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Magnesium in PDB 6y5x: Structure of Apo New Jersey Polyomavirus VP1

Protein crystallography data

The structure of Structure of Apo New Jersey Polyomavirus VP1, PDB code: 6y5x 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) 48.31 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.480, 151.760, 130.910, 90.00, 106.85, 90.00
R / Rfree (%) 20.2 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Apo New Jersey Polyomavirus VP1 (pdb code 6y5x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of Apo New Jersey Polyomavirus VP1, PDB code: 6y5x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6y5x

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Magnesium binding site 1 out of 9 in the Structure of Apo New Jersey Polyomavirus VP1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Apo New Jersey Polyomavirus VP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:39.5
occ:1.00
 OE2 A:GLU53 2.6 40.7 1.0
O B:HOH569 2.7 29.1 1.0
OE2 B:GLU240 3.0 37.5 1.0
CD A:GLU53 3.5 32.5 1.0
O B:SER237 3.5 24.5 1.0
NZ A:LYS312 3.7 36.0 1.0
CE A:LYS312 3.8 37.8 1.0
CD B:GLU240 3.9 36.4 1.0
OE1 A:GLU53 3.9 33.6 1.0
CG B:GLU240 4.0 31.5 1.0
C B:SER237 4.3 27.1 1.0
OH A:TYR310 4.4 28.0 1.0
CG A:GLU53 4.7 30.5 1.0
OE1 A:GLU51 4.9 42.2 1.0
CD A:LYS312 4.9 35.0 1.0

Magnesium binding site 2 out of 9 in 6y5x

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Magnesium binding site 2 out of 9 in the Structure of Apo New Jersey Polyomavirus VP1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Apo New Jersey Polyomavirus VP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:34.3
occ:1.00
 O E:HOH581 2.3 27.4 1.0
OE2 E:GLU53 2.4 27.2 1.0
O A:HOH574 2.5 21.9 1.0
O E:HOH569 2.5 29.9 1.0
O A:SER237 2.7 21.7 1.0
CD E:GLU53 3.4 27.3 1.0
C A:SER237 3.6 18.2 1.0
OE1 E:GLU53 3.7 30.8 1.0
CA A:ARG238 4.3 20.0 1.0
N A:ARG238 4.3 17.4 1.0
CE E:LYS312 4.3 31.7 1.0
OH E:TYR310 4.4 21.3 1.0
CA A:SER237 4.5 19.5 1.0
NZ E:LYS312 4.5 31.6 1.0
CG E:GLU53 4.7 28.8 1.0
O A:ARG238 4.8 20.0 1.0
C A:ARG238 4.9 20.0 1.0
O A:PRO236 4.9 21.4 1.0

Magnesium binding site 3 out of 9 in 6y5x

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Magnesium binding site 3 out of 9 in the Structure of Apo New Jersey Polyomavirus VP1


Mono view


Stereo pair view

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

b:43.7
occ:1.00
 O C:SER237 2.3 27.5 1.0
OE1 C:GLU240 2.6 33.4 1.0
O C:HOH573 2.8 27.3 1.0
OE1 B:GLU53 3.1 44.4 1.0
OE2 B:GLU53 3.2 33.8 1.0
C C:SER237 3.4 27.8 1.0
CD B:GLU53 3.5 35.1 1.0
CD C:GLU240 3.7 38.3 1.0
CA C:ARG238 4.1 25.6 1.0
N C:ARG238 4.1 25.0 1.0
CG C:GLU240 4.3 34.4 1.0
CA C:SER237 4.4 25.7 1.0
OH B:TYR310 4.5 28.4 1.0
OE2 C:GLU240 4.6 35.1 1.0
CE B:LYS312 4.8 32.9 1.0
O C:ARG238 4.8 24.5 1.0
C C:ARG238 4.9 23.6 1.0
CG B:GLU53 4.9 30.0 1.0

Magnesium binding site 4 out of 9 in 6y5x

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Magnesium binding site 4 out of 9 in the Structure of Apo New Jersey Polyomavirus VP1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Apo New Jersey Polyomavirus VP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:42.5
occ:1.00
 OE1 D:GLU240 2.5 37.1 1.0
OE2 C:GLU53 2.6 32.9 1.0
O D:SER237 2.7 27.4 1.0
O D:HOH567 3.0 27.1 1.0
CD C:GLU53 3.4 34.2 1.0
OE1 C:GLU53 3.5 37.8 1.0
CD D:GLU240 3.6 35.9 1.0
C D:SER237 3.7 25.0 1.0
CG D:GLU240 4.1 25.9 1.0
CE C:LYS312 4.5 38.5 1.0
CA D:ARG238 4.5 26.9 1.0
N D:ARG238 4.5 23.1 1.0
OH C:TYR310 4.6 26.6 1.0
CA D:SER237 4.6 23.2 1.0
NZ C:LYS312 4.6 37.0 1.0
OE2 D:GLU240 4.6 29.2 1.0
CG C:GLU53 4.7 27.8 1.0

