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Nickel in PDB 3l6p: Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease

Enzymatic activity of Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease

All present enzymatic activity of Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease:
2.1.1.56; 2.1.1.57; 2.7.7.48; 3.4.21.91; 3.6.1.15; 3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease, PDB code: 3l6p was solved by S.Chandramouli, J.S.Joseph, S.Daudenarde, J.Gatchalian, C.Cornillez-Ty, P.Kuhn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.95 / 2.20
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 56.721, 60.848, 161.644, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 28.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease (pdb code 3l6p). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease, PDB code: 3l6p:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3l6p

Go back to Nickel Binding Sites List in 3l6p
Nickel binding site 1 out of 3 in the Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:57.2
occ:0.50
NE2 A:HIS28 2.5 61.4 1.0
CE1 A:HIS28 3.4 57.5 1.0
CD2 A:HIS28 3.5 59.5 1.0
O A:GLY25 3.9 58.5 1.0
ND1 A:HIS28 4.5 58.5 1.0
CG A:HIS28 4.6 57.2 1.0

Nickel binding site 2 out of 3 in 3l6p

Go back to Nickel Binding Sites List in 3l6p
Nickel binding site 2 out of 3 in the Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:60.6
occ:0.74
NE2 A:HIS101 2.5 29.7 1.0
O A:HOH415 3.1 42.1 1.0
CD2 A:HIS101 3.1 34.7 1.0
OD1 A:ASN202 3.4 60.5 1.0
CB A:SER185 3.6 33.7 1.0
CE1 A:HIS101 3.6 31.9 1.0
CG A:ASN202 4.2 58.6 1.0
OG A:SER185 4.3 43.3 1.0
CG A:HIS101 4.4 35.2 1.0
ND2 A:ASN202 4.4 60.8 1.0
ND1 A:HIS101 4.6 29.7 1.0
O A:VAL86 4.9 30.7 1.0
CA A:SER185 4.9 33.0 1.0

Nickel binding site 3 out of 3 in 3l6p

Go back to Nickel Binding Sites List in 3l6p
Nickel binding site 3 out of 3 in the Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Dengue Virus 1 NS2B/NS3 Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni303

b:0.7
occ:1.00
NE2 A:HIS3 1.8 44.3 1.0
CD2 A:HIS3 2.5 54.4 1.0
CE1 A:HIS3 2.6 44.4 1.0
ND1 A:HIS3 3.4 49.7 1.0
CG A:HIS3 3.4 52.1 1.0
CB A:MET4 4.1 20.0 1.0
N A:MET4 4.4 20.0 1.0
C A:HIS3 4.6 62.5 1.0
O A:HIS3 4.7 62.2 1.0
CB A:HIS3 4.7 58.7 1.0
CA A:MET4 4.7 20.0 1.0

Reference:

S.Chandramouli, J.S.Joseph, S.Daudenarde, J.Gatchalian, C.Cornillez-Ty, P.Kuhn. Serotype-Specific Structural Differences in the Protease-Cofactor Complexes of the Dengue Virus Family. J.Virol. V. 84 3059 2010.
ISSN: ISSN 0022-538X
PubMed: 20042502
DOI: 10.1128/JVI.02044-09
Page generated: Fri Sep 25 08:26:37 2020
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