Sodium in PDB 5meh: Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin

Enzymatic activity of Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin

All present enzymatic activity of Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin:
3.2.1.113;

Protein crystallography data

The structure of Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin, PDB code: 5meh was solved by A.Males, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	47.14 / 0.95
*Space group*	H 3
*Cell size a, b, c (Å), α, β, γ (°)*	145.371, 145.371, 50.838, 90.00, 90.00, 120.00
*R / R_free (%)*	9.1 / 10.3

Other elements in 5meh:

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

Calcium

(Ca)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin (pdb code 5meh). 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 Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin, PDB code: 5meh:

Sodium binding site 1 out of 1 in 5meh

Go back to

Sodium Binding Sites List in 5meh

Sodium binding site 1 out of 1 in the Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Alpha-1,2-Mannosidase From Caulobacter K31 Strain in Complex with 1-Deoxymannojirimycin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na505 b:5.6 occ:1.00	OD1	A:ASN454	2.4	6.0	1.0
	O	A:GLU84	2.4	5.9	1.0
	OD1	A:ASP87	2.4	5.6	1.0
	O	A:HOH766	2.5	6.0	1.0
	OG	A:SER426	2.6	5.7	1.0
	CG	A:ASP87	3.3	5.3	1.0
	C	A:GLU84	3.4	5.5	1.0
	CB	A:SER426	3.5	5.4	1.0
	CG	A:ASN454	3.5	5.6	1.0
	O	A:HOH824	3.6	6.0	1.0
	OD2	A:ASP87	3.8	6.0	1.0
	CA	A:GLU84	3.8	5.4	1.0
	NZ	A:LYS430	4.0	5.9	1.0
	OG	A:SER132	4.0	5.8	1.0
	ND2	A:ASN454	4.1	5.6	1.0
	CA	A:SER426	4.1	5.4	1.0
	O	A:VAL83	4.2	6.2	1.0
	N	A:ASP87	4.3	5.4	1.0
	CA	A:GLY129	4.4	5.5	1.0
	CB	A:ASP87	4.4	5.6	1.0
	N	A:ALA85	4.5	5.3	1.0
	CA	A:ASN454	4.6	5.2	1.0
	CB	A:ASN454	4.6	5.3	1.0
	N	A:LEU86	4.7	5.5	1.0
	CB	A:GLU84	4.8	5.7	1.0
	C	A:ALA85	4.9	5.4	1.0
	OG1	A:THR88	4.9	6.2	1.0
	CA	A:ASP87	4.9	5.4	1.0
	N	A:GLU84	4.9	5.3	1.0

Reference:

E.R.Van Rijssel, A.P.A.Janssen, A.Males, G.J.Davies, G.A.Van Der Marel, H.S.Overkleeft, J.D.C.Codee. Conformational Behaviour of Azasugars Based on Mannuronic Acid. Chembiochem V. 18 1297 2017.
ISSN: ESSN 1439-7633
PubMed: 28256791
DOI: 10.1002/CBIC.201700080

Page generated: Mon Aug 18 01:02:36 2025

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