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Magnesium in PDB 5kw9: Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody

Protein crystallography data

The structure of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody, PDB code: 5kw9 was solved by S.Shanker, B.V.V.Prasad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.00 / 2.30
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 162.000, 162.000, 146.810, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 21.2

Other elements in 5kw9:

The structure of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody (pdb code 5kw9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody, PDB code: 5kw9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5kw9

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Magnesium binding site 1 out of 5 in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:35.7
occ:1.00
CD2 A:HIS286 2.6 23.9 1.0
O A:HOH902 2.6 35.0 1.0
O A:HOH833 2.7 23.2 1.0
O A:HOH735 2.8 19.5 1.0
NE2 A:HIS286 3.4 25.6 1.0
CG A:HIS286 3.8 22.3 1.0
CB A:ILE318 3.8 22.6 1.0
CG2 A:ILE318 3.9 22.2 1.0
CD1 A:LEU304 3.9 30.3 1.0
CB A:LEU304 4.0 28.1 1.0
CG A:LEU304 4.1 31.5 1.0
N A:LEU304 4.1 25.0 1.0
O A:ILE318 4.2 19.5 1.0
CB A:HIS286 4.4 20.4 1.0
OE1 A:GLU303 4.4 23.6 1.0
C A:ILE318 4.6 21.4 1.0
CE1 A:HIS286 4.6 24.4 1.0
CA A:LEU304 4.7 26.4 1.0
O A:HOH842 4.7 55.6 1.0
CA A:ILE318 4.7 22.5 1.0
CG1 A:ILE318 4.7 24.4 1.0
CB A:GLU303 4.8 23.4 1.0
ND1 A:HIS286 4.8 23.8 1.0

Magnesium binding site 2 out of 5 in 5kw9

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Magnesium binding site 2 out of 5 in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:54.8
occ:1.00
ND1 A:HIS337 3.1 39.4 1.0
CB A:HIS337 3.8 33.2 1.0
CG A:HIS337 3.9 36.3 1.0
CA A:HIS337 4.1 30.5 1.0
N A:SER338 4.1 29.0 1.0
CE1 A:HIS337 4.2 39.3 1.0
O A:HOH774 4.4 41.4 1.0
O A:HOH765 4.5 49.9 1.0
C A:HIS337 4.6 28.5 1.0
O A:SER338 4.9 29.4 1.0
O A:GLY336 5.0 34.0 1.0

Magnesium binding site 3 out of 5 in 5kw9

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Magnesium binding site 3 out of 5 in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:38.6
occ:1.00
O A:ASP478 2.7 24.9 1.0
NE A:ARG269 2.9 21.9 1.0
O A:GLY479 3.0 25.3 1.0
N A:CYS270 3.3 21.2 1.0
CA A:ARG269 3.4 20.4 1.0
CD A:ARG269 3.5 20.6 1.0
CA A:GLY479 3.6 25.3 1.0
C A:GLY479 3.6 25.8 1.0
O A:HOH776 3.6 29.1 1.0
C A:ASP478 3.7 25.3 1.0
O A:CYS270 3.7 23.9 1.0
CB A:ARG269 3.8 20.1 1.0
C A:ARG269 3.8 20.2 1.0
CZ A:ARG269 4.0 23.5 1.0
N A:GLY479 4.1 24.5 1.0
C A:CYS270 4.1 23.4 1.0
NH2 A:ARG269 4.2 21.5 1.0
CG A:ARG269 4.3 20.1 1.0
CA A:CYS270 4.3 21.5 1.0
O A:GLY268 4.4 21.3 1.0
CD1 A:LEU437 4.6 25.5 1.0
CD1 A:LEU436 4.7 20.5 1.0
N A:ARG269 4.7 20.5 1.0
N A:PHE480 4.8 25.6 1.0
N A:THR271 4.8 23.5 1.0
O A:ARG269 4.9 21.9 1.0
CA A:ASP478 5.0 26.6 1.0

Magnesium binding site 4 out of 5 in 5kw9

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Magnesium binding site 4 out of 5 in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:48.2
occ:1.00
NH2 H:ARG100 3.3 80.8 1.0
NE1 L:TRP56 3.6 40.1 1.0
OH H:TYR110 3.6 50.5 1.0
CE1 L:TYR55 4.1 50.5 1.0
CE1 H:TYR110 4.2 43.8 1.0
CZ H:TYR110 4.4 46.4 1.0
CE2 L:TRP56 4.4 38.7 1.0
CD1 L:TRP56 4.5 40.7 1.0
CZ H:ARG100 4.6 79.0 1.0
CZ2 L:TRP56 4.6 37.6 1.0
OH L:TYR55 4.7 55.8 1.0
CZ L:TYR55 4.7 53.5 1.0
CD1 L:TYR55 4.8 48.4 1.0

Magnesium binding site 5 out of 5 in 5kw9

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Magnesium binding site 5 out of 5 in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg302

b:65.4
occ:1.00
NZ L:LYS45 3.4 68.6 1.0
NZ L:LYS51 3.6 75.1 1.0
CE L:LYS51 4.1 72.2 1.0
O L:HOH442 4.3 54.9 1.0
CD L:LYS51 4.4 69.1 1.0
CE L:LYS45 4.6 65.6 1.0
OE1 L:GLN43 4.8 58.4 1.0
CD L:LYS45 4.8 63.4 1.0

Reference:

S.Shanker, R.Czako, G.Sapparapu, G.Alvarado, M.Viskovska, B.Sankaran, R.L.Atmar, J.E.Crowe, M.K.Estes, B.V.Prasad. Structural Basis For Norovirus Neutralization By An Hbga Blocking Human Iga Antibody. Proc.Natl.Acad.Sci.Usa V. 113 E5830 2016.
ISSN: ESSN 1091-6490
PubMed: 27647885
DOI: 10.1073/PNAS.1609990113
Page generated: Mon Dec 14 20:38:32 2020

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