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Magnesium in PDB 8iib: Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)

Protein crystallography data

The structure of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546), PDB code: 8iib was solved by X.Fang, G.Lu, C.Hou, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.41 / 2.69
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.51, 150.51, 104.626, 90, 90, 120
R / Rfree (%) 21.3 / 25.4

Other elements in 8iib:

The structure of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) also contains other interesting chemical elements:

Cadmium (Cd) 4 atoms
Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) (pdb code 8iib). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546), PDB code: 8iib:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8iib

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Magnesium binding site 1 out of 8 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:49.9
occ:1.00
 OD2 A:ASP399 2.3 48.1 1.0
OD2 A:ASP398 2.4 48.7 1.0
O A:HOH722 2.8 40.4 1.0
CG A:ASP398 3.4 40.4 1.0
CG A:ASP399 3.4 38.8 1.0
OD1 A:ASP398 3.6 50.4 1.0
OD1 A:ASP399 3.9 50.9 1.0
O A:HOH750 4.5 20.7 1.0
CB A:ASP399 4.7 32.1 1.0
CB A:ASP398 4.8 32.3 1.0
N A:ASP398 4.8 29.8 1.0
N A:ASP399 4.9 33.2 1.0
O A:TYR396 4.9 28.5 1.0

Magnesium binding site 2 out of 8 in 8iib

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Magnesium binding site 2 out of 8 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:54.7
occ:1.00
 O B:HOH728 2.2 43.9 1.0
O A:HOH771 2.2 44.5 1.0
OD2 A:ASP471 2.2 45.1 1.0
O A:HOH717 3.2 48.9 1.0
CG A:ASP471 3.2 42.9 1.0
O A:ASP471 3.5 29.8 1.0
OE2 A:GLU475 3.7 51.1 1.0
OD1 A:ASP471 3.7 46.8 1.0
O A:HOH729 4.2 30.0 1.0
C A:ASP471 4.3 25.1 1.0
CB A:ASP471 4.4 24.1 1.0
CA A:ASP471 4.5 25.7 1.0
CB A:GLU475 4.5 26.5 1.0
CD A:GLU475 4.6 46.7 1.0
O B:GLU475 4.6 35.3 1.0
CD1 B:TRP479 4.7 23.0 1.0
CA B:GLU475 4.8 30.8 1.0
O B:PRO477 4.8 29.8 1.0
CB B:GLU475 5.0 30.8 1.0

Magnesium binding site 3 out of 8 in 8iib

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Magnesium binding site 3 out of 8 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:50.9
occ:1.00
 O B:HOH704 2.3 46.3 1.0
OD2 B:ASP398 2.3 55.0 1.0
OD1 B:ASP399 2.7 43.6 1.0
CG B:ASP398 3.3 45.9 1.0
OD1 B:ASP398 3.6 54.5 1.0
CG B:ASP399 3.7 40.3 1.0
OD2 B:ASP399 4.0 60.0 1.0
O B:HOH757 4.4 51.8 1.0
O B:HOH732 4.6 31.7 1.0
CB B:ASP398 4.7 38.0 1.0
N B:ASP398 4.7 34.7 1.0
N B:ASP399 4.8 33.5 1.0
O B:TYR396 4.8 31.0 1.0
CB B:ASP399 4.9 33.4 1.0

Magnesium binding site 4 out of 8 in 8iib

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Magnesium binding site 4 out of 8 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:57.5
occ:1.00
 O B:HOH727 2.4 45.9 1.0
O B:HOH763 2.4 46.4 1.0
O B:HOH705 2.5 51.3 1.0
OD2 B:ASP526 2.7 57.0 1.0
CG B:ASP526 3.6 49.5 1.0
OD1 B:ASP529 3.6 39.6 1.0
OD1 B:ASP526 3.6 46.1 1.0
CE1 B:HIS527 3.7 62.3 1.0
ND1 B:HIS527 4.0 62.4 1.0
O B:HIS527 4.0 41.8 1.0
CE B:LYS491 4.3 32.7 1.0
NE2 B:HIS527 4.6 61.7 1.0
NZ B:LYS491 4.6 31.8 1.0
CG B:ASP529 4.7 43.3 1.0
N B:HIS527 4.8 52.5 1.0
CG B:HIS527 4.9 63.1 1.0

