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Magnesium in PDB 3vv1: Crystal Structure of Caenorhabditis Elegans Galectin Lec-6

Protein crystallography data

The structure of Crystal Structure of Caenorhabditis Elegans Galectin Lec-6, PDB code: 3vv1 was solved by H.Makyio, T.Takeuchi, M.Tamura, K.Nishiyama, H.Takahashi, H.Natsugari, Y.Arata, K.Kasai, Y.Yamada, S.Wakatsuki, R.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.50
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 69.323, 69.323, 120.131, 90.00, 90.00, 120.00
R / Rfree (%) 14.7 / 17.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Caenorhabditis Elegans Galectin Lec-6 (pdb code 3vv1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Caenorhabditis Elegans Galectin Lec-6, PDB code: 3vv1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3vv1

Go back to Magnesium Binding Sites List in 3vv1
Magnesium binding site 1 out of 3 in the Crystal Structure of Caenorhabditis Elegans Galectin Lec-6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Caenorhabditis Elegans Galectin Lec-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:73.8
occ:0.33
O A:HOH447 2.5 61.2 1.0
O A:HOH435 2.8 37.8 1.0
OD1 A:ASP44 4.0 35.7 1.0
O A:ALA43 4.5 31.0 1.0
O A:HOH478 4.9 44.3 1.0

Magnesium binding site 2 out of 3 in 3vv1

Go back to Magnesium Binding Sites List in 3vv1
Magnesium binding site 2 out of 3 in the Crystal Structure of Caenorhabditis Elegans Galectin Lec-6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Caenorhabditis Elegans Galectin Lec-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:17.8
occ:0.33
O B:HOH308 2.4 13.3 1.0
O B:HOH309 2.5 13.6 1.0
MG B:MG204 3.2 16.4 0.3
ND2 B:ASN30 4.3 15.2 1.0
OD1 B:ASN30 4.3 15.1 1.0
O B:ASN103 4.4 18.2 1.0
O B:HOH354 4.7 24.1 1.0
CG B:ASN30 4.7 14.6 1.0
O B:HOH317 4.9 14.9 1.0
ND2 B:ASN103 4.9 13.9 1.0

Magnesium binding site 3 out of 3 in 3vv1

Go back to Magnesium Binding Sites List in 3vv1
Magnesium binding site 3 out of 3 in the Crystal Structure of Caenorhabditis Elegans Galectin Lec-6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Caenorhabditis Elegans Galectin Lec-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:16.4
occ:0.33
O B:HOH309 2.4 13.6 1.0
O B:HOH317 2.4 14.9 1.0
MG B:MG203 3.2 17.8 0.3
OD1 B:ASN30 3.9 15.1 1.0
O B:HOH349 4.1 23.8 1.0
O B:HOH374 4.2 23.6 1.0
ND2 B:ASN103 4.5 13.9 1.0
CG B:ASN30 4.8 14.6 1.0
O B:HOH308 5.0 13.3 1.0

Reference:

H.Makyio, T.Takeuchi, M.Tamura, K.Nishiyama, H.Takahashi, H.Natsugari, Y.Arata, K.Kasai, Y.Yamada, S.Wakatsuki, R.Kato. Structural Basis of Preferential Binding of Fucose-Containing Saccharide By the Caenorhabditis Elegans Galectin Lec-6 Glycobiology V. 23 797 2013.
ISSN: ISSN 0959-6658
PubMed: 23481096
DOI: 10.1093/GLYCOB/CWT017
Page generated: Mon Dec 14 08:59:53 2020

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