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Magnesium in PDB 6c6q: Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor

Protein crystallography data

The structure of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor, PDB code: 6c6q 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) 62.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.712, 135.245, 139.516, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.2

Other elements in 6c6q:

The structure of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

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 (pdb code 6c6q). 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, PDB code: 6c6q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6c6q

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:30.6
occ:1.00
 OD1 A:ASP366 2.0 24.9 1.0
O A:HOH763 2.0 23.8 1.0
OD1 A:ASP410 2.1 30.2 1.0
O A:HOH826 2.1 32.0 1.0
O A:HOH739 2.1 23.5 1.0
O A:HOH871 2.1 32.1 1.0
CG A:ASP410 3.1 30.0 1.0
CG A:ASP366 3.2 28.8 1.0
HA A:ASP366 3.2 29.2 1.0
OD2 A:ASP410 3.6 38.4 1.0
H A:ASP366 3.7 31.3 1.0
CA A:ASP366 3.9 24.3 1.0
CB A:ASP366 3.9 25.9 1.0
HB3 A:ASP366 4.0 31.1 1.0
N A:ASP366 4.1 26.1 1.0
O A:HOH923 4.1 38.8 1.0
HA A:ASP410 4.1 32.3 1.0
O A:THR363 4.2 22.1 1.0
HA A:ASN364 4.2 31.3 1.0
OD2 A:ASP366 4.2 28.4 1.0
OE2 A:GLU407 4.2 26.1 1.0
O A:ASP410 4.3 29.2 1.0
O A:HOH896 4.3 37.0 1.0
CB A:ASP410 4.4 25.0 1.0
CA A:ASP410 4.6 26.9 1.0
C A:ASP410 4.7 26.5 1.0
O A:HOH917 4.8 43.7 1.0
HB2 A:ASP366 4.8 31.1 1.0
HB2 A:ASP410 4.8 30.0 1.0
O F:HOH384 4.9 38.3 1.0

Magnesium binding site 2 out of 6 in 6c6q

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:27.2
occ:1.00
 O A:HOH757 1.9 26.0 1.0
OD2 A:ASP440 2.1 23.8 1.0
OE1 A:GLN438 2.1 21.9 1.0
O A:HOH732 2.1 19.6 1.0
O A:HOH830 2.2 24.9 1.0
O A:HOH768 2.2 25.4 1.0
CD A:GLN438 3.1 22.0 1.0
CG A:ASP440 3.2 24.8 1.0
HE22 A:GLN438 3.2 22.0 1.0
HB2 A:ASP440 3.3 30.0 1.0
HB3 A:ASP443 3.5 32.0 1.0
NE2 A:GLN438 3.6 18.3 1.0
HO2 A:EDO603 3.7 49.6 1.0
CB A:ASP440 3.8 25.0 1.0
OE2 A:GLU447 4.1 24.2 1.0
HB3 A:ASP440 4.1 30.0 1.0
O A:HOH758 4.1 26.1 1.0
O A:ALA445 4.1 22.8 1.0
H22 A:EDO603 4.2 47.0 1.0
OD2 A:ASP443 4.3 32.5 1.0
OD1 A:ASP440 4.3 25.2 1.0
O A:ASP443 4.3 27.2 1.0
CB A:ASP443 4.4 26.6 1.0
O A:HOH841 4.4 35.5 1.0
O A:HOH870 4.4 31.3 1.0
HE21 A:GLN438 4.4 22.0 1.0
HB3 A:ALA445 4.4 30.0 1.0
CG A:GLN438 4.5 19.0 1.0
O2 A:EDO603 4.5 41.4 1.0
HD12 B:LEU350 4.6 33.2 1.0
CG A:ASP443 4.6 27.2 1.0
HG2 A:GLN438 4.6 22.8 1.0
HG3 A:GLN438 4.7 22.8 1.0
O A:HOH833 4.7 23.6 1.0
C2 A:EDO603 4.8 39.2 1.0
HB2 A:GLU447 4.9 26.1 1.0
HB2 A:ASP443 5.0 32.0 1.0
C A:ASP443 5.0 29.2 1.0

