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Magnesium in PDB 6y64: Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine

Protein crystallography data

The structure of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine, PDB code: 6y64 was solved by L.J.Stroh, N.H.Rustmeier, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.47 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 129.620, 81.260, 146.660, 90.00, 115.52, 90.00
R / Rfree (%) 15.2 / 18.2

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine (pdb code 6y64). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine, PDB code: 6y64:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 6y64

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Magnesium binding site 1 out of 14 in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:21.2
occ:1.00
 O A:HOH810 2.1 41.7 1.0
O B:HOH611 2.3 45.5 1.0
O A:HOH601 2.4 22.0 1.0
O B:PHE207 2.5 15.9 1.0
OE2 B:GLU210 2.5 30.7 1.0
OE2 A:GLU38 2.5 19.3 1.0
OE1 A:GLU38 2.7 22.8 1.0
CD A:GLU38 2.9 19.4 1.0
NH2 A:ARG281 3.3 30.1 1.0
C B:PHE207 3.3 15.0 1.0
O A:HOH617 3.4 53.0 1.0
CD B:GLU210 3.7 28.6 1.0
CA B:PHE207 4.0 14.7 1.0
CZ A:ARG281 4.1 29.5 1.0
N B:LYS208 4.2 14.4 1.0
CG A:GLU38 4.4 18.4 1.0
CA B:LYS208 4.5 15.0 1.0
O A:HOH655 4.5 36.9 1.0
O B:PRO206 4.5 13.4 1.0
NH1 A:ARG281 4.6 32.8 1.0
OE1 B:GLU210 4.6 32.0 1.0
O B:LYS208 4.6 14.3 1.0
CG B:GLU210 4.6 25.3 1.0
O B:HOH502 4.7 32.7 1.0
OH A:TYR279 4.7 16.0 1.0
NE A:ARG281 4.8 26.7 1.0
O A:HOH685 4.9 32.8 1.0
CB B:PHE207 4.9 14.5 1.0
C B:LYS208 5.0 14.5 1.0

Magnesium binding site 2 out of 14 in 6y64

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Magnesium binding site 2 out of 14 in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:20.8
occ:1.00
 O E:HOH585 2.2 31.2 0.5
O E:HOH585 2.3 31.4 0.5
O E:HOH501 2.3 22.0 1.0
O A:HOH816 2.5 48.5 1.0
OE2 A:GLU210 2.5 34.9 1.0
OE2 E:GLU38 2.6 23.5 1.0
O A:PHE207 2.6 18.3 1.0
OE1 E:GLU38 2.7 25.6 1.0
CD E:GLU38 2.9 23.1 1.0
C A:PHE207 3.4 16.9 1.0
NH2 E:ARG281 3.4 38.8 1.0
CD A:GLU210 3.8 30.9 1.0
O E:HOH649 3.8 45.5 1.0
CA A:PHE207 4.0 16.4 1.0
N A:LYS208 4.2 16.8 1.0
CZ E:ARG281 4.3 37.6 1.0
O E:HOH643 4.4 47.1 1.0
CG E:GLU38 4.4 22.0 1.0
O E:HOH602 4.4 41.0 1.0
CA A:LYS208 4.4 17.1 1.0
O A:PRO206 4.4 15.6 1.0
O A:HOH605 4.6 41.9 1.0
O A:LYS208 4.6 16.0 1.0
OE1 A:GLU210 4.7 32.8 1.0
CG A:GLU210 4.7 27.5 1.0
OH E:TYR279 4.7 18.9 1.0
NH1 E:ARG281 4.7 40.5 1.0
O A:HOH817 4.9 42.0 1.0
CB A:PHE207 4.9 16.6 1.0
C A:LYS208 5.0 16.4 1.0

