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Nickel in PDB 1w9h: The Structure of A Piwi Protein From Archaeoglobus Fