Magnesium in PDB 5ltn: Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba

Enzymatic activity of Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba

All present enzymatic activity of Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba, PDB code: 5ltn was solved by M.Saez-Ayala, E.L.Yekwa, B.Canard, K.Alvarez, F.Ferron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.59 / 1.88
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 107.185, 107.185, 53.807, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.6

Other elements in 5ltn:

The structure of Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba (pdb code 5ltn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba, PDB code: 5ltn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ltn

Go back to Magnesium Binding Sites List in 5ltn
Magnesium binding site 1 out of 4 in the Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba


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 Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:30.2
occ:1.00
 O11 A:XI7205 1.6 58.3 1.0
O A:HOH339 1.8 44.0 1.0
O A:HOH314 2.0 53.4 1.0
OE2 A:GLU101 2.0 46.7 1.0
O A:HOH315 2.1 39.4 1.0
OD1 A:ASP88 2.6 40.7 1.0
O A:HOH301 2.6 24.8 1.0
C10 A:XI7205 2.7 50.3 0.0
O8 A:XI7205 2.9 58.2 1.0
CD A:GLU101 3.2 47.4 1.0
C9 A:XI7205 3.2 54.1 1.0
MG A:MG202 3.3 42.0 1.0
CG A:ASP88 3.4 38.5 1.0
O A:HOH376 3.5 49.5 1.0
OD2 A:ASP88 3.7 40.3 1.0
O10 A:XI7205 3.7 24.3 1.0
OE1 A:GLU101 3.9 49.1 1.0
O A:HOH303 3.9 47.5 1.0
O A:CYS102 4.1 30.9 1.0
NZ A:LYS121 4.3 51.5 1.0
OD2 A:ASP118 4.3 34.7 1.0
O A:HOH308 4.3 33.3 1.0
CG A:GLU101 4.3 33.6 1.0
CB A:GLU101 4.3 35.5 1.0
N A:CYS102 4.4 32.6 1.0
CA A:GLU101 4.4 36.4 1.0
CB A:ASP88 4.6 32.6 1.0
CE A:LYS121 4.6 56.7 1.0
C8 A:XI7205 4.7 53.1 0.4
OD1 A:ASP118 4.7 35.5 1.0
N A:ASP88 4.7 35.9 1.0
NZ A:LYS114 4.7 36.4 1.0
CG A:ASP118 4.8 35.3 1.0
O A:ILE86 4.9 46.4 1.0
C A:GLU101 4.9 34.2 1.0
O A:HOH304 4.9 50.9 1.0

Magnesium binding site 2 out of 4 in 5ltn

Go back to Magnesium Binding Sites List in 5ltn
Magnesium binding site 2 out of 4 in the Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba


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 Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:42.0
occ:1.00
 O A:HOH304 1.9 50.9 1.0
C10 A:XI7205 2.0 50.3 0.0
O11 A:XI7205 2.2 58.3 1.0
OD2 A:ASP88 2.2 40.3 1.0
O10 A:XI7205 2.2 24.3 1.0
O A:HOH315 2.3 39.4 1.0
O A:HOH394 2.4 42.8 1.0
C9 A:XI7205 2.9 54.1 1.0
CG A:ASP88 3.1 38.5 1.0
MG A:MG201 3.3 30.2 1.0
C8 A:XI7205 3.5 53.1 0.4
OD1 A:ASP88 3.6 40.7 1.0
O8 A:XI7205 3.6 58.2 1.0
OE2 A:GLU50 3.7 39.1 1.0
O A:HOH301 3.9 24.8 1.0
O14 A:XI7205 4.2 49.0 0.6
C7 A:XI7205 4.2 52.0 1.0
O A:HOH310 4.2 49.2 1.0
CA A:ASP88 4.3 35.6 1.0
O A:HOH308 4.3 33.3 1.0
CB A:ASP88 4.3 32.6 1.0
N A:ASP88 4.3 35.9 1.0
O A:ILE86 4.4 46.4 1.0
O A:HOH314 4.4 53.4 1.0
CD A:GLU50 4.5 38.7 1.0
C A:PRO87 4.6 40.0 1.0
O A:PRO87 4.7 41.2 1.0
OE2 A:GLU101 4.8 46.7 1.0
O A:HOH339 4.8 44.0 1.0
OE1 A:GLU50 5.0 41.4 1.0
O A:HOH376 5.0 49.5 1.0

Magnesium binding site 3 out of 4 in 5ltn

Go back to Magnesium Binding Sites List in 5ltn
Magnesium binding site 3 out of 4 in the Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba


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 Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:72.1
occ:1.00
 OD1 B:ASP88 2.2 43.8 1.0
O B:HOH384 2.4 58.7 1.0
O B:HOH397 2.5 60.0 1.0
MG B:MG202 2.5 60.7 1.0
O B:HOH307 2.6 56.2 1.0
OE2 B:GLU50 2.8 66.2 1.0
CG B:ASP88 3.1 43.1 1.0
CD B:GLU50 3.3 58.0 1.0
OD2 B:ASP88 3.3 41.5 1.0
CG B:GLU50 3.7 38.9 1.0
O B:HOH301 3.8 52.0 1.0
OE1 B:GLU50 4.1 58.5 1.0
CB B:ASP88 4.5 34.9 1.0
O B:CYS102 4.5 36.7 1.0
O B:HOH405 4.7 64.2 1.0
O B:HOH386 4.9 67.5 1.0

Magnesium binding site 4 out of 4 in 5ltn

Go back to Magnesium Binding Sites List in 5ltn
Magnesium binding site 4 out of 4 in the Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba


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 Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:60.7
occ:1.00
 OD2 B:ASP88 2.2 41.5 1.0
O B:HOH301 2.3 52.0 1.0
O B:CYS102 2.3 36.7 1.0
O B:HOH397 2.4 60.0 1.0
O B:HOH384 2.5 58.7 1.0
MG B:MG201 2.5 72.1 1.0
O B:HOH314 2.7 44.4 1.0
CG B:ASP88 3.0 43.1 1.0
OD1 B:ASP88 3.1 43.8 1.0
C B:CYS102 3.5 39.3 1.0
O B:HOH307 3.6 56.2 1.0
N B:CYS102 3.7 31.8 1.0
O B:HOH386 3.8 67.5 1.0
OE2 B:GLU101 4.1 52.6 1.0
CA B:CYS102 4.2 38.4 1.0
SG B:CYS102 4.3 55.8 1.0
CB B:ASP88 4.4 34.9 1.0
N B:PHE103 4.6 32.8 1.0
C B:GLU101 4.7 36.7 1.0
O B:HOH405 4.8 64.2 1.0
CA B:PHE103 4.8 34.4 1.0
CA B:GLU101 4.9 36.4 1.0
CB B:CYS102 4.9 39.3 1.0

Reference:

M.Saez-Ayala, E.L.Yekwa, M.Carcelli, B.Canard, K.Alvarez, F.Ferron. Crystal Structures of Lymphocytic Choriomeningitis Virusendonuclease Domain Complexed with Diketo-Acid Ligands. Iucrj V. 5 223 2018.
ISSN: ESSN 2052-2525
PubMed: 29765612
DOI: 10.1107/S2052252518001021
Page generated: Mon Dec 14 20:49:24 2020

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