Magnesium binding site 3 out of 14 in 6y64

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Magnesium binding site 3 out of 14 in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:13.6
occ:1.00
 OE2 C:GLU210 2.3 25.6 1.0
O C:HOH614 2.3 33.9 1.0
O B:HOH721 2.4 37.7 1.0
O C:HOH615 2.4 17.9 1.0
O C:PHE207 2.4 17.5 1.0
OE1 B:GLU38 2.5 19.7 1.0
OE2 B:GLU38 2.6 17.8 1.0
CD B:GLU38 2.9 18.2 1.0
C C:PHE207 3.3 16.0 1.0
CD C:GLU210 3.5 24.3 1.0
CA C:PHE207 4.1 15.6 1.0
N C:LYS208 4.1 16.0 1.0
CG C:GLU210 4.2 22.6 1.0
NH1 B:ARG281 4.3 34.1 1.0
CA C:LYS208 4.3 16.8 1.0
CG B:GLU38 4.4 16.9 1.0
OE1 C:GLU210 4.4 25.7 1.0
O B:HOH735 4.4 43.4 1.0
O B:HOH633 4.5 30.4 1.0
O C:LYS208 4.5 15.8 1.0
O C:PRO206 4.5 15.5 1.0
O C:HOH717 4.6 36.0 1.0
O C:HOH545 4.6 32.1 1.0
OH B:TYR279 4.9 14.7 1.0
C C:LYS208 4.9 16.3 1.0
CB C:PHE207 5.0 15.9 1.0

Magnesium binding site 4 out of 14 in 6y64

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Magnesium binding site 4 out of 14 in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:28.3
occ:1.00
 O C:HOH690 2.0 45.4 1.0
O D:HOH706 2.1 39.0 1.0
O C:HOH501 2.3 23.6 1.0
O D:PHE207 2.5 19.1 1.0
OE2 C:GLU38 2.6 23.6 1.0
OE1 C:GLU38 2.8 26.5 1.0
O D:HOH726 2.8 47.0 1.0
CD C:GLU38 3.0 23.1 1.0
O C:HOH511 3.1 43.1 1.0
NH1 C:ARG281 3.3 30.7 1.0
C D:PHE207 3.3 17.9 1.0
CA D:PHE207 4.0 17.2 1.0
CZ C:ARG281 4.1 30.8 1.0
N D:LYS208 4.2 17.7 1.0
O C:HOH533 4.3 39.3 1.0
CG C:GLU38 4.4 21.9 1.0
O D:PRO206 4.5 15.7 1.0
CA D:LYS208 4.5 17.7 1.0
NH2 C:ARG281 4.6 32.3 1.0
CG D:GLU210 4.6 20.6 1.0
OH C:TYR279 4.6 19.4 1.0
O D:LYS208 4.6 15.2 1.0
NE C:ARG281 4.9 28.9 1.0
CB D:PHE207 4.9 17.3 1.0

Magnesium binding site 5 out of 14 in 6y64

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Magnesium binding site 5 out of 14 in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg405

b:29.0
occ:1.00
 O C:HOH719 2.2 28.2 1.0
O C:HOH687 2.4 25.1 1.0
O C:HOH734 2.4 32.9 1.0
O C:THR190 2.5 17.4 1.0
OG1 C:THR192 2.5 20.6 1.0
OG1 C:THR190 2.5 21.5 1.0
CG2 C:THR192 3.3 21.0 1.0
C C:THR190 3.4 18.4 1.0
CB C:THR192 3.4 20.6 1.0
N C:THR190 3.6 18.4 1.0
CB C:THR190 3.7 19.8 1.0
CA C:THR190 3.7 18.7 1.0
N C:THR192 4.2 19.4 1.0
CZ C:PHE197 4.2 18.4 1.0
O C:HOH566 4.3 39.0 1.0
O C:HOH735 4.4 45.5 1.0
CA C:THR192 4.4 19.6 1.0
N C:LEU191 4.5 18.1 1.0
O C:HOH529 4.5 39.3 1.0
CE2 C:PHE197 4.7 18.2 1.0
CG2 C:THR190 4.8 20.1 1.0
C C:GLY189 4.8 18.5 1.0
C C:LEU191 4.9 18.9 1.0