Magnesium binding site 5 out of 8 in 8iib

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Magnesium binding site 5 out of 8 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:48.8
occ:1.00
 OD2 B:ASP399 3.0 60.0 1.0
O B:HOH766 3.2 55.3 1.0
N B:LEU451 3.3 21.5 1.0
O B:GLN449 3.8 28.3 1.0
N B:LYS452 3.8 18.9 1.0
CA B:TYR450 3.9 18.9 1.0
C B:TYR450 4.0 23.3 1.0
CA B:LEU451 4.0 18.1 1.0
OE1 B:GLN449 4.1 29.9 1.0
CG B:ASP399 4.2 40.3 1.0
C B:GLN449 4.2 24.8 1.0
N B:TYR450 4.3 24.1 1.0
C B:LEU451 4.4 20.5 1.0
MG B:MG607 4.5 52.4 1.0
CB B:ASP399 4.6 33.4 1.0
CG B:GLN449 4.7 22.4 1.0
CA B:LYS452 4.7 18.7 1.0
CD B:GLN449 4.8 23.0 1.0
O B:HOH757 4.8 51.8 1.0

Magnesium binding site 6 out of 8 in 8iib

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Magnesium binding site 6 out of 8 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:41.0
occ:1.00
 O B:HOH772 2.4 37.9 1.0
O B:HOH776 2.4 30.3 1.0
OH B:TYR544 2.7 23.2 1.0
O B:HOH768 2.9 40.6 1.0
O B:HOH769 3.3 35.0 1.0
CZ B:TYR544 3.6 23.7 1.0
CE2 B:TYR544 3.6 20.9 1.0
CD1 B:TYR267 4.0 20.4 1.0
CG B:TYR267 4.3 22.3 1.0
CB B:TYR267 4.5 21.5 1.0
CE1 B:TYR267 4.6 18.7 1.0
CE1 B:TYR544 4.9 22.7 1.0
CD2 B:TYR544 4.9 19.5 1.0

Magnesium binding site 7 out of 8 in 8iib

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Magnesium binding site 7 out of 8 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg606

b:52.5
occ:1.00
 O B:HOH764 2.4 45.8 1.0
O A:HOH772 2.6 44.1 1.0
OD2 B:ASP471 2.6 48.7 1.0
O B:HOH759 2.8 43.9 1.0
OD1 B:ASP471 3.0 31.6 1.0
CG B:ASP471 3.2 33.1 1.0
O A:PRO477 3.7 30.4 1.0
O A:GLU475 4.0 25.1 1.0
O A:HOH746 4.2 40.0 1.0
O B:ASP471 4.5 26.6 1.0
CB B:ASP471 4.6 23.9 1.0
C A:GLU475 4.8 24.5 1.0
CA A:GLU475 4.8 25.7 1.0
C A:PRO477 4.9 22.2 1.0
CD1 A:TRP479 4.9 13.4 1.0
OE1 B:GLU475 4.9 59.4 1.0

Magnesium binding site 8 out of 8 in 8iib

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Magnesium binding site 8 out of 8 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:52.4
occ:1.00
 O B:HOH766 2.1 55.3 1.0
O B:HOH720 2.1 53.5 1.0
O B:HOH761 2.5 44.1 1.0
O B:GLN449 3.8 28.3 1.0
N B:GLU431 4.2 64.3 1.0
CB B:GLU431 4.3 57.4 1.0
MG B:MG604 4.5 48.8 1.0
O B:ALA287 4.5 45.2 1.0
CA B:GLY288 4.7 40.8 1.0
C B:ALA287 4.8 39.3 1.0
C B:GLN449 4.8 24.8 1.0
CB B:GLN449 4.9 22.8 1.0
CB B:ALA287 4.9 29.6 1.0
CA B:GLU431 4.9 65.6 1.0
N B:GLY288 5.0 39.3 1.0
OE1 B:GLN449 5.0 29.9 1.0

Reference:

X.Fang, G.Lu, Y.Deng, S.Yang, C.Hou, P.Gong. Unusual Substructure Conformations Observed in Crystal Structures of A Dicistrovirus Rna-Dependent Rna Polymerase Suggest Contribution of the N-Terminal Extension in Proper Folding. Virol Sin 2023.
ISSN: ISSN 1995-820X
PubMed: 37156298
DOI: 10.1016/J.VIRS.2023.05.002
Page generated: Fri Oct 4 09:25:28 2024

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