Atomistry » Calcium » PDB 6e48-6eku » 6e48
Atomistry »
  Calcium »
    PDB 6e48-6eku »
      6e48 »

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

Go back to Calcium Binding Sites List in 6e48
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

Go back to Calcium Binding Sites List in 6e48
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

Go back to Calcium Binding Sites List in 6e48
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

Go back to Calcium Binding Sites List in 6e48
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: Mon Jul 15 18:10:14 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy