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Magnesium in PDB 6y5y: Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose

Protein crystallography data

The structure of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose, PDB code: 6y5y 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) 48.20 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.381, 151.082, 130.617, 90.00, 106.56, 90.00
R / Rfree (%) 16.6 / 20.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose (pdb code 6y5y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose, PDB code: 6y5y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6y5y

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Magnesium binding site 1 out of 10 in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:37.7
occ:1.00
 OE2 A:GLU53 2.2 32.6 1.0
O A:HOH700 2.5 40.3 1.0
O B:SER237 2.6 19.2 1.0
O B:HOH605 2.7 20.4 1.0
O B:HOH720 2.9 35.8 1.0
CD A:GLU53 3.2 33.9 1.0
C B:SER237 3.5 23.5 1.0
O B:HOH637 3.6 48.2 1.0
OE1 A:GLU53 3.7 46.8 1.0
O B:HOH734 3.9 37.2 1.0
OH A:TYR310 4.1 23.3 1.0
NZ A:LYS312 4.2 34.3 1.0
CA B:SER237 4.2 18.0 1.0
N B:ARG238 4.3 18.4 1.0
CA B:ARG238 4.4 20.1 1.0
CG B:GLU240 4.4 29.4 1.0
CG A:GLU53 4.5 29.5 1.0
CD A:LYS312 4.7 31.6 1.0
O B:ARG238 4.7 19.4 1.0
O B:PRO236 4.9 19.1 1.0
CB B:SER237 5.0 16.9 1.0

Magnesium binding site 2 out of 10 in 6y5y

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Magnesium binding site 2 out of 10 in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:48.4
occ:1.00
 OE2 E:GLU53 2.4 43.5 1.0
O A:HOH662 2.7 33.9 1.0
O A:SER237 2.8 24.2 1.0
O A:HOH708 2.8 41.4 1.0
CD E:GLU53 3.3 39.8 1.0
C A:SER237 3.7 26.5 1.0
OE1 E:GLU53 3.8 52.6 1.0
OH E:TYR310 4.1 28.4 1.0
CA A:SER237 4.5 27.6 1.0
N A:ARG238 4.5 22.5 1.0
CE E:LYS312 4.5 45.2 1.0
CG E:GLU53 4.5 34.7 1.0
CA A:ARG238 4.6 21.4 1.0
NZ E:LYS312 4.7 49.2 1.0
O A:ARG238 4.8 21.5 1.0

Magnesium binding site 3 out of 10 in 6y5y

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Magnesium binding site 3 out of 10 in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg409

b:36.7
occ:1.00
 OE2 B:GLU53 2.4 32.2 1.0
O C:HOH594 2.4 24.2 1.0
O C:SER237 2.5 18.6 1.0
O C:HOH717 2.7 43.5 1.0
O B:HOH666 2.8 50.8 1.0
CD B:GLU53 3.4 39.5 1.0
C C:SER237 3.4 19.3 1.0
OE1 B:GLU53 3.7 45.6 1.0
O B:HOH632 3.8 39.8 1.0
OH B:TYR310 4.0 22.1 1.0
N C:ARG238 4.1 15.9 1.0
CA C:SER237 4.2 19.4 1.0
CA C:ARG238 4.2 18.7 1.0
CG C:GLU240 4.4 32.4 1.0
NZ B:LYS312 4.4 39.6 1.0
O C:ARG238 4.5 15.8 1.0
CE B:LYS312 4.6 44.9 1.0
CG B:GLU53 4.7 29.0 1.0
O C:PRO236 4.7 17.3 1.0
C C:ARG238 4.8 15.7 1.0

