Magnesium in PDB 6e47: Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid

Protein crystallography data

The structure of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid, PDB code: 6e47 was solved by C.A.Nelson, D.H.Fremont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.70 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.105, 134.824, 139.592, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid (pdb code 6e47). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid, PDB code: 6e47:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6e47

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Magnesium binding site 1 out of 6 in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid


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 the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:35.4
occ:1.00
OD1 A:ASP410 2.0 28.9 1.0
O A:HOH788 2.0 29.2 1.0
O A:HOH702 2.1 23.7 1.0
OD1 A:ASP366 2.1 36.1 1.0
O A:HOH826 2.1 34.8 1.0
O A:HOH782 2.2 30.4 1.0
HA A:ASP366 3.0 30.5 1.0
CG A:ASP410 3.1 33.7 1.0
CG A:ASP366 3.2 28.4 1.0
OD2 A:ASP410 3.5 38.7 1.0
CA A:ASP366 3.8 25.4 1.0
CB A:ASP366 3.8 25.4 1.0
H A:ASP366 3.8 34.3 1.0
HB3 A:ASP366 3.9 30.5 1.0
OE2 A:GLU407 4.0 30.9 1.0
HA A:ASP410 4.0 34.4 1.0
O A:THR363 4.0 28.0 1.0
O A:ASP410 4.1 33.5 1.0
O F:HOH320 4.1 46.4 1.0
N A:ASP366 4.2 28.6 1.0
OD2 A:ASP366 4.2 31.9 1.0
O A:HOH842 4.3 35.0 1.0
HA A:ASN364 4.3 41.8 1.0
CB A:ASP410 4.4 29.3 1.0
CA A:ASP410 4.5 28.6 1.0
C A:ASP410 4.5 38.9 1.0
O F:HOH332 4.7 41.3 1.0
HB2 A:ASP366 4.8 30.5 1.0
HB2 A:ASP410 4.9 35.2 1.0
HB3 A:ASP410 5.0 35.2 1.0

Magnesium binding site 2 out of 6 in 6e47

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid


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 the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:32.1
occ:1.00
O A:HOH709 2.0 31.1 1.0
OE1 A:GLN438 2.0 30.1 1.0
OD2 A:ASP440 2.1 26.1 1.0
O A:HOH799 2.1 32.7 1.0
O A:HOH725 2.1 31.9 1.0
O A:HOH708 2.2 39.3 1.0
CD A:GLN438 3.1 26.4 1.0
CG A:ASP440 3.2 34.9 1.0
HB2 A:ASP440 3.2 37.9 1.0
HB3 A:ASP443 3.3 42.4 1.0
HE22 A:GLN438 3.4 32.7 1.0
O A:HOH845 3.7 44.6 1.0
CB A:ASP440 3.7 31.5 1.0
NE2 A:GLN438 3.7 27.2 1.0
OE2 A:GLU447 4.0 34.5 1.0
HB3 A:ASP440 4.1 37.9 1.0
O A:HOH749 4.1 28.6 1.0
O A:ALA445 4.2 32.3 1.0
OD2 A:ASP443 4.2 47.3 1.0
CB A:ASP443 4.3 35.3 1.0
OD1 A:ASP440 4.3 32.9 1.0
O A:ASP443 4.3 39.4 1.0
CG A:GLN438 4.4 33.1 1.0
HG2 A:GLN438 4.5 39.7 1.0
CG A:ASP443 4.5 41.6 1.0
HE21 A:GLN438 4.5 32.7 1.0
HG3 A:GLN438 4.6 39.7 1.0
HD12 B:LEU350 4.7 38.3 1.0
HB2 A:ASP443 4.8 42.4 1.0
HB2 A:GLU447 4.8 29.2 1.0
HB3 A:ALA445 4.8 40.7 1.0
O A:HOH784 4.8 23.3 1.0
CD A:GLU447 4.9 31.4 1.0
C A:ASP443 5.0 36.1 1.0
H A:ASP443 5.0 52.3 1.0

Magnesium binding site 3 out of 6 in 6e47

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid


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 the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:34.8
occ:1.00
OD1 B:ASP410 2.1 30.5 1.0
OD1 B:ASP366 2.1 30.5 1.0
O B:HOH792 2.1 33.8 1.0
O B:HOH727 2.1 31.8 1.0
O B:HOH721 2.2 35.6 1.0
O B:HOH802 2.2 39.1 1.0
HA B:ASP366 3.1 30.5 1.0
CG B:ASP410 3.1 31.2 1.0
CG B:ASP366 3.2 31.2 1.0
OD2 B:ASP410 3.5 46.3 1.0
CA B:ASP366 3.8 25.4 1.0
H B:ASP366 3.8 36.2 1.0
CB B:ASP366 3.9 32.7 1.0
HB3 B:ASP366 3.9 39.2 1.0
N B:ASP366 4.2 30.1 1.0
HA B:ASP410 4.2 38.9 1.0
OE2 B:GLU407 4.3 28.9 1.0
O G:HOH332 4.3 36.2 1.0
OD2 B:ASP366 4.3 35.7 1.0
O B:ASP410 4.3 32.9 1.0
CB B:ASP410 4.4 29.6 1.0
O B:THR363 4.4 22.5 1.0
HA B:ASN364 4.4 40.3 1.0
O B:HOH858 4.6 42.3 1.0
O B:HOH846 4.6 38.3 1.0
CA B:ASP410 4.6 32.4 1.0
C B:ASP410 4.7 34.3 1.0
HB2 B:ASP410 4.7 35.6 1.0
HB2 B:ASP366 4.8 39.2 1.0

