Calcium in PDB 6e48: Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid

Protein crystallography data

The structure of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid, PDB code: 6e48 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) 63.67 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.091, 152.891, 70.037, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid (pdb code 6e48). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid, PDB code: 6e48:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6e48

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:26.0
occ:1.00
 OD2 A:ASP440 2.1 18.8 1.0
OE1 A:GLN438 2.2 22.4 1.0
O A:HOH922 2.4 34.5 1.0
O A:HOH728 2.5 18.5 1.0
O A:HOH931 2.6 31.0 1.0
O A:HOH942 2.6 33.2 1.0
CG A:ASP440 3.2 19.2 1.0
CD A:GLN438 3.3 16.2 1.0
HB2 A:ASP440 3.3 21.1 1.0
HB3 A:ASP443 3.5 27.2 1.0
HE22 A:GLN438 3.6 18.7 1.0
OE2 A:GLU447 3.7 22.0 1.0
CB A:ASP440 3.8 17.6 1.0
NE2 A:GLN438 3.8 15.6 1.0
HB3 A:ASP440 4.1 21.1 1.0
O A:HOH745 4.2 15.6 1.0
OD1 A:ASP440 4.3 23.1 1.0
O A:ALA445 4.4 18.6 1.0
CB A:ASP443 4.4 22.6 1.0
CG A:GLN438 4.5 22.6 1.0
O A:ASP443 4.5 17.8 1.0
OD2 A:ASP443 4.6 28.3 1.0
HG3 A:GLN438 4.6 27.2 1.0
HG2 A:GLN438 4.6 27.2 1.0
CD A:GLU447 4.7 20.2 1.0
HE21 A:GLN438 4.7 18.7 1.0
CG A:ASP443 4.7 25.0 1.0
O A:HOH751 4.8 31.2 1.0
HD12 B:LEU350 4.8 21.8 1.0
HB2 A:GLU447 4.8 18.7 1.0
O A:HOH866 4.9 14.1 1.0
HB2 A:ASP443 4.9 27.2 1.0
O A:HOH892 4.9 37.8 1.0

Calcium binding site 2 out of 6 in 6e48

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:16.5
occ:1.00
 OD1 A:ASP366 2.3 17.1 1.0
O A:HOH874 2.4 25.3 1.0
OD1 A:ASP410 2.4 15.4 1.0
O A:HOH727 2.5 15.3 1.0
O A:HOH970 2.6 25.2 1.0
O A:HOH888 2.6 28.4 1.0
HA A:ASP366 3.4 19.6 1.0
CG A:ASP410 3.4 23.1 1.0
CG A:ASP366 3.5 18.1 1.0
OD2 A:ASP410 3.8 25.0 1.0
HB3 A:ASP366 3.9 18.4 1.0
H A:ASP366 4.0 14.6 1.0
CB A:ASP366 4.1 15.3 1.0
CA A:ASP366 4.1 16.4 1.0
O A:HOH979 4.3 18.8 1.0
OE2 A:GLU407 4.4 18.7 1.0
O A:ASP410 4.4 21.1 1.0
N A:ASP366 4.4 12.2 1.0
HA A:ASP410 4.4 17.4 1.0
O A:HOH994 4.5 36.2 1.0
OD2 A:ASP366 4.5 18.6 1.0
O A:THR363 4.5 15.4 1.0
O A:HOH1046 4.5 33.4 1.0
HA A:ASN364 4.5 19.9 1.0
CB A:ASP410 4.7 16.9 1.0
C A:ASP410 4.8 18.1 1.0
CA A:ASP410 4.9 14.5 1.0