Magnesium binding site 5 out of 9 in 6y5x

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Magnesium binding site 5 out of 9 in the Structure of Apo New Jersey Polyomavirus VP1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Apo New Jersey Polyomavirus VP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg405

b:39.6
occ:1.00
 O D:HOH600 2.4 35.3 1.0
O E:HOH603 2.5 32.8 1.0
OE2 D:GLU53 2.6 31.5 1.0
OE2 E:GLU240 2.7 33.7 1.0
O E:HOH558 2.8 23.5 1.0
O E:SER237 2.9 26.5 1.0
CD D:GLU53 3.5 33.5 1.0
CD E:GLU240 3.7 36.2 1.0
C E:SER237 3.8 22.5 1.0
OE1 D:GLU53 3.9 35.3 1.0
CG E:GLU240 4.0 28.7 1.0
CA E:ARG238 4.4 21.9 1.0
OH D:TYR310 4.5 23.9 1.0
N E:ARG238 4.5 19.7 1.0
CE D:LYS312 4.6 33.4 1.0
CA E:SER237 4.6 21.9 1.0
CG D:GLU53 4.7 29.8 1.0
O E:ARG238 4.8 21.8 1.0
OE1 E:GLU240 4.8 29.3 1.0
NZ D:LYS312 4.9 31.0 1.0

Magnesium binding site 6 out of 9 in 6y5x

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Magnesium binding site 6 out of 9 in the Structure of Apo New Jersey Polyomavirus VP1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Apo New Jersey Polyomavirus VP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg403

b:41.7
occ:1.00
 OE2 F:GLU53 2.7 36.5 1.0
OE2 G:GLU240 2.7 39.5 1.0
O G:HOH567 3.0 28.1 1.0
O G:SER237 3.0 25.2 1.0
CD F:GLU53 3.6 39.7 1.0
CD G:GLU240 3.7 37.4 1.0
C G:SER237 4.0 22.6 1.0
OE1 F:GLU53 4.1 38.0 1.0
CG G:GLU240 4.1 31.7 1.0
CA G:ARG238 4.6 25.5 1.0
CE F:LYS312 4.6 39.0 1.0
NZ F:LYS312 4.7 37.5 1.0
N G:ARG238 4.7 23.7 1.0
OH F:TYR310 4.7 33.8 1.0
CG F:GLU53 4.8 33.8 1.0
OE1 G:GLU240 4.9 28.2 1.0
CA G:SER237 4.9 26.0 1.0

Magnesium binding site 7 out of 9 in 6y5x

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Magnesium binding site 7 out of 9 in the Structure of Apo New Jersey Polyomavirus VP1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Apo New Jersey Polyomavirus VP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg404

b:44.5
occ:1.00
 OE1 F:GLU240 2.5 35.1 1.0
O J:HOH566 2.9 27.0 1.0
OE2 J:GLU53 2.9 31.7 1.0
O F:SER237 3.0 28.2 1.0
OE1 J:GLU53 3.3 39.0 1.0
CD J:GLU53 3.4 37.1 1.0
CD F:GLU240 3.6 38.1 1.0
C F:SER237 4.0 26.3 1.0
CG F:GLU240 4.1 33.2 1.0
CE J:LYS312 4.3 35.5 1.0
NZ J:LYS312 4.4 37.9 1.0
OE2 F:GLU240 4.6 32.8 1.0
CA F:ARG238 4.7 25.1 1.0
N F:ARG238 4.8 25.2 1.0
OH J:TYR310 4.8 28.6 1.0
CG J:GLU53 4.8 33.6 1.0
CA F:SER237 4.9 24.6 1.0

Magnesium binding site 8 out of 9 in 6y5x

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Magnesium binding site 8 out of 9 in the Structure of Apo New Jersey Polyomavirus VP1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Apo New Jersey Polyomavirus VP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg403

b:36.1
occ:1.00
 OE2 I:GLU240 2.4 38.9 1.0
OE2 H:GLU53 2.6 36.4 1.0
O I:HOH542 2.7 32.4 1.0
O I:SER237 2.9 29.7 1.0
CD H:GLU53 3.5 37.3 1.0
CD I:GLU240 3.5 38.7 1.0
OE1 H:GLU53 3.7 35.8 1.0
C I:SER237 3.8 28.5 1.0
CG I:GLU240 4.1 33.6 1.0
OH H:TYR310 4.3 29.7 1.0
NZ H:LYS312 4.4 42.8 1.0
CA I:ARG238 4.5 27.8 1.0
CE H:LYS312 4.5 41.5 1.0
N I:ARG238 4.5 27.8 1.0
OE1 I:GLU240 4.5 31.4 1.0
CA I:SER237 4.6 27.4 1.0
CG H:GLU53 4.7 34.2 1.0
O I:ARG238 4.9 28.8 1.0

Magnesium binding site 9 out of 9 in 6y5x

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Magnesium binding site 9 out of 9 in the Structure of Apo New Jersey Polyomavirus VP1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Apo New Jersey Polyomavirus VP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg403

b:37.6
occ:1.00
 O I:HOH574 2.4 32.2 1.0
OE2 I:GLU53 2.4 41.5 1.0
O J:SER237 2.6 29.3 1.0
O I:HOH540 2.6 31.9 1.0
C J:SER237 3.5 27.3 1.0
CD I:GLU53 3.6 39.6 1.0
CG J:GLU240 3.9 26.9 1.0
OE1 I:GLU53 4.0 38.2 1.0
CA J:ARG238 4.1 27.1 1.0
N J:ARG238 4.1 26.6 1.0
NZ I:LYS312 4.3 39.0 1.0
CE I:LYS312 4.4 39.8 1.0
OH I:TYR310 4.4 27.1 1.0
CA J:SER237 4.4 25.9 1.0
O J:ARG238 4.5 27.3 1.0
C J:ARG238 4.7 22.7 1.0
CG I:GLU53 4.8 32.2 1.0
O J:PRO236 4.8 26.3 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 00:09:44 2024

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