Magnesium binding site 6 out of 14 in 6y64

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Magnesium binding site 6 out of 14 in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg406

b:21.5
occ:1.00
 O D:HOH501 2.4 22.5 1.0
OE1 E:GLU210 2.5 33.2 1.0
O E:PHE207 2.5 19.3 1.0
OE2 D:GLU38 2.6 22.4 1.0
O D:HOH714 2.6 44.8 1.0
OE1 D:GLU38 2.7 24.1 1.0
CD D:GLU38 2.9 21.3 1.0
C E:PHE207 3.3 17.7 1.0
NH2 D:ARG281 3.4 34.5 1.0
CD E:GLU210 3.7 30.4 1.0
CA E:PHE207 4.0 17.1 1.0
CZ D:ARG281 4.2 32.8 1.0
N E:LYS208 4.2 17.0 1.0
O D:HOH529 4.3 31.4 1.0
CG D:GLU38 4.4 20.0 1.0
O D:HOH644 4.4 46.0 1.0
CA E:LYS208 4.5 17.3 1.0
O E:PRO206 4.5 16.4 1.0
O E:LYS208 4.6 16.2 1.0
NH1 D:ARG281 4.6 34.7 1.0
CG E:GLU210 4.6 27.4 1.0
OE2 E:GLU210 4.6 33.2 1.0
OH D:TYR279 4.7 18.8 1.0
O E:HOH551 4.8 39.4 1.0
O D:HOH535 4.8 37.3 1.0
O D:HOH649 4.9 43.6 1.0
CB E:PHE207 5.0 17.1 1.0
NE D:ARG281 5.0 29.5 1.0
C E:LYS208 5.0 16.8 1.0

Magnesium binding site 7 out of 14 in 6y64

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Magnesium binding site 7 out of 14 in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg405

b:23.3
occ:1.00
 O F:HOH678 2.3 48.3 1.0
O F:HOH501 2.4 23.0 1.0
OE2 G:GLU210 2.4 32.5 1.0
O G:HOH700 2.5 39.8 1.0
OE2 F:GLU38 2.6 23.3 1.0
O G:PHE207 2.6 17.7 1.0
OE1 F:GLU38 2.7 26.5 1.0
CD F:GLU38 3.0 23.5 1.0
NH2 F:ARG281 3.2 34.7 1.0
C G:PHE207 3.4 16.3 1.0
CD G:GLU210 3.6 28.2 1.0
CZ F:ARG281 4.0 34.1 1.0
CA G:PHE207 4.1 16.0 1.0
N G:LYS208 4.3 15.9 1.0
NH1 F:ARG281 4.4 36.1 1.0
CG F:GLU38 4.4 21.5 1.0
CG G:GLU210 4.5 25.4 1.0
O G:PRO206 4.5 14.7 1.0
CA G:LYS208 4.5 15.8 1.0
OE1 G:GLU210 4.5 32.0 1.0
O G:LYS208 4.6 15.2 1.0
OH F:TYR279 4.7 17.6 1.0
O G:HOH502 4.8 34.2 1.0
NE F:ARG281 4.9 30.4 1.0
O F:HOH535 4.9 36.2 1.0
CB G:PHE207 5.0 16.7 1.0

Magnesium binding site 8 out of 14 in 6y64

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Magnesium binding site 8 out of 14 in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg406

b:37.0
occ:1.00
 O F:THR190 2.4 19.8 1.0
O F:HOH712 2.4 36.8 1.0
OG1 F:THR192 2.5 24.2 1.0
OG1 F:THR190 2.5 26.4 1.0
O F:HOH713 2.5 37.6 1.0
O F:HOH704 2.6 26.0 1.0
C F:THR190 3.3 21.0 1.0
CG2 F:THR192 3.3 24.7 1.0
CB F:THR192 3.4 23.8 1.0
N F:THR190 3.6 20.6 1.0
CB F:THR190 3.6 23.7 1.0
CA F:THR190 3.6 21.5 1.0
N F:THR192 4.0 21.0 1.0
CZ F:PHE197 4.2 17.8 1.0
CA F:THR192 4.4 22.4 1.0
N F:LEU191 4.4 20.1 1.0
CE2 F:PHE197 4.7 17.8 1.0
CG2 F:THR190 4.7 23.8 1.0
C F:LEU191 4.8 21.1 1.0
C F:GLY189 4.8 19.6 1.0
CA F:LEU191 4.9 20.1 1.0

