Magnesium in PDB 6h6l: Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)

Protein crystallography data

The structure of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca), PDB code: 6h6l was solved by T.Kilic, G.S.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.71 / 2.50
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 87.000, 87.000, 276.810, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.6

Other elements in 6h6l:

The structure of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) (pdb code 6h6l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca), PDB code: 6h6l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6h6l

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Magnesium binding site 1 out of 8 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:48.7
occ:1.00
 O A:HOH705 2.0 49.8 1.0
OD1 A:ASP410 2.0 83.1 1.0
OD1 A:ASP366 2.6 58.2 1.0
O A:HOH709 2.8 37.6 1.0
CG A:ASP410 3.1 77.5 1.0
OD2 A:ASP410 3.5 80.8 1.0
CG A:ASP366 3.7 56.6 1.0
O A:ASP410 4.0 69.2 1.0
CB A:ASP366 4.2 53.9 1.0
CA A:ASP366 4.3 52.2 1.0
CB A:ASP410 4.4 70.7 1.0
C A:ASP410 4.5 65.2 1.0
CA A:ASP410 4.6 64.6 1.0
OE2 A:GLU407 4.6 61.0 1.0
O A:THR363 4.7 52.8 1.0
N A:ASP366 4.7 51.6 1.0
OD2 A:ASP366 4.8 58.0 1.0

Magnesium binding site 2 out of 8 in 6h6l

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Magnesium binding site 2 out of 8 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:40.4
occ:1.00
 OE1 A:GLN438 2.1 75.4 1.0
O A:HOH714 2.3 35.8 1.0
OD2 A:ASP440 2.6 55.9 1.0
OE2 A:GLU447 2.6 57.4 1.0
CD A:GLN438 3.2 68.0 1.0
CG A:ASP440 3.7 55.6 1.0
CD A:GLU447 3.8 55.8 1.0
NE2 A:GLN438 3.8 66.8 1.0
O A:ALA445 4.2 47.3 1.0
CG A:GLN438 4.4 62.0 1.0
OD2 A:ASP443 4.4 68.5 1.0
CB A:ASP440 4.4 52.9 1.0
OE1 A:GLU447 4.5 57.2 1.0
O A:HOH715 4.6 42.9 1.0
OD1 A:ASP440 4.7 57.2 1.0
CB A:ASP443 4.7 64.2 1.0
CG A:GLU447 4.8 51.0 1.0
CB A:GLU447 4.8 47.5 1.0
CG A:ASP443 4.9 67.2 1.0
O A:ASP443 4.9 56.0 1.0

Magnesium binding site 3 out of 8 in 6h6l

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Magnesium binding site 3 out of 8 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:37.5
occ:1.00
 O B:HOH735 2.0 39.5 1.0
OD1 B:ASP366 2.1 70.0 1.0
O B:HOH739 2.1 39.8 1.0
O B:HOH759 2.2 36.1 1.0
OD1 B:ASP410 2.6 52.7 1.0
O B:HOH710 2.7 39.1 1.0
CG B:ASP366 3.3 65.2 1.0
CG B:ASP410 3.6 52.6 1.0
OD2 B:ASP410 4.0 55.0 1.0
CA B:ASP366 4.0 51.2 1.0
O F:HOH507 4.0 57.3 1.0
CB B:ASP366 4.1 57.8 1.0
N B:ASP366 4.1 47.7 1.0
OD2 B:ASP366 4.2 67.8 1.0
O B:THR363 4.3 44.6 1.0
O B:ASP410 4.8 49.3 1.0
OE2 B:GLU407 4.9 50.8 1.0
CB B:ASP410 5.0 48.5 1.0
CA B:ASN364 5.0 44.1 1.0

Magnesium binding site 4 out of 8 in 6h6l

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Magnesium binding site 4 out of 8 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:48.0
occ:1.00
 O B:HOH724 2.1 48.5 1.0
O B:HOH738 2.3 48.4 1.0
OE1 B:GLN438 2.4 41.7 1.0
OD2 B:ASP440 2.7 51.1 1.0
OE1 B:GLU447 2.7 47.5 1.0
CD B:GLN438 3.5 41.1 1.0
CG B:ASP440 3.8 50.5 1.0
CD B:GLU447 3.8 45.5 1.0
NE2 B:GLN438 3.9 41.2 1.0
O B:ALA445 4.1 43.4 1.0
CB B:ASP440 4.2 48.0 1.0
OD2 B:ASP443 4.3 64.4 1.0
OE2 B:GLU447 4.5 44.8 1.0
O B:HOH755 4.5 29.7 1.0
O B:HOH729 4.6 40.6 1.0
CB B:GLU447 4.6 39.5 1.0
CG B:GLU447 4.7 42.4 1.0
CB B:ASP443 4.8 60.9 1.0
O B:ASP443 4.8 53.4 1.0
CG B:GLN438 4.8 38.6 1.0
OD1 B:ASP440 4.9 51.7 1.0
CG B:ASP443 4.9 63.8 1.0

