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Nickel in PDB 2h9j: Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam

Enzymatic activity of Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam

All present enzymatic activity of Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam:
3.2.1.17;

Protein crystallography data

The structure of Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam, PDB code: 2h9j was solved by I.W.Mcnae, T.M.Hunter, P.J.Sadler, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.38 / 1.75
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.577, 77.577, 38.355, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam (pdb code 2h9j). 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 Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam, PDB code: 2h9j:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 2h9j

Go back to Nickel Binding Sites List in 2h9j
Nickel binding site 1 out of 3 in the Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni206

b:61.2
occ:1.00
O A:HOH288 2.2 31.7 1.0
O A:HOH325 2.3 37.4 1.0
OD2 A:ASP52 2.3 26.9 1.0
O A:HOH281 2.4 28.4 1.0
O A:HOH218 2.5 27.9 1.0
CG A:ASP52 3.2 20.6 1.0
O A:HOH249 3.4 33.0 1.0
OD1 A:ASP52 3.5 21.0 1.0
O A:HOH313 3.6 27.8 1.0
O A:HOH309 4.1 37.7 1.0
OE1 A:GLU35 4.2 20.3 1.0
CB A:ASP52 4.4 14.4 1.0
O A:GLN57 4.4 16.9 1.0
ND2 A:ASN46 4.4 25.4 1.0
CB A:GLN57 4.7 16.6 1.0
OE2 A:GLU35 4.8 25.2 1.0
O A:HOH308 4.8 39.1 1.0
CD A:GLU35 4.9 19.6 1.0

Nickel binding site 2 out of 3 in 2h9j

Go back to Nickel Binding Sites List in 2h9j
Nickel binding site 2 out of 3 in the Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:0.9
occ:1.00
NI1 A:MM5201 0.0 0.9 1.0
N11 A:MM5201 2.0 0.0 1.0
N4 A:MM5201 2.0 0.7 1.0
N14 A:MM5201 2.0 0.8 1.0
N7 A:MM5201 2.0 0.8 1.0
O A:HOH278 2.5 55.8 1.0
OD1 A:ASP101 2.6 37.9 1.0
C5 A:MM5201 2.9 0.5 1.0
C6 A:MM5201 3.0 0.7 1.0
C12 A:MM5201 3.0 0.1 1.0
C13 A:MM5201 3.0 0.0 1.0
C10 A:MM5201 3.0 0.9 1.0
C1 A:MM5201 3.0 0.6 1.0
C2 A:MM5201 3.0 0.6 1.0
C3 A:MM5201 3.0 0.6 1.0
C8 A:MM5201 3.1 0.7 1.0
C9 A:MM5201 3.1 0.8 1.0
CG A:ASP101 3.6 34.6 1.0
OD2 A:ASP101 3.9 37.0 1.0
O A:HOH248 4.3 42.9 1.0
O A:ASP101 4.7 31.1 1.0
CB A:ASP101 4.9 31.3 1.0

Nickel binding site 3 out of 3 in 2h9j

Go back to Nickel Binding Sites List in 2h9j
Nickel binding site 3 out of 3 in the Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Hen Egg White Lysozyme Soaked with NI2- Xylylbicyclam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni202

b:0.8
occ:1.00
NI1 A:MM5202 0.0 0.8 1.0
N11 A:MM5202 2.0 0.4 1.0
N4 A:MM5202 2.0 0.5 1.0
N7 A:MM5202 2.0 0.0 1.0
N14 A:MM5202 2.0 0.6 1.0
C5 A:MM5202 3.0 0.9 1.0
C6 A:MM5202 3.0 0.6 1.0
C12 A:MM5202 3.0 0.3 1.0
C13 A:MM5202 3.0 0.4 1.0
C8 A:MM5202 3.0 0.8 1.0
C1 A:MM5202 3.0 0.6 1.0
C2 A:MM5202 3.0 0.7 1.0
C3 A:MM5202 3.0 0.6 1.0
C10 A:MM5202 3.0 0.2 1.0
C9 A:MM5202 3.1 0.9 1.0
O A:HOH327 3.3 60.1 1.0
O A:HOH332 4.0 35.8 1.0
CH2 A:TRP123 5.0 24.8 1.0

Reference:

T.M.Hunter, I.W.Mcnae, D.P.Simpson, A.M.Smith, S.Moggach, F.White, M.D.Walkinshaw, S.Parsons, P.J.Sadler. Configurations of Nickel-Cyclam Antiviral Complexes and Protein Recognition. Chemistry V. 13 40 2007.
ISSN: ISSN 0947-6539
PubMed: 17120266
DOI: 10.1002/CHEM.200601334
Page generated: Fri Sep 25 08:09:48 2020
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