Calcium binding site 3 out of 6 in 6e48

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:14.1
occ:1.00
 OD1 G:ASP98 2.3 15.6 1.0
O B:ASN364 2.3 16.3 1.0
O B:HOH981 2.3 15.0 1.0
O G:LYS94 2.3 16.3 1.0
OD2 B:ASP366 2.3 17.9 1.0
O G:GLY96 2.4 17.4 1.0
CG G:ASP98 3.3 16.8 1.0
CG B:ASP366 3.4 18.0 1.0
C B:ASN364 3.4 17.7 1.0
H G:LYS94 3.4 23.4 1.0
C G:GLY96 3.5 13.7 1.0
C G:LYS94 3.5 19.3 1.0
HA B:ALA365 3.7 18.9 1.0
H G:GLY96 3.8 21.3 1.0
N G:GLY96 3.8 17.8 1.0
OD1 B:ASP366 3.8 18.4 1.0
OD2 G:ASP98 3.9 16.1 1.0
H G:ASP98 3.9 19.5 1.0
HB2 B:ASN364 4.0 24.4 1.0
HA2 G:GLY95 4.0 24.9 1.0
C G:GLY95 4.1 20.1 1.0
O G:HOH216 4.1 19.7 1.0
N G:LYS94 4.2 19.5 1.0
N G:ASP98 4.2 16.2 1.0
CA G:GLY96 4.2 17.7 1.0
CA B:ALA365 4.2 15.8 1.0
N B:ALA365 4.3 18.0 1.0
O B:HOH1006 4.3 34.6 1.0
HA B:ASN364 4.3 22.4 1.0
HG23 G:THR93 4.4 23.9 1.0
C B:ALA365 4.4 15.4 1.0
CA B:ASN364 4.4 18.7 1.0
CA G:GLY95 4.4 20.8 1.0
O B:HOH701 4.4 19.4 1.0
N G:GLY95 4.4 15.2 1.0
CB G:ASP98 4.4 18.2 1.0
HA G:ASP98 4.5 20.8 1.0
CA G:LYS94 4.5 20.0 1.0
HG3 G:LYS94 4.5 24.6 1.0
HA G:THR93 4.5 20.0 1.0
HA2 G:GLY96 4.6 21.3 1.0
HA G:LEU97 4.6 19.7 1.0
N B:ASP366 4.6 15.1 1.0
CA G:ASP98 4.6 17.3 1.0
HB2 B:ASP366 4.6 20.8 1.0
N G:LEU97 4.6 16.6 1.0
CB B:ASP366 4.6 17.4 1.0
H B:ASP366 4.6 18.1 1.0
CB B:ASN364 4.7 20.4 1.0
C G:LEU97 4.7 20.7 1.0
O G:GLY95 4.7 14.4 1.0
HB2 G:ASP98 4.8 21.8 1.0
O B:ALA365 4.8 13.7 1.0
O B:HOH989 4.8 32.8 1.0
CA G:LEU97 4.9 16.4 1.0
HG2 G:LYS94 4.9 24.6 1.0

Calcium binding site 4 out of 6 in 6e48

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:20.6
occ:1.00
 OD1 B:ASP410 2.3 18.8 1.0
OD1 B:ASP366 2.4 18.4 1.0
O B:HOH849 2.4 23.5 1.0
O B:HOH794 2.4 24.9 1.0
O B:HOH1007 2.5 34.6 1.0
O B:HOH739 2.6 19.5 1.0
O B:HOH989 2.7 32.8 1.0
CG B:ASP410 3.3 21.5 1.0
HA B:ASP366 3.4 17.6 1.0
CG B:ASP366 3.5 18.0 1.0
OD2 B:ASP410 3.7 23.7 1.0
HB3 B:ASP366 4.0 20.8 1.0
CB B:ASP366 4.1 17.4 1.0
CA B:ASP366 4.1 14.6 1.0
H B:ASP366 4.2 18.1 1.0
OE2 B:GLU407 4.3 23.2 1.0
O B:ASP410 4.4 17.9 1.0
HA B:ASP410 4.4 19.5 1.0
O B:HOH983 4.5 37.3 1.0
OD2 B:ASP366 4.5 17.9 1.0
N B:ASP366 4.6 15.1 1.0
O B:THR363 4.6 20.7 1.0
O B:HOH981 4.6 15.0 1.0
O B:HOH1006 4.6 34.6 1.0
HA B:ASN364 4.6 22.4 1.0
CB B:ASP410 4.7 17.3 1.0
C B:ASP410 4.8 20.9 1.0
CA B:ASP410 4.8 16.2 1.0
O B:HOH1049 4.8 42.1 1.0