Magnesium binding site 4 out of 10 in 6y5y

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Magnesium binding site 4 out of 10 in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:52.5
occ:1.00
 O C:HOH743 2.3 47.7 1.0
O D:HOH667 2.6 25.5 1.0
O D:HOH708 2.7 46.0 1.0
O D:SER237 2.8 21.1 1.0
OE2 C:GLU53 3.1 40.1 1.0
C D:SER237 3.7 19.5 1.0
O D:HOH581 3.9 40.5 1.0
CD C:GLU53 4.1 38.4 1.0
OH C:TYR310 4.1 24.0 1.0
CG D:GLU240 4.4 35.5 1.0
OE1 C:GLU53 4.4 56.7 1.0
CE C:LYS312 4.4 39.3 1.0
CA D:SER237 4.5 19.4 1.0
O D:HOH718 4.5 49.4 1.0
N D:ARG238 4.5 17.1 1.0
CA D:ARG238 4.6 19.1 1.0
NZ C:LYS312 4.6 49.9 1.0
O D:ARG238 4.9 17.0 1.0

Magnesium binding site 5 out of 10 in 6y5y

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Magnesium binding site 5 out of 10 in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg408

b:43.3
occ:1.00
 OE2 D:GLU53 2.5 24.4 1.0
O E:HOH694 2.7 42.1 1.0
O E:HOH618 2.7 27.3 1.0
O E:SER237 3.0 22.7 1.0
CD D:GLU53 3.2 32.3 1.0
OE1 D:GLU53 3.3 35.9 1.0
C E:SER237 3.8 20.2 1.0
CE D:LYS312 4.1 35.3 1.0
OH D:TYR310 4.2 25.0 1.0
O D:HOH742 4.3 50.7 1.0
CG E:GLU240 4.4 39.6 1.0
N E:ARG238 4.5 20.0 1.0
CA E:SER237 4.6 23.8 1.0
CG D:GLU53 4.6 30.1 1.0
CA E:ARG238 4.6 22.2 1.0
O E:ARG238 4.8 22.9 1.0
O D:HOH665 4.8 33.8 1.0
O E:PRO236 5.0 22.3 1.0

Magnesium binding site 6 out of 10 in 6y5y

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Magnesium binding site 6 out of 10 in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg407

b:39.4
occ:1.00
 O J:HOH733 2.3 38.8 1.0
O F:HOH729 2.5 34.8 1.0
OE2 J:GLU53 2.5 30.0 1.0
O F:SER237 2.5 21.6 1.0
O F:HOH637 2.7 21.2 1.0
CD J:GLU53 3.3 37.3 1.0
C F:SER237 3.4 24.8 1.0
OE1 J:GLU53 3.5 37.9 1.0
O F:HOH605 3.6 40.3 1.0
OH J:TYR310 4.2 21.9 1.0
CA F:SER237 4.2 18.7 1.0
N F:ARG238 4.2 19.6 1.0
CA F:ARG238 4.3 17.9 1.0
NZ J:LYS312 4.5 37.4 1.0
CG F:GLU240 4.6 35.7 1.0
CG J:GLU53 4.6 29.8 1.0
CE J:LYS312 4.6 42.0 1.0
O F:ARG238 4.7 17.4 1.0
C F:ARG238 5.0 18.9 1.0
CB F:SER237 5.0 18.8 1.0

Magnesium binding site 7 out of 10 in 6y5y

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Magnesium binding site 7 out of 10 in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg408

b:41.7
occ:1.00
 O F:HOH538 2.5 45.9 1.0
OE2 F:GLU53 2.7 29.9 1.0
O G:SER237 2.7 14.3 1.0
O G:HOH677 2.8 23.6 1.0
O G:HOH767 2.8 44.0 1.0
CD F:GLU53 3.5 40.5 1.0
OE1 F:GLU53 3.6 46.4 1.0
C G:SER237 3.6 17.1 1.0
O G:HOH626 3.7 39.2 1.0
OH F:TYR310 3.9 21.4 1.0
CE F:LYS312 4.2 39.8 1.0
CA G:SER237 4.3 17.2 1.0
NZ F:LYS312 4.5 43.1 1.0
O G:HOH789 4.5 41.9 1.0
N G:ARG238 4.5 13.0 1.0
CA G:ARG238 4.6 13.4 1.0
CG G:GLU240 4.8 31.0 1.0
O G:ARG238 4.9 13.3 1.0
O G:PRO236 5.0 14.8 1.0
CG F:GLU53 5.0 30.0 1.0