Magnesium binding site 9 out of 14 in 6y64

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Magnesium binding site 9 out of 14 in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg407

b:22.7
occ:1.00
 O J:HOH719 2.1 51.3 1.0
O F:HOH674 2.2 37.0 1.0
O J:HOH501 2.3 23.0 1.0
O F:PHE207 2.5 20.2 1.0
OE2 J:GLU38 2.5 23.9 1.0
O F:HOH662 2.6 41.7 1.0
OE1 J:GLU38 2.7 24.6 1.0
CD J:GLU38 2.9 23.1 1.0
C F:PHE207 3.3 18.7 1.0
NH2 J:ARG281 3.5 35.1 1.0
CA F:PHE207 4.0 18.0 1.0
N F:LYS208 4.2 18.8 1.0
O J:HOH557 4.3 41.8 1.0
CZ J:ARG281 4.3 35.0 1.0
CG J:GLU38 4.4 21.4 1.0
CG F:GLU210 4.4 23.7 1.0
CA F:LYS208 4.5 19.0 1.0
O F:PRO206 4.5 16.7 1.0
O F:LYS208 4.6 18.0 1.0
OH J:TYR279 4.7 19.2 1.0
O F:HOH691 4.7 45.2 1.0
O F:HOH671 4.8 37.0 1.0
NH1 J:ARG281 4.9 37.8 1.0
O F:HOH730 4.9 39.3 1.0
CB F:PHE207 4.9 17.8 1.0
C F:LYS208 5.0 18.3 1.0

Magnesium binding site 10 out of 14 in 6y64

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Magnesium binding site 10 out of 14 in the Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Sheep Polyomavirus VP1 in Complex with 6'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg407

b:18.3
occ:1.00
 O G:HOH587 2.3 40.8 1.0
OE2 H:GLU210 2.3 30.0 1.0
O H:HOH667 2.4 41.3 1.0
O G:HOH556 2.4 20.4 1.0
O H:PHE207 2.4 16.4 1.0
OE2 G:GLU38 2.6 20.6 1.0
OE1 G:GLU38 2.8 23.2 1.0
CD G:GLU38 3.0 19.5 1.0
C H:PHE207 3.3 14.8 1.0
CD H:GLU210 3.6 28.5 1.0
NH1 G:ARG281 3.7 37.0 1.0
CA H:PHE207 4.0 14.0 1.0
N H:LYS208 4.1 14.4 1.0
O G:HOH564 4.2 41.3 1.0
O G:HOH605 4.2 40.6 1.0
O H:HOH514 4.3 38.2 1.0
CA H:LYS208 4.4 14.8 1.0
CG H:GLU210 4.4 24.9 1.0
CG G:GLU38 4.4 18.2 1.0
O H:HOH689 4.5 39.6 1.0
OE1 H:GLU210 4.5 32.5 1.0
O H:PRO206 4.5 13.5 1.0
O H:LYS208 4.6 13.6 1.0
OH G:TYR279 4.7 16.0 1.0
CZ G:ARG281 4.7 35.1 1.0
O G:HOH728 4.9 15.4 0.5
CB H:PHE207 4.9 13.9 1.0
C H:LYS208 4.9 13.8 1.0

Reference:

L.J.Stroh, N.H.Rustmeier, B.S.Blaum, J.Botsch, P.Rossler, F.Wedekink, W.I.Lipkin, N.Mishra, T.Stehle. Structural Basis and Evolution of Glycan Receptor Specificities Within the Polyomavirus Family. Mbio V. 11 2020.
ISSN: ESSN 2150-7511
PubMed: 32723915
DOI: 10.1128/MBIO.00745-20
Page generated: Wed Oct 2 00:10:31 2024

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