Magnesium binding site 3 out of 6 in 6c6q

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:30.2
occ:1.00
 OD1 B:ASP366 2.1 23.0 1.0
O B:HOH760 2.1 20.9 1.0
O B:HOH878 2.1 28.1 1.0
O B:HOH771 2.1 30.6 1.0
OD1 B:ASP410 2.1 28.8 1.0
O B:HOH843 2.1 27.9 1.0
CG B:ASP410 3.2 29.0 1.0
CG B:ASP366 3.2 26.7 1.0
HA B:ASP366 3.3 28.8 1.0
OD2 B:ASP410 3.5 38.1 1.0
H B:ASP366 3.8 26.3 1.0
CA B:ASP366 3.9 24.0 1.0
CB B:ASP366 3.9 25.6 1.0
HB3 B:ASP366 4.0 30.7 1.0
O B:HOH899 4.1 29.0 1.0
OD2 B:ASP366 4.1 31.1 1.0
N B:ASP366 4.2 21.9 1.0
O B:HOH894 4.2 34.4 1.0
OE2 B:GLU407 4.3 26.4 1.0
HA B:ASP410 4.3 33.2 1.0
O B:ASP410 4.3 28.4 1.0
O B:THR363 4.3 23.7 1.0
HA B:ASN364 4.3 32.9 1.0
O B:HOH936 4.4 35.4 1.0
CB B:ASP410 4.5 24.0 1.0
CA B:ASP410 4.7 27.6 1.0
C B:ASP410 4.8 26.0 1.0
HB2 B:ASP366 4.9 30.7 1.0
HB2 B:ASP410 4.9 28.8 1.0

Magnesium binding site 4 out of 6 in 6c6q

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:27.5
occ:1.00
 O B:HOH776 2.1 23.1 1.0
OE1 B:GLN438 2.1 24.1 1.0
O B:HOH747 2.1 24.6 1.0
OD2 B:ASP440 2.1 27.1 1.0
O B:HOH758 2.1 22.9 1.0
O B:HOH801 2.1 22.5 1.0
CD B:GLN438 3.1 21.6 1.0
CG B:ASP440 3.2 26.0 1.0
HE22 B:GLN438 3.2 24.9 1.0
HB2 B:ASP440 3.3 31.7 1.0
HB3 B:ASP443 3.3 38.0 1.0
NE2 B:GLN438 3.6 20.8 1.0
CB B:ASP440 3.7 26.4 1.0
O B:HOH830 4.0 30.4 1.0
HB3 B:ASP440 4.1 31.7 1.0
O B:HOH812 4.1 20.4 1.0
OE2 B:GLU447 4.1 30.2 1.0
O B:ALA445 4.1 24.3 1.0
OD2 B:ASP443 4.2 30.0 1.0
O B:ASP443 4.2 26.8 1.0
CB B:ASP443 4.2 31.6 1.0
OD1 B:ASP440 4.3 24.4 1.0
HD12 A:LEU350 4.4 32.0 1.0
HE21 B:GLN438 4.4 24.9 1.0
CG B:GLN438 4.4 21.4 1.0
CG B:ASP443 4.5 26.7 1.0
HB3 B:ALA445 4.6 33.6 1.0
O B:HOH838 4.6 35.7 1.0
HG2 B:GLN438 4.6 25.7 1.0
HG3 B:GLN438 4.7 25.7 1.0
O B:HOH797 4.7 31.5 1.0
HB2 B:ASP443 4.8 38.0 1.0
O B:HOH784 4.8 19.6 1.0
HB2 B:GLU447 4.9 28.2 1.0
C B:ASP443 4.9 28.8 1.0

