.1 1.0
CB A:ASP87 4.4 4.2 1.0
N A:ALA85 4.5 4.0 1.0
CA A:ASN454 4.6 3.8 1.0
CB A:ASN454 4.6 3.8 1.0
N A:LEU86 4.7 4.2 1.0
CB A:GLU84 4.7 4.5 1.0
OG1 A:THR88 4.8 4.8 1.0
CA A:ASP87 4.8 4.2 1.0
C A:ALA85 4.8 4.0 1.0
N A:GLU84 4.9 4.1 1.0
C A:VAL83 4.9 4.1 1.0
CA A:ALA85 5.0 4.3 1.0
N A:ASN454 5.0 3.6 1.0
N A:THR88 5.0 4.5 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 14:25:53 2024

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