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Manganese in PDB 5ize: Hantaan Virus L Protein Cap-Snatching Endonuclease

Enzymatic activity of Hantaan Virus L Protein Cap-Snatching Endonuclease

All present enzymatic activity of Hantaan Virus L Protein Cap-Snatching Endonuclease:
2.7.7.48;

Protein crystallography data

The structure of Hantaan Virus L Protein Cap-Snatching Endonuclease, PDB code: 5ize was solved by J.Reguera, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.200, 76.150, 63.720, 90.00, 103.97, 90.00
R / Rfree (%) 16.6 / 21.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Hantaan Virus L Protein Cap-Snatching Endonuclease (pdb code 5ize). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Hantaan Virus L Protein Cap-Snatching Endonuclease, PDB code: 5ize:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5ize

Go back to Manganese Binding Sites List in 5ize
Manganese binding site 1 out of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:18.6
occ:1.00
 OD2 A:ASP97 2.2 14.0 1.0
O A:VAL111 2.2 14.9 1.0
O A:HOH1198 2.2 19.0 1.0
OE2 A:GLU110 2.2 19.6 1.0
O A:HOH1196 2.2 20.7 1.0
NE2 A:HIS36 2.3 15.6 1.0
CG A:ASP97 3.1 14.6 1.0
CD A:GLU110 3.2 18.3 1.0
CE1 A:HIS36 3.3 15.6 1.0
CD2 A:HIS36 3.3 16.2 1.0
C A:VAL111 3.3 15.1 1.0
OD1 A:ASP97 3.3 14.3 1.0
MN A:MN31002 3.7 38.4 1.0
N A:VAL111 3.8 13.0 1.0
OE1 A:GLU110 3.9 18.6 1.0
CA A:VAL111 4.0 14.6 1.0
O A:HOH1141 4.0 21.2 1.0
CG A:GLU110 4.1 17.4 1.0
CB A:VAL111 4.2 15.2 1.0
NZ A:LYS124 4.3 31.0 1.0
ND1 A:HIS36 4.4 15.5 1.0
N A:THR112 4.4 16.3 1.0
CG A:HIS36 4.4 14.8 1.0
CE A:LYS124 4.5 25.2 1.0
CB A:ASP97 4.5 14.6 1.0
O A:HOH1200 4.7 28.7 1.0
CA A:THR112 4.7 16.4 1.0
C A:GLU110 4.7 12.9 1.0
O A:HOH1167 4.8 29.6 1.0
O A:HOH1203 4.9 31.7 1.0

Manganese binding site 2 out of 6 in 5ize

Go back to Manganese Binding Sites List in 5ize
Manganese binding site 2 out of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1002

b:38.4
occ:1.00
 O A:HOH1198 2.1 19.0 1.0
O A:HOH1130 2.1 35.2 1.0
OD1 A:ASP97 2.2 14.3 1.0
OE2 A:GLU54 2.3 37.6 1.0
O A:HOH1141 2.3 21.2 1.0
O A:HOH1203 2.4 31.7 1.0
CG A:ASP97 3.2 14.6 1.0
CD A:GLU54 3.3 39.2 1.0
OE1 A:GLU54 3.7 43.2 1.0
MN A:MN31001 3.7 18.6 1.0
OD2 A:ASP97 3.8 14.0 1.0
O A:HOH1127 3.9 32.7 1.0
O A:HOH1214 4.0 41.3 1.0
O A:THR95 4.2 20.7 1.0
OE2 A:GLU110 4.3 19.6 1.0
CE1 A:HIS36 4.3 15.6 1.0
CB A:ASP97 4.4 14.6 1.0
CA A:ASP97 4.4 14.4 1.0
OE1 A:GLU110 4.5 18.6 1.0
N A:ASP97 4.5 14.2 1.0
NE2 A:HIS36 4.6 15.6 1.0
CG A:GLU54 4.6 34.0 1.0
O A:HOH1196 4.8 20.7 1.0
CD A:GLU110 4.8 18.3 1.0
CB A:GLU54 4.8 30.9 1.0

Manganese binding site 3 out of 6 in 5ize

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Manganese binding site 3 out of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1003

b:27.0
occ:1.00
 OG A:SER15 2.1 33.9 1.0
NE2 A:HIS8 2.3 27.2 1.0
O A:GLY17 2.4 34.3 1.0
CD2 A:HIS8 3.2 30.3 1.0
CE1 A:HIS8 3.4 27.9 1.0
CB A:SER15 3.4 36.1 1.0
C A:GLY17 3.5 37.1 1.0
O A:SER15 3.9 39.0 1.0
C A:SER15 4.0 35.0 1.0
N A:GLY17 4.0 39.0 1.0
CA A:SER15 4.1 33.9 1.0
CA A:GLY17 4.1 38.1 1.0
O A:THR18 4.3 28.7 1.0
OE1 A:GLU23 4.3 27.4 1.0
OE2 A:GLU23 4.4 24.7 1.0
C A:THR18 4.4 32.3 1.0
CG A:HIS8 4.4 31.3 1.0
ND1 A:HIS8 4.4 29.3 1.0
N A:LEU19 4.5 29.4 1.0
N A:THR18 4.6 38.2 1.0
CA A:LEU19 4.7 30.9 1.0
CD A:GLU23 4.7 28.7 1.0
N A:PRO16 4.8 38.3 1.0
CA A:THR18 5.0 34.7 1.0

