Magnesium in PDB 5lkg: Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl)

Protein crystallography data

The structure of Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl), PDB code: 5lkg was solved by B.K.Singh, V.Morozov, G.S.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.30 / 1.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.200, 86.680, 97.060, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl) (pdb code 5lkg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl), PDB code: 5lkg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5lkg

Go back to Magnesium Binding Sites List in 5lkg
Magnesium binding site 1 out of 2 in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:20.6
occ:1.00
H A:LEU229 2.3 23.8 1.0
H A:PHE517 2.3 25.9 1.0
HE A:ARG516 2.5 38.9 1.0
HB3 A:PHE517 3.0 28.5 1.0
HA A:SER228 3.1 23.9 1.0
N A:LEU229 3.1 19.8 1.0
N A:PHE517 3.2 21.6 1.0
HA A:ARG516 3.2 25.0 1.0
HH21 A:ARG516 3.2 43.1 1.0
NE A:ARG516 3.3 32.4 1.0
HB2 A:SER228 3.4 25.1 1.0
HB2 A:LEU229 3.4 21.3 1.0
HB3 A:ARG516 3.6 29.0 1.0
HG A:LEU229 3.6 23.4 1.0
CB A:PHE517 3.7 23.8 1.0
HB2 A:PHE517 3.8 28.5 1.0
O A:LEU229 3.8 20.6 1.0
CA A:SER228 3.8 19.9 1.0
HD11 A:ILE231 3.9 32.9 1.0
CA A:ARG516 3.9 20.9 1.0
NH2 A:ARG516 3.9 35.9 1.0
CB A:LEU229 4.0 17.8 1.0
HD2 A:ARG516 4.0 35.8 1.0
C A:SER228 4.0 19.0 1.0
CA A:LEU229 4.0 19.2 1.0
CB A:SER228 4.0 20.9 1.0
CA A:PHE517 4.0 22.4 1.0
C A:ARG516 4.1 21.7 1.0
CZ A:ARG516 4.1 33.5 1.0
CB A:ARG516 4.2 24.2 1.0
CD A:ARG516 4.2 29.8 1.0
CG A:LEU229 4.2 19.5 1.0
HD12 A:LEU229 4.3 23.4 1.0
C A:LEU229 4.4 18.6 1.0
HB3 A:SER228 4.4 25.1 1.0
O A:PHE517 4.5 25.9 1.0
HD13 A:ILE231 4.5 32.9 1.0
CD1 A:ILE231 4.6 27.4 1.0
O A:HOH733 4.7 32.0 1.0
HH22 A:ARG516 4.7 43.1 1.0
C A:PHE517 4.8 23.6 1.0
CD1 A:LEU229 4.8 19.5 1.0
HA A:PHE517 4.8 26.9 1.0
CG A:ARG516 4.8 27.8 1.0
HB3 A:LEU229 4.9 21.3 1.0
HD2 A:PHE517 4.9 30.8 1.0
HA A:LEU229 4.9 23.1 1.0
HB2 A:ARG516 5.0 29.0 1.0

Magnesium binding site 2 out of 2 in 5lkg

Go back to Magnesium Binding Sites List in 5lkg
Magnesium binding site 2 out of 2 in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:18.6
occ:1.00
H B:LEU229 2.4 23.4 1.0
HE B:ARG516 2.4 43.9 1.0
H B:PHE517 2.4 26.0 1.0
HB3 B:PHE517 3.1 26.9 1.0
O B:HOH927 3.1 45.5 1.0
HA B:ARG516 3.2 27.1 1.0
N B:LEU229 3.2 19.5 1.0
NE B:ARG516 3.2 36.6 1.0
N B:PHE517 3.3 21.6 1.0
HA B:SER228 3.3 23.8 1.0
HH21 B:ARG516 3.3 49.1 1.0
HB2 B:LEU229 3.3 21.3 1.0
HB2 B:SER228 3.5 24.9 1.0
HG B:LEU229 3.7 23.3 1.0
HB2 B:PHE517 3.7 26.9 1.0
CB B:PHE517 3.8 22.4 1.0
O B:LEU229 3.8 20.5 1.0
HD2 B:ARG516 3.8 40.2 1.0
HB3 B:ARG516 3.8 30.3 1.0
HD11 B:ILE231 3.9 36.1 1.0
CA B:SER228 3.9 19.8 1.0
NH2 B:ARG516 3.9 41.0 1.0
CA B:ARG516 4.0 22.6 1.0
CB B:LEU229 4.0 17.7 1.0
CA B:LEU229 4.1 18.7 1.0
CZ B:ARG516 4.1 39.8 1.0
C B:SER228 4.1 18.8 1.0
CD B:ARG516 4.1 33.5 1.0
CA B:PHE517 4.1 22.5 1.0
C B:ARG516 4.1 22.6 1.0
CB B:SER228 4.1 20.8 1.0
HD12 B:LEU229 4.2 25.0 1.0
CG B:LEU229 4.3 19.4 1.0
CB B:ARG516 4.3 25.2 1.0
HD13 B:ILE231 4.4 36.1 1.0
C B:LEU229 4.4 18.7 1.0
HB3 B:SER228 4.5 24.9 1.0
CD1 B:ILE231 4.6 30.1 1.0
O B:HOH726 4.6 33.8 1.0
O B:PHE517 4.7 22.9 1.0
HH22 B:ARG516 4.7 49.1 1.0
O B:HOH729 4.8 34.6 1.0
CD1 B:LEU229 4.8 20.8 1.0
HD12 B:ILE231 4.8 36.1 1.0
HB3 B:LEU229 4.8 21.3 1.0
HA B:PHE517 4.8 26.9 1.0
CG B:ARG516 4.9 29.2 1.0
HD3 B:ARG516 4.9 40.2 1.0
HD2 B:PHE517 4.9 30.4 1.0
HA B:LEU229 4.9 22.5 1.0
C B:PHE517 4.9 22.4 1.0
O B:PHE515 5.0 21.0 1.0

Reference:

A.Koromyslova, S.Tripathi, V.Morozov, H.Schroten, G.S.Hansman. Human Norovirus Inhibition By A Human Milk Oligosaccharide. Virology V. 508 81 2017.
ISSN: ISSN 1096-0341
PubMed: 28505592
DOI: 10.1016/J.VIROL.2017.04.032
Page generated: Mon Dec 14 20:47:31 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy