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Nickel in PDB 2o3b: Crystal Structure Complex of Nuclease A (Nuca) with Intra-Cellular Inhibitor Nuia

Protein crystallography data

The structure of Crystal Structure Complex of Nuclease A (Nuca) with Intra-Cellular Inhibitor Nuia, PDB code: 2o3b was solved by M.Ghosh, G.Meiss, A.M.Pingoud, R.E.London, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.61 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.225, 87.225, 138.977, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure Complex of Nuclease A (Nuca) with Intra-Cellular Inhibitor Nuia (pdb code 2o3b). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure Complex of Nuclease A (Nuca) with Intra-Cellular Inhibitor Nuia, PDB code: 2o3b:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2o3b

Go back to Nickel Binding Sites List in 2o3b
Nickel binding site 1 out of 2 in the Crystal Structure Complex of Nuclease A (Nuca) with Intra-Cellular Inhibitor Nuia


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure Complex of Nuclease A (Nuca) with Intra-Cellular Inhibitor Nuia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:61.5
occ:1.00
O A:HOH1081 2.1 60.1 1.0
OE1 A:GLU249 2.3 41.6 1.0
O A:HOH933 2.3 40.6 1.0
OE1 A:GLU269 2.5 38.4 1.0
OD1 A:ASP246 2.6 32.8 0.7
CD A:GLU249 3.4 38.7 1.0
CG A:ASP246 3.5 32.8 0.7
CD A:GLU269 3.7 39.2 1.0
NI A:NI302 3.8 56.5 1.0
OE2 A:GLU249 3.9 36.5 1.0
OD2 A:ASP246 4.1 32.1 0.7
CB A:GLU269 4.2 40.1 1.0
O A:HOH998 4.3 52.5 1.0
CA A:ASP246 4.4 34.1 1.0
CB A:ASP246 4.5 32.6 0.7
OE2 A:GLU269 4.6 39.9 1.0
CG A:GLU249 4.6 38.1 1.0
CG A:GLU269 4.6 36.8 1.0
O A:HOH946 4.6 43.4 1.0
O A:HOH1075 5.0 51.0 1.0
OE1 A:GLN265 5.0 42.1 1.0

Nickel binding site 2 out of 2 in 2o3b

Go back to Nickel Binding Sites List in 2o3b
Nickel binding site 2 out of 2 in the Crystal Structure Complex of Nuclease A (Nuca) with Intra-Cellular Inhibitor Nuia


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure Complex of Nuclease A (Nuca) with Intra-Cellular Inhibitor Nuia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:56.5
occ:1.00
OE1 A:GLN265 2.3 42.1 1.0
OE2 A:GLU249 2.5 36.5 1.0
OD1 A:ASP255 2.5 36.2 1.0
OE2 A:GLU269 2.5 39.9 1.0
O A:PHE256 2.6 30.6 1.0
OE1 A:GLU269 2.7 38.4 1.0
CD A:GLU269 3.0 39.2 1.0
CD A:GLU249 3.4 38.7 1.0
CD A:GLN265 3.4 40.9 1.0
OE1 A:GLU249 3.6 41.6 1.0
C A:PHE256 3.7 34.5 1.0
CG A:ASP255 3.7 39.0 1.0
N A:PHE256 3.8 37.0 1.0
NI A:NI301 3.8 61.5 1.0
C A:ASP255 4.1 38.1 1.0
CG A:GLN265 4.2 42.3 1.0
CA A:PHE256 4.2 34.7 1.0
O A:HOH943 4.3 39.7 1.0
CA A:ASP255 4.4 37.1 1.0
NE2 A:GLN265 4.4 42.3 1.0
CB A:GLN265 4.5 43.6 1.0
CG A:GLU269 4.5 36.8 1.0
OD2 A:ASP255 4.5 40.5 1.0
CB A:ASP255 4.6 37.1 1.0
CG A:GLU249 4.8 38.1 1.0
O A:ASP255 4.8 40.5 1.0
N A:LEU257 4.8 34.4 1.0
O A:HOH1081 4.8 60.1 1.0
C A:LEU257 4.9 35.2 1.0
CB A:PHE256 4.9 32.6 1.0
O A:LEU257 4.9 35.5 1.0
O A:HOH965 4.9 43.6 1.0
CB A:LEU257 5.0 35.9 1.0

Reference:

M.Ghosh, G.Meiss, A.M.Pingoud, R.E.London, L.C.Pedersen. The Nuclease A-Inhibitor Complex Is Characterized By A Novel Metal Ion Bridge. J.Biol.Chem. V. 282 5682 2007.
ISSN: ISSN 0021-9258
PubMed: 17138564
DOI: 10.1074/JBC.M605986200
Page generated: Fri Sep 25 08:12:14 2020
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