Magnesium binding site 5 out of 6 in 6c6q

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg207

b:25.6
occ:1.00
 OD1 D:ASP98 2.1 30.7 1.0
O B:ASN364 2.2 25.8 1.0
O D:LYS94 2.3 24.7 1.0
O B:HOH899 2.4 29.0 1.0
O D:GLY96 2.4 28.6 1.0
CG D:ASP98 3.1 24.0 1.0
H D:LYS94 3.3 30.5 1.0
C B:ASN364 3.3 23.9 1.0
OD2 B:ASP366 3.5 31.1 1.0
C D:GLY96 3.5 27.3 1.0
C D:LYS94 3.5 29.0 1.0
HA B:ALA365 3.6 31.8 1.0
OD2 D:ASP98 3.6 27.9 1.0
H D:GLY96 3.7 30.3 1.0
HB2 B:ASN364 3.8 28.9 1.0
N D:GLY96 3.8 25.3 1.0
H D:ASP98 3.9 33.3 1.0
CG B:ASP366 4.0 26.7 1.0
OD1 B:ASP366 4.0 23.0 1.0
O D:HOH305 4.1 24.9 1.0
N D:ASP98 4.1 27.7 1.0
N D:LYS94 4.1 25.4 1.0
HA2 D:GLY95 4.1 37.5 1.0
O B:HOH713 4.1 25.2 1.0
C D:GLY95 4.2 27.4 1.0
N B:ALA365 4.2 22.9 1.0
CA B:ALA365 4.2 26.5 1.0
CA D:GLY96 4.2 29.6 1.0
O B:HOH894 4.3 34.4 1.0
HG3 D:LYS94 4.3 37.5 1.0
CB D:ASP98 4.3 25.1 1.0
HA D:ASP98 4.3 28.8 1.0
CA B:ASN364 4.3 27.4 1.0
HA B:ASN364 4.3 32.9 1.0
HG23 D:THR93 4.3 35.7 1.0
N D:GLY95 4.4 25.2 1.0
CA D:GLY95 4.4 31.3 1.0
CA D:LYS94 4.4 31.7 1.0
CA D:ASP98 4.5 24.0 1.0
C B:ALA365 4.5 27.2 1.0
CB B:ASN364 4.5 24.1 1.0
HA D:THR93 4.5 30.7 1.0
C D:LEU97 4.5 24.1 1.0
HA D:LEU97 4.5 30.9 1.0
N D:LEU97 4.5 26.6 1.0
HA2 D:GLY96 4.6 35.5 1.0
HB2 D:ASP98 4.6 30.1 1.0
O B:HOH843 4.7 27.9 1.0
O D:GLY95 4.8 30.5 1.0
CA D:LEU97 4.8 25.7 1.0
N B:ASP366 4.8 21.9 1.0
HG2 D:LYS94 4.9 37.5 1.0
H B:ASP366 4.9 26.3 1.0
O B:ALA365 4.9 24.0 1.0
CG D:LYS94 5.0 31.3 1.0
H B:ALA365 5.0 27.4 1.0

Magnesium binding site 6 out of 6 in 6c6q

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg204

b:27.1
occ:1.00
 O A:ASN364 2.2 24.1 1.0
OD1 F:ASP98 2.2 23.6 1.0
O F:GLY96 2.3 24.0 1.0
O A:HOH896 2.3 37.0 1.0
O F:LYS94 2.3 30.0 1.0
CG F:ASP98 3.1 26.6 1.0
H F:LYS94 3.3 34.3 1.0
OD2 A:ASP366 3.3 28.4 1.0
C A:ASN364 3.3 21.7 1.0
C F:GLY96 3.4 24.7 1.0
C F:LYS94 3.5 30.2 1.0
OD2 F:ASP98 3.6 28.5 1.0
HA A:ALA365 3.6 24.0 1.0
H F:GLY96 3.6 35.0 1.0
HB2 A:ASN364 3.7 27.5 1.0
N F:GLY96 3.7 29.2 1.0
H F:ASP98 3.8 30.9 1.0
O A:HOH731 3.9 25.4 1.0
CG A:ASP366 4.0 28.8 1.0
N F:ASP98 4.0 25.8 1.0
CA F:GLY96 4.1 28.8 1.0
N F:LYS94 4.1 28.6 1.0
C F:GLY95 4.1 31.9 1.0
O F:HOH304 4.2 26.6 1.0
HA2 F:GLY95 4.2 33.4 1.0
OD1 A:ASP366 4.2 24.9 1.0
N A:ALA365 4.2 24.6 1.0
CA A:ALA365 4.2 20.0 1.0
CB F:ASP98 4.3 20.8 1.0
CA A:ASN364 4.3 26.1 1.0
HA A:ASN364 4.3 31.3 1.0
HA F:LEU97 4.3 30.9 1.0
O F:HOH384 4.3 38.3 1.0
N F:LEU97 4.3 27.1 1.0
HA F:ASP98 4.4 33.1 1.0
HG23 F:THR93 4.4 35.2 1.0
C F:LEU97 4.4 24.3 1.0
CB A:ASN364 4.4 22.9 1.0
N F:GLY95 4.5 31.2 1.0
CA F:GLY95 4.5 27.8 1.0
HA2 F:GLY96 4.5 34.5 1.0
CA F:LYS94 4.5 30.9 1.0
CA F:ASP98 4.5 27.6 1.0
C A:ALA365 4.5 25.7 1.0
HG3 F:LYS94 4.5 34.8 1.0
HG2 F:LYS94 4.6 34.8 1.0
HA F:THR93 4.6 34.5 1.0
CA F:LEU97 4.6 25.8 1.0
HB2 F:ASP98 4.6 24.9 1.0
O A:HOH763 4.6 23.8 1.0
O F:GLY95 4.7 26.9 1.0
N A:ASP366 4.8 26.1 1.0
H A:ASP366 4.9 31.3 1.0
HA3 F:GLY96 4.9 34.5 1.0
O A:ALA365 4.9 25.4 1.0
CG F:LYS94 5.0 29.0 1.0
H A:ALA365 5.0 29.5 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 Sep 30 20:13:06 2024

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