Magnesium binding site 8 out of 10 in 6y5y

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Magnesium binding site 8 out of 10 in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg409

b:38.6
occ:1.00
 OE2 G:GLU53 2.3 41.8 1.0
O G:HOH731 2.4 46.3 1.0
O H:SER237 2.5 18.0 1.0
O H:HOH647 2.5 21.1 1.0
O H:HOH721 2.6 36.9 1.0
O G:HOH758 2.7 48.0 1.0
CD G:GLU53 3.4 36.7 1.0
C H:SER237 3.4 17.6 1.0
O G:HOH512 3.7 39.5 1.0
OE1 G:GLU53 3.8 48.3 1.0
OH G:TYR310 4.1 24.6 1.0
CA H:SER237 4.2 19.7 1.0
N H:ARG238 4.2 10.7 1.0
NZ G:LYS312 4.3 41.2 1.0
CA H:ARG238 4.3 14.4 1.0
CE G:LYS312 4.3 40.6 1.0
CG H:GLU240 4.4 32.1 1.0
CG G:GLU53 4.6 33.6 1.0
O G:HOH519 4.6 44.4 1.0
O H:ARG238 4.6 14.7 1.0
O H:PRO236 4.8 12.3 1.0
C H:ARG238 4.9 15.7 1.0

Magnesium binding site 9 out of 10 in 6y5y

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Magnesium binding site 9 out of 10 in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg407

b:40.3
occ:1.00
 O H:HOH724 2.2 36.2 1.0
OE2 H:GLU53 2.3 31.4 1.0
O I:HOH673 2.5 23.4 1.0
O I:SER237 2.7 19.2 1.0
CD H:GLU53 3.1 32.9 1.0
O I:HOH750 3.1 39.6 1.0
OE1 H:GLU53 3.4 41.1 1.0
C I:SER237 3.5 17.7 1.0
O I:HOH538 3.6 46.5 1.0
O H:HOH668 3.9 43.6 1.0
OH H:TYR310 4.0 23.2 1.0
CA I:SER237 4.2 17.1 1.0
CG H:GLU53 4.3 34.8 1.0
NZ H:LYS312 4.3 34.2 1.0
N I:ARG238 4.4 12.4 1.0
O I:HOH761 4.4 41.0 1.0
CA I:ARG238 4.5 17.9 1.0
CD H:LYS312 4.5 33.1 1.0
O I:ARG238 4.7 16.1 1.0
CG I:GLU240 4.8 32.7 1.0
O I:PRO236 4.8 15.7 1.0

Magnesium binding site 10 out of 10 in 6y5y

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Magnesium binding site 10 out of 10 in the Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of New Jersey Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg407

b:40.9
occ:1.00
 OE2 I:GLU53 2.6 33.4 1.0
O J:HOH604 2.6 23.4 1.0
O J:HOH740 2.7 37.2 1.0
O J:SER237 3.0 18.5 1.0
CD I:GLU53 3.4 37.0 1.0
C J:SER237 3.7 18.5 1.0
OE1 I:GLU53 3.8 41.6 1.0
OH I:TYR310 4.1 21.5 1.0
CE I:LYS312 4.2 41.6 1.0
CG J:GLU240 4.3 29.3 1.0
CA J:SER237 4.5 17.0 1.0
N J:ARG238 4.5 20.0 1.0
CA J:ARG238 4.5 18.4 1.0
CG I:GLU53 4.6 32.6 1.0
O J:ARG238 4.7 16.8 1.0
O J:PRO236 4.9 16.4 1.0
O J:HOH653 5.0 26.4 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 00:10:28 2024

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