Calcium in PDB 6aq6: X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with N-Acetyllactosamine

The structure of X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with N-Acetyllactosamine, PDB code: 6aq6 was solved by O.Gerlits, R.J.Woods, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.08 / 1.90
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	134.669, 134.669, 81.212, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 25.5

The structure of X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with N-Acetyllactosamine also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with N-Acetyllactosamine (pdb code 6aq6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with N-Acetyllactosamine, PDB code: 6aq6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with N-Acetyllactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with N-Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca309 b:20.2 occ:1.00 OD2 A:ASP136 2.2 16.1 1.0 O A:HOH451 2.3 19.3 1.0 O A:PHE131 2.3 19.0 1.0 OD1 A:ASP129 2.4 18.4 1.0 OD1 A:ASN133 2.4 20.9 1.0 OD2 A:ASP129 2.6 22.1 1.0 O A:HOH418 2.6 20.7 1.0 CG A:ASP129 2.8 23.9 1.0 CG A:ASP136 3.3 22.0 1.0 C A:PHE131 3.5 25.1 1.0 CG A:ASN133 3.6 24.4 1.0 OD1 A:ASP136 3.8 20.5 1.0 N A:ASN133 4.0 22.1 1.0 MN A:MN310 4.2 22.0 1.0 CB A:ASN133 4.2 23.1 1.0 N A:PHE131 4.3 19.8 1.0 CB A:ASP129 4.3 18.3 1.0 CA A:PHE131 4.4 21.2 1.0 CB A:ASP136 4.5 19.6 1.0 NE1 A:TRP135 4.5 17.1 1.0 N A:SER132 4.5 20.1 1.0 O A:GLY107 4.5 20.1 1.0 CA A:GLY107 4.6 17.9 1.0 O A:HOH413 4.6 21.3 1.0 OD2 A:ASP89 4.6 16.8 1.0 CB A:PHE131 4.6 19.4 1.0 CA A:SER132 4.6 24.2 1.0 ND2 A:ASN133 4.6 18.9 1.0 O A:ASP89 4.7 15.7 1.0 CA A:ASN133 4.8 24.0 1.0 C A:SER132 4.8 28.3 1.0 CD2 A:PHE131 4.9 24.5 1.0

Calcium binding site 2 out of 2 in the X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with N-Acetyllactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with N-Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:15.1 occ:1.00 O B:PHE131 2.2 14.2 1.0 OD2 B:ASP136 2.3 15.5 1.0 OD1 B:ASN133 2.3 17.9 1.0 OD2 B:ASP129 2.4 18.5 1.0 OD1 B:ASP129 2.4 14.9 1.0 O B:HOH431 2.5 12.9 1.0 O B:HOH422 2.6 18.4 1.0 CG B:ASP129 2.7 12.8 1.0 CG B:ASP136 3.4 17.3 1.0 CG B:ASN133 3.4 19.4 1.0 C B:PHE131 3.5 12.0 1.0 OD1 B:ASP136 3.8 17.9 1.0 N B:ASN133 3.9 17.1 1.0 CB B:ASN133 4.1 15.4 1.0 MN B:MN306 4.2 20.9 1.0 CB B:ASP129 4.3 15.2 1.0 CA B:PHE131 4.3 17.0 1.0 N B:PHE131 4.3 17.7 1.0 N B:SER132 4.4 16.8 1.0 NE1 B:TRP135 4.5 18.7 1.0 ND2 B:ASN133 4.5 19.6 1.0 CA B:SER132 4.5 18.9 1.0 O B:HOH413 4.6 22.1 1.0 CB B:PHE131 4.6 20.0 1.0 CB B:ASP136 4.6 17.1 1.0 O B:ASP89 4.6 18.1 1.0 O B:GLY107 4.6 18.3 1.0 C B:SER132 4.6 20.3 1.0 CA B:ASN133 4.6 17.1 1.0 CA B:GLY107 4.6 18.0 1.0 OD2 B:ASP89 4.7 16.6 1.0 CD2 B:PHE131 4.8 21.1 1.0 CZ2 B:TRP135 4.9 20.6 1.0 CE2 B:TRP135 4.9 22.9 1.0

A.Sood, O.O.Gerlits, Y.Ji, N.V.Bovin, L.Coates, R.J.Woods. Defining the Specificity of Carbohydrate-Protein Interactions By Quantifying Functional Group Contributions. J Chem Inf Model V. 58 1889 2018.
ISSN: ESSN 1549-960X
PubMed: 30086239
DOI: 10.1021/ACS.JCIM.8B00120