Magnesium binding site 5 out of 8 in 6h6l

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Magnesium binding site 5 out of 8 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:40.8
occ:1.00
 OD1 C:ASP366 2.1 85.2 1.0
OD1 C:ASP410 2.2 71.1 1.0
O C:HOH730 2.3 55.1 1.0
O C:HOH711 2.4 54.8 1.0
O C:HOH747 2.4 46.4 1.0
CG C:ASP410 3.1 70.5 1.0
CG C:ASP366 3.3 80.3 1.0
OD2 C:ASP410 3.3 72.2 1.0
CB C:ASP366 3.9 73.0 1.0
CA C:ASP366 4.1 65.6 1.0
OD2 C:ASP366 4.2 82.7 1.0
N C:ASP366 4.3 62.6 1.0
O C:ASP410 4.4 68.1 1.0
CB C:ASP410 4.5 67.4 1.0
O C:THR363 4.6 59.6 1.0
OE1 C:GLU407 4.9 64.5 1.0
CA C:ASP410 4.9 64.4 1.0
C C:ASP410 4.9 65.6 1.0

Magnesium binding site 6 out of 8 in 6h6l

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Magnesium binding site 6 out of 8 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:48.3
occ:1.00
 O C:HOH707 2.1 47.2 1.0
O C:HOH718 2.1 47.3 1.0
OE1 C:GLN438 2.4 42.5 1.0
OE2 C:GLU447 2.5 63.7 1.0
OD2 C:ASP440 2.6 58.6 1.0
CD C:GLN438 3.3 40.6 1.0
NE2 C:GLN438 3.5 39.6 1.0
CD C:GLU447 3.7 61.1 1.0
CG C:ASP440 3.7 58.3 1.0
O C:ALA445 3.8 46.1 1.0
OD2 C:ASP443 4.2 66.7 1.0
CB C:ASP440 4.2 54.9 1.0
OE1 C:GLU447 4.4 61.5 1.0
CB C:ASP443 4.6 60.9 1.0
CB C:GLU447 4.6 54.9 1.0
O C:ASP443 4.6 52.9 1.0
CG C:GLN438 4.7 39.4 1.0
CG C:GLU447 4.7 57.0 1.0
OD1 C:ASP440 4.8 60.6 1.0
CG C:ASP443 4.8 64.9 1.0
O C:HOH734 4.8 44.8 1.0
C C:ALA445 4.9 45.5 1.0

Magnesium binding site 7 out of 8 in 6h6l

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Magnesium binding site 7 out of 8 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:36.2
occ:1.00
 OD1 D:ASP366 2.0 69.1 1.0
O D:HOH738 2.1 38.2 1.0
O D:HOH758 2.1 39.5 1.0
OD1 D:ASP410 2.3 54.3 1.0
O D:HOH757 2.4 74.8 1.0
O D:HOH720 2.5 41.9 1.0
CG D:ASP366 3.1 64.9 1.0
CG D:ASP410 3.2 53.8 1.0
OD2 D:ASP410 3.4 55.8 1.0
CB D:ASP366 3.8 58.3 1.0
CA D:ASP366 4.0 51.3 1.0
OD2 D:ASP366 4.1 67.8 1.0
O H:HOH511 4.2 54.0 1.0
N D:ASP366 4.2 46.4 1.0
O D:ASP410 4.6 50.2 1.0
O D:THR363 4.6 41.7 1.0
CB D:ASP410 4.6 50.0 1.0
OE2 D:GLU407 4.8 48.0 1.0
CA D:ASP410 4.9 47.5 1.0

Magnesium binding site 8 out of 8 in 6h6l

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Magnesium binding site 8 out of 8 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:47.1
occ:1.00
 O D:HOH750 2.3 50.3 1.0
O D:HOH706 2.4 41.2 1.0
OE1 D:GLN438 2.4 41.9 1.0
OD2 D:ASP440 2.5 54.9 1.0
OE1 D:GLU447 2.6 49.6 1.0
CD D:GLN438 3.4 40.6 1.0
NE2 D:GLN438 3.7 40.5 1.0
CG D:ASP440 3.7 53.9 1.0
CD D:GLU447 3.8 48.9 1.0
O D:ALA445 4.0 48.7 1.0
CB D:ASP440 4.3 50.3 1.0
OD2 D:ASP443 4.4 68.5 1.0
CB D:GLU447 4.5 43.3 1.0
OE2 D:GLU447 4.5 49.2 1.0
CG D:GLU447 4.6 46.0 1.0
O D:HOH740 4.7 35.9 1.0
OD1 D:ASP440 4.7 55.7 1.0
CG D:GLN438 4.8 38.3 1.0
CB D:ASP443 4.9 63.2 1.0
O D:ASP443 4.9 59.9 1.0
CA D:GLU447 5.0 41.0 1.0

Reference:

T.Kilic, A.Koromyslova, V.Malak, G.S.Hansman. Crystal Structures of Murine Norovirus Protruding Domain with Conjugated Bile Acid Reveal A Novel Binding Pocket. To Be Published.
Page generated: Mon Dec 14 22:47:39 2020

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