Magnesium binding site 4 out of 6 in 6e47

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:27.9
occ:1.00
OE1 B:GLN438 2.1 29.1 1.0
O B:HOH731 2.1 24.7 1.0
OD2 B:ASP440 2.1 32.7 1.0
O B:HOH707 2.1 30.7 1.0
O B:HOH783 2.2 27.9 1.0
O B:HOH705 2.2 30.4 1.0
CD B:GLN438 3.1 24.8 1.0
HE22 B:GLN438 3.1 29.6 1.0
CG B:ASP440 3.2 34.1 1.0
HB2 B:ASP440 3.3 37.2 1.0
HB3 B:ASP443 3.3 39.9 1.0
NE2 B:GLN438 3.5 24.7 1.0
H21 B:EDO605 3.7 57.7 1.0
CB B:ASP440 3.7 31.0 1.0
OE2 B:GLU447 3.9 32.5 1.0
O B:ALA445 4.0 25.5 1.0
HB3 B:ASP440 4.0 37.2 1.0
O B:HOH801 4.0 29.2 1.0
CB B:ASP443 4.2 33.2 1.0
OD1 B:ASP440 4.2 35.6 1.0
O B:HOH780 4.3 40.7 1.0
O B:ASP443 4.3 37.9 1.0
HE21 B:GLN438 4.3 29.6 1.0
OD2 B:ASP443 4.4 42.9 1.0
HB3 B:ALA445 4.4 31.1 1.0
HD12 A:LEU350 4.4 42.3 1.0
CG B:GLN438 4.4 27.9 1.0
C2 B:EDO605 4.5 48.1 1.0
CG B:ASP443 4.5 37.8 1.0
HG2 B:GLN438 4.6 33.5 1.0
H22 B:EDO605 4.7 57.7 1.0
HG3 B:GLN438 4.7 33.5 1.0
HB2 B:ASP443 4.8 39.9 1.0
H B:ALA445 4.8 35.6 1.0
O2 B:EDO605 4.8 48.3 1.0
HB2 B:GLU447 4.9 31.3 1.0
C B:ASP443 4.9 37.8 1.0
HO2 B:EDO605 4.9 58.0 1.0
CD B:GLU447 5.0 26.8 1.0
O B:HOH748 5.0 26.1 1.0

Magnesium binding site 5 out of 6 in 6e47

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Magnesium binding site 5 out of 6 in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:25.3
occ:1.00
O A:ASN364 2.1 33.7 1.0
OD1 F:ASP98 2.1 35.7 1.0
O A:HOH842 2.2 35.0 1.0
O F:LYS94 2.3 34.9 1.0
O F:GLY96 2.3 30.4 1.0
OD2 A:ASP366 2.8 31.9 1.0
CG F:ASP98 3.2 22.9 1.0
C A:ASN364 3.3 28.4 1.0
H F:LYS94 3.4 47.5 1.0
C F:GLY96 3.5 33.1 1.0
H F:GLY96 3.5 36.5 1.0
C F:LYS94 3.5 37.9 1.0
CG A:ASP366 3.6 28.4 1.0
HB2 A:ASN364 3.7 33.1 1.0
N F:GLY96 3.7 30.4 1.0
OD2 F:ASP98 3.7 27.0 1.0
HA A:ALA365 3.8 34.2 1.0
H F:ASP98 3.8 34.0 1.0
OD1 A:ASP366 3.9 36.1 1.0
N F:ASP98 4.0 28.3 1.0
HA2 F:GLY95 4.0 42.9 1.0
CA F:GLY96 4.1 22.3 1.0
N F:LYS94 4.2 39.5 1.0
HA A:ASN364 4.2 41.8 1.0
C F:GLY95 4.2 30.1 1.0
CA A:ASN364 4.2 34.8 1.0
N A:ALA365 4.2 29.6 1.0
CA A:ALA365 4.3 28.5 1.0
HA F:ASP98 4.3 32.8 1.0
CB F:ASP98 4.3 31.3 1.0
CB A:ASN364 4.4 27.5 1.0
C A:ALA365 4.4 26.5 1.0
CA F:GLY95 4.4 35.7 1.0
N F:GLY95 4.4 38.2 1.0
CA F:ASP98 4.5 27.3 1.0
CA F:LYS94 4.5 37.8 1.0
C F:LEU97 4.5 31.9 1.0
HA F:LEU97 4.5 37.4 1.0
N F:LEU97 4.5 35.8 1.0
HA2 F:GLY96 4.5 26.8 1.0
HG3 F:LYS94 4.6 43.0 1.0
HB2 F:ASP98 4.6 37.6 1.0
HA F:THR93 4.7 36.1 1.0
HG23 F:THR93 4.7 39.0 1.0
O2 F:EDO202 4.7 32.1 1.0
N A:ASP366 4.7 28.6 1.0
O A:ALA365 4.7 24.5 1.0
HB2 A:ASP366 4.7 30.5 1.0
CA F:LEU97 4.8 31.1 1.0
CB A:ASP366 4.8 25.4 1.0
HG2 F:LYS94 4.8 43.0 1.0
H A:ASP366 4.9 34.3 1.0
O F:GLY95 4.9 36.8 1.0
OD1 A:ASN364 4.9 37.4 1.0
O A:HOH788 5.0 29.2 1.0
HA3 F:GLY96 5.0 26.8 1.0
HO2 F:EDO202 5.0 38.6 1.0

