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Nickel in PDB 2hje: Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain

Enzymatic activity of Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain

All present enzymatic activity of Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain:
2.7.13.3;

Protein crystallography data

The structure of Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain, PDB code: 2hje was solved by M.B.Neiditch, R.C.Kelly, F.M.Hughson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.10 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 33.446, 36.152, 49.185, 82.18, 86.14, 67.28
R / Rfree (%) 19.4 / 23.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain (pdb code 2hje). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain, PDB code: 2hje:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 2hje

Go back to Nickel Binding Sites List in 2hje
Nickel binding site 1 out of 4 in the Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain


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 Vibrio Harveyi Luxq Periplasmic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni272

b:16.8
occ:1.00
O A:HOH462 1.9 18.6 1.0
OD2 A:ASP271 2.0 17.9 1.0
OD1 A:ASP209 2.2 15.6 1.0
O A:HOH289 2.2 17.2 1.0
O A:HOH459 2.2 18.3 1.0
CG A:ASP271 3.0 20.7 1.0
CG A:ASP209 3.0 19.2 1.0
OD2 A:ASP209 3.2 20.9 1.0
OD1 A:ASP271 3.3 17.4 1.0
O A:HOH356 4.0 28.2 1.0
O A:HOH393 4.1 35.6 1.0
CB A:ASP209 4.4 17.2 1.0
CB A:ASP271 4.4 22.9 1.0
O A:HOH432 4.5 39.1 1.0
O A:ASP271 4.6 25.7 1.0
N A:ASP271 4.6 22.8 1.0
C A:ASP271 4.6 24.2 1.0
CA A:ASP271 4.8 23.2 1.0
OXT A:ASP271 5.0 25.5 1.0

Nickel binding site 2 out of 4 in 2hje

Go back to Nickel Binding Sites List in 2hje
Nickel binding site 2 out of 4 in the Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain


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 Vibrio Harveyi Luxq Periplasmic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni273

b:17.4
occ:1.00
O A:HOH343 2.0 23.8 1.0
O A:HOH436 2.1 19.8 1.0
O A:HOH456 2.1 17.5 1.0
NE2 A:HIS131 2.1 12.0 1.0
O A:HOH362 2.1 18.6 1.0
O A:HOH370 2.2 20.7 1.0
CE1 A:HIS131 3.1 13.5 1.0
CD2 A:HIS131 3.1 13.1 1.0
OD1 A:ASP126 4.1 12.8 1.0
OD2 A:ASP126 4.1 11.8 1.0
ND1 A:HIS131 4.2 12.5 1.0
OD1 A:ASP137 4.2 26.2 1.0
CG A:HIS131 4.2 10.9 1.0
O A:HOH446 4.4 23.7 1.0
CG A:ASP126 4.5 11.6 1.0
OD2 A:ASP137 4.8 23.6 1.0
CG A:ASP137 4.9 21.2 1.0

Nickel binding site 3 out of 4 in 2hje

Go back to Nickel Binding Sites List in 2hje
Nickel binding site 3 out of 4 in the Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain


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 Vibrio Harveyi Luxq Periplasmic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni274

b:34.1
occ:1.00
O A:HOH445 1.9 27.6 1.0
NE2 A:HIS61 2.1 26.4 1.0
OD2 A:ASP65 2.1 27.1 1.0
O A:HOH444 2.1 33.1 1.0
CD2 A:HIS61 3.0 26.1 1.0
CG A:ASP65 3.0 23.9 1.0
CE1 A:HIS61 3.1 27.6 1.0
OD1 A:ASP65 3.3 23.8 1.0
O A:VAL256 4.1 24.8 1.0
O A:HOH457 4.1 50.7 1.0
ND1 A:HIS61 4.2 26.0 1.0
CG A:HIS61 4.2 25.8 1.0
CB A:ASP65 4.4 22.6 1.0
O A:HOH412 4.9 54.4 1.0
CB A:VAL256 5.0 25.7 1.0

Nickel binding site 4 out of 4 in 2hje

Go back to Nickel Binding Sites List in 2hje
Nickel binding site 4 out of 4 in the Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Vibrio Harveyi Luxq Periplasmic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni275

b:42.4
occ:1.00
O A:HOH466 2.0 40.1 1.0
O A:HOH435 2.1 24.5 1.0
O A:HOH438 2.3 36.9 1.0
NE2 A:HIS110 2.3 31.4 1.0
O A:HOH414 2.4 35.4 1.0
NZ A:LYS201 2.9 16.8 1.0
CE1 A:HIS110 3.2 31.1 1.0
CD2 A:HIS110 3.3 30.8 1.0
CE A:LYS201 3.7 23.3 1.0
O A:HOH415 3.7 43.0 1.0
OE2 A:GLU205 4.3 33.8 1.0
ND1 A:HIS110 4.4 30.4 1.0
CG A:HIS110 4.4 27.7 1.0
OE1 A:GLU205 4.6 33.1 1.0
CD A:GLU205 4.9 31.1 1.0
CD A:LYS201 4.9 24.5 1.0

Reference:

M.B.Neiditch, M.J.Federle, A.J.Pompeani, R.C.Kelly, D.L.Swem, P.D.Jeffrey, B.L.Bassler, F.M.Hughson. Ligand-Induced Asymmetry in Histidine Sensor Kinase Complex Regulates Quorum Sensing. Cell(Cambridge,Mass.) V. 126 1095 2006.
ISSN: ISSN 0092-8674
PubMed: 16990134
DOI: 10.1016/J.CELL.2006.07.032
Page generated: Fri Sep 25 08:10:10 2020
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