Calcium binding site 5 out of 6 in 6e48

Go back to Calcium Binding Sites List in 6e48
Calcium binding site 5 out of 6 in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:25.1
occ:1.00
 OE1 B:GLN438 2.1 20.8 1.0
OD2 B:ASP440 2.3 24.9 1.0
O B:HOH938 2.4 29.2 1.0
O B:HOH834 2.5 31.8 1.0
O B:HOH736 2.6 23.9 1.0
O B:HOH924 2.6 32.6 1.0
O B:HOH761 2.6 30.4 1.0
CD B:GLN438 3.3 17.6 1.0
CG B:ASP440 3.4 20.6 1.0
OE2 B:GLU447 3.5 23.6 1.0
HB2 B:ASP440 3.5 26.3 1.0
HE22 B:GLN438 3.5 22.5 1.0
HB3 B:ASP443 3.8 29.9 1.0
NE2 B:GLN438 3.8 18.8 1.0
CB B:ASP440 4.0 21.9 1.0
O B:HOH744 4.3 17.5 1.0
HB3 B:ASP440 4.3 26.3 1.0
O B:ALA445 4.3 20.7 1.0
O B:HOH1004 4.4 48.5 1.0
OD1 B:ASP440 4.4 22.4 1.0
CD B:GLU447 4.4 21.5 1.0
CG B:GLN438 4.5 21.9 1.0
HG3 B:GLN438 4.6 26.2 1.0
O B:HOH966 4.6 41.6 1.0
O B:ASP443 4.6 22.9 1.0
HE21 B:GLN438 4.7 22.5 1.0
HG2 B:GLN438 4.7 26.2 1.0
CB B:ASP443 4.7 24.9 1.0
OD2 B:ASP443 4.7 34.1 1.0
O B:HOH884 4.8 16.4 1.0
HB2 B:GLU447 4.8 21.6 1.0
HB3 B:ALA445 4.8 29.6 1.0
OE1 B:GLU447 4.9 20.9 1.0
HD12 A:LEU350 4.9 25.6 1.0
CG B:ASP443 4.9 27.6 1.0

Calcium binding site 6 out of 6 in 6e48

Go back to Calcium Binding Sites List in 6e48
Calcium binding site 6 out of 6 in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor and Lithocholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:15.0
occ:1.00
 O F:LYS94 2.2 16.0 1.0
OD1 F:ASP98 2.3 16.3 1.0
O A:ASN364 2.3 15.4 1.0
O F:GLY96 2.3 16.9 1.0
O A:HOH979 2.4 18.8 1.0
OD2 A:ASP366 2.4 18.6 1.0
CG F:ASP98 3.3 17.1 1.0
H F:LYS94 3.3 21.3 1.0
CG A:ASP366 3.4 18.1 1.0
C A:ASN364 3.4 15.4 1.0
C F:LYS94 3.5 19.3 1.0
C F:GLY96 3.5 12.8 1.0
H F:GLY96 3.6 18.4 1.0
HA A:ALA365 3.6 17.2 1.0
OD1 A:ASP366 3.8 17.1 1.0
OD2 F:ASP98 3.8 14.0 1.0
N F:GLY96 3.8 15.4 1.0
H F:ASP98 3.9 17.7 1.0
HB2 A:ASN364 3.9 18.6 1.0
HA2 F:GLY95 3.9 24.8 1.0
N F:LYS94 4.0 17.7 1.0
N F:ASP98 4.1 14.8 1.0
O F:HOH303 4.2 19.3 1.0
C F:GLY95 4.2 18.2 1.0
CA F:GLY96 4.2 16.6 1.0
CA A:ALA365 4.2 14.3 1.0
N A:ALA365 4.2 16.5 1.0
HG23 F:THR93 4.3 22.9 1.0
O A:HOH701 4.3 20.0 1.0
C A:ALA365 4.3 13.8 1.0
N F:GLY95 4.4 20.9 1.0
CA F:GLY95 4.4 20.6 1.0
O F:HOH419 4.4 37.2 1.0
HA A:ASN364 4.4 19.9 1.0
CA A:ASN364 4.4 16.6 1.0
CA F:LYS94 4.4 20.4 1.0
HA F:ASP98 4.4 17.7 1.0
HA F:THR93 4.5 19.9 1.0
CB F:ASP98 4.5 16.6 1.0
HA2 F:GLY96 4.5 19.9 1.0
O A:HOH970 4.6 25.2 1.0
N F:LEU97 4.6 16.3 1.0
CA F:ASP98 4.6 14.7 1.0
HA F:LEU97 4.6 19.2 1.0
N A:ASP366 4.6 12.2 1.0
HG2 F:LYS94 4.6 23.4 1.0
CB A:ASN364 4.6 15.5 1.0
C F:LEU97 4.6 16.3 1.0
H A:ASP366 4.7 14.6 1.0
HG3 F:LYS94 4.7 23.4 1.0
CB A:ASP366 4.7 15.3 1.0
HB2 A:ASP366 4.7 18.4 1.0
O A:ALA365 4.7 13.7 1.0
HB2 F:ASP98 4.8 19.9 1.0
CA F:LEU97 4.9 16.0 1.0
O F:GLY95 4.9 20.2 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: Sat Dec 12 06:04:13 2020

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