Magnesium binding site 6 out of 6 in 6e47

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Magnesium binding site 6 out of 6 in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg201

b:25.6
occ:1.00
OD1 G:ASP98 2.1 41.2 1.0
O G:HOH332 2.1 36.2 1.0
O B:ASN364 2.2 31.0 1.0
O G:GLY96 2.2 27.4 1.0
O G:LYS94 2.4 35.8 1.0
OD2 B:ASP366 2.8 35.7 1.0
CG G:ASP98 3.1 22.9 1.0
C G:GLY96 3.3 32.1 1.0
C B:ASN364 3.4 28.4 1.0
H G:GLY96 3.4 33.5 1.0
H G:LYS94 3.4 51.1 1.0
OD2 G:ASP98 3.5 36.5 1.0
HO2 G:EDO203 3.5 44.9 1.0
C G:LYS94 3.6 34.6 1.0
CG B:ASP366 3.6 31.2 1.0
N G:GLY96 3.6 27.9 1.0
HA B:ALA365 3.6 32.4 1.0
HB2 B:ASN364 3.8 38.6 1.0
H G:ASP98 3.9 44.2 1.0
OD1 B:ASP366 3.9 30.5 1.0
CA G:GLY96 4.0 30.9 1.0
N G:ASP98 4.1 36.8 1.0
C G:GLY95 4.1 33.1 1.0
HA2 G:GLY95 4.1 36.9 1.0
O2 G:EDO203 4.1 37.4 1.0
CA B:ALA365 4.2 27.0 1.0
N G:LYS94 4.2 42.5 1.0
N B:ALA365 4.2 29.4 1.0
C B:ALA365 4.3 27.8 1.0
CB G:ASP98 4.3 34.2 1.0
O B:HOH721 4.3 35.6 1.0
HA2 G:GLY96 4.3 37.1 1.0
HA B:ASN364 4.4 40.3 1.0
CA B:ASN364 4.4 33.5 1.0
N G:LEU97 4.4 27.1 1.0
O B:HOH846 4.4 38.3 1.0
HA G:LEU97 4.4 36.9 1.0
HG3 G:LYS94 4.4 44.9 1.0
HA G:ASP98 4.5 37.2 1.0
CA G:GLY95 4.5 30.7 1.0
N G:GLY95 4.5 37.0 1.0
C G:LEU97 4.5 35.3 1.0
CB B:ASN364 4.5 32.1 1.0
CA G:LYS94 4.5 37.4 1.0
CA G:ASP98 4.6 31.0 1.0
HG23 G:THR93 4.6 45.5 1.0
N B:ASP366 4.6 30.1 1.0
O B:ALA365 4.6 28.6 1.0
CA G:LEU97 4.7 30.7 1.0
HB2 G:ASP98 4.7 41.1 1.0
HB2 B:ASP366 4.7 39.2 1.0
HA G:THR93 4.7 34.9 1.0
H B:ASP366 4.7 36.2 1.0
CB B:ASP366 4.8 32.7 1.0
HA3 G:GLY96 4.8 37.1 1.0
O G:GLY95 4.8 32.1 1.0

Reference:

C.A.Nelson, C.B.Wilen, Y.N.Dai, R.C.Orchard, A.S.Kim, R.A.Stegeman, L.L.Hsieh, T.J.Smith, H.W.Virgin, D.H.Fremont. Structural Basis For Murine Norovirus Engagement of Bile Acids and the CD300LF Receptor. Proc. Natl. Acad. Sci. V. 115 E9201 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30194229
DOI: 10.1073/PNAS.1805797115
Page generated: Mon Dec 14 22:37:57 2020

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