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Nickel in PDB 3ii2: Structure of ORF157 From Acidianus Filamentous Virus 1

Protein crystallography data

The structure of Structure of ORF157 From Acidianus Filamentous Virus 1, PDB code: 3ii2 was solved by A.Goulet, S.Porciero, D.Prangishvili, H.Van Tilbeurgh, C.Cambillau, V.Campanacci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.35 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.637, 65.637, 85.568, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 23.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of ORF157 From Acidianus Filamentous Virus 1 (pdb code 3ii2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Structure of ORF157 From Acidianus Filamentous Virus 1, PDB code: 3ii2:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3ii2

Go back to Nickel Binding Sites List in 3ii2
Nickel binding site 1 out of 3 in the Structure of ORF157 From Acidianus Filamentous Virus 1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of ORF157 From Acidianus Filamentous Virus 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni164

b:23.6
occ:0.50
OD1 A:ASP79 2.4 41.0 0.8
NE2 A:HIS77 2.8 28.9 1.0
OD2 A:ASP79 2.9 42.5 0.8
CG A:ASP79 3.0 43.2 0.3
CD2 A:HIS77 3.2 31.2 1.0
CE1 A:HIS77 3.9 28.9 1.0
O A:HOH216 4.4 24.5 1.0
CG A:HIS77 4.4 24.1 1.0
NZ A:LYS83 4.5 81.4 1.0
CB A:ASP79 4.5 45.7 1.0
O A:HOH296 4.6 40.0 1.0
ND1 A:HIS77 4.7 26.7 1.0

Nickel binding site 2 out of 3 in 3ii2

Go back to Nickel Binding Sites List in 3ii2
Nickel binding site 2 out of 3 in the Structure of ORF157 From Acidianus Filamentous Virus 1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of ORF157 From Acidianus Filamentous Virus 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni165

b:17.5
occ:0.44
OE1 A:GLU144 2.3 43.6 0.9
NZ A:LYS147 2.5 54.8 1.0
OE2 A:GLU144 2.9 42.3 0.9
CD A:GLU144 2.9 38.5 0.7
CE A:LYS147 3.3 45.1 1.0
CD A:LYS147 3.9 37.6 1.0
O A:HOH227 4.0 30.9 1.0
O A:HOH223 4.1 37.2 1.0
CG A:GLU144 4.4 38.3 1.0

Nickel binding site 3 out of 3 in 3ii2

Go back to Nickel Binding Sites List in 3ii2
Nickel binding site 3 out of 3 in the Structure of ORF157 From Acidianus Filamentous Virus 1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of ORF157 From Acidianus Filamentous Virus 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni166

b:33.1
occ:0.70
NE2 A:HIS39 2.4 49.7 0.7
NE A:ARG41 2.8 55.5 0.3
CD2 A:HIS39 3.1 49.1 0.4
O A:HOH291 3.2 42.9 1.0
CZ A:ARG41 3.3 55.3 1.0
NH1 A:ARG41 3.3 59.3 0.8
CE1 A:HIS39 3.4 48.1 0.8
CD A:ARG41 3.6 54.6 0.2
CG A:ARG41 4.0 49.2 0.5
CG A:HIS39 4.3 45.0 1.0
NH2 A:ARG41 4.3 61.6 0.7
ND1 A:HIS39 4.4 46.1 0.3
O A:HOH271 4.9 36.7 1.0
O A:HIS39 4.9 48.9 1.0

Reference:

A.Goulet, M.Pina, P.Redder, D.Prangishvili, L.Vera, J.Lichiere, N.Leulliot, H.Van Tilbeurgh, M.Ortiz-Lombardia, V.Campanacci, C.Cambillau. ORF157 From the Archaeal Virus Acidianus Filamentous Virus 1 Defines A New Class of Nuclease J.Virol. V. 84 5025 2010.
ISSN: ISSN 0022-538X
PubMed: 20200253
DOI: 10.1128/JVI.01664-09
Page generated: Fri Sep 25 08:25:07 2020
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