Manganese binding site 4 out of 6 in 5ize

Go back to Manganese Binding Sites List in 5ize
Manganese binding site 4 out of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1001

b:49.8
occ:1.00
 O B:HOH1170 2.1 26.2 1.0
OE2 B:GLU54 2.2 49.1 1.0
OD1 B:ASP97 2.3 21.0 1.0
O B:HOH1122 2.3 31.4 1.0
O B:HOH1174 2.4 40.8 1.0
CD B:GLU54 3.3 45.8 1.0
CG B:ASP97 3.3 20.6 1.0
OE1 B:GLU54 3.7 55.0 1.0
MN B:MN31002 3.8 24.2 1.0
OD2 B:ASP97 3.8 20.4 1.0
O B:HOH1127 3.9 34.2 1.0
O B:THR95 4.1 27.3 1.0
OE2 B:GLU110 4.3 26.4 1.0
CE1 B:HIS36 4.3 23.6 1.0
CA B:ASP97 4.4 20.4 1.0
CB B:ASP97 4.5 20.9 1.0
OE1 B:GLU110 4.5 24.4 1.0
NE2 B:HIS36 4.6 21.3 1.0
N B:ASP97 4.6 19.9 1.0
CG B:GLU54 4.6 38.0 1.0
O B:HOH1163 4.8 25.8 1.0
CB B:GLU54 4.8 33.2 1.0
CD B:GLU110 4.8 26.8 1.0

Manganese binding site 5 out of 6 in 5ize

Go back to Manganese Binding Sites List in 5ize
Manganese binding site 5 out of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1002

b:24.2
occ:1.00
 O B:VAL111 2.1 20.9 1.0
OD2 B:ASP97 2.2 20.4 1.0
O B:HOH1163 2.2 25.8 1.0
OE2 B:GLU110 2.2 26.4 1.0
O B:HOH1170 2.3 26.2 1.0
NE2 B:HIS36 2.3 21.3 1.0
CG B:ASP97 3.1 20.6 1.0
CD B:GLU110 3.2 26.8 1.0
CE1 B:HIS36 3.3 23.6 1.0
CD2 B:HIS36 3.3 24.6 1.0
C B:VAL111 3.3 21.4 1.0
OD1 B:ASP97 3.4 21.0 1.0
N B:VAL111 3.8 21.7 1.0
MN B:MN31001 3.8 49.8 1.0
OE1 B:GLU110 3.8 24.4 1.0
CA B:VAL111 3.9 22.4 1.0
O B:HOH1122 4.0 31.4 1.0
CB B:VAL111 4.1 23.9 1.0
CG B:GLU110 4.1 25.0 1.0
NZ B:LYS124 4.4 35.2 1.0
ND1 B:HIS36 4.4 23.8 1.0
N B:THR112 4.4 22.1 1.0
CG B:HIS36 4.4 24.1 1.0
CE B:LYS124 4.5 31.9 1.0
CB B:ASP97 4.5 20.9 1.0
O B:HOH1168 4.6 32.1 1.0
CA B:THR112 4.7 23.6 1.0
C B:GLU110 4.7 20.4 1.0
O B:HOH1174 4.9 40.8 1.0
O B:HOH1110 5.0 35.7 1.0

Manganese binding site 6 out of 6 in 5ize

Go back to Manganese Binding Sites List in 5ize
Manganese binding site 6 out of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1003

b:17.6
occ:1.00
 O B:HOH1117 2.2 19.4 1.0
O B:HOH1107 2.2 16.1 1.0
NE2 B:HIS8 2.2 16.6 1.0
OG B:SER15 2.3 18.1 1.0
O B:GLY17 2.3 20.0 1.0
CD2 B:HIS8 3.2 17.3 1.0
CE1 B:HIS8 3.3 17.4 1.0
C B:GLY17 3.4 20.9 1.0
CB B:SER15 3.5 19.1 1.0
O B:SER15 3.8 22.8 1.0
N B:GLY17 3.9 22.0 1.0
CA B:GLY17 4.0 22.5 1.0
C B:SER15 4.0 21.6 1.0
CA B:SER15 4.2 20.6 1.0
O B:THR18 4.2 18.0 1.0
C B:THR18 4.3 18.9 1.0
CG B:HIS8 4.3 18.3 1.0
OE1 B:GLU23 4.3 20.7 1.0
ND1 B:HIS8 4.3 18.2 1.0
OE2 B:GLU23 4.4 19.9 1.0
N B:LEU19 4.5 20.5 1.0
N B:THR18 4.5 21.6 1.0
CA B:LEU19 4.7 21.9 1.0
N B:PRO16 4.8 22.6 1.0
CD B:GLU23 4.8 23.1 1.0
CA B:THR18 4.8 21.9 1.0
C B:PRO16 5.0 24.8 1.0

Reference:

J.Reguera, P.Gerlach, M.Rosenthal, S.Gaudon, F.Coscia, S.Gunther, S.Cusack. Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases. Plos Pathog. V. 12 05636 2016.
ISSN: ESSN 1553-7374
PubMed: 27304209
DOI: 10.1371/JOURNAL.PPAT.1005636
Page generated: Tue Dec 15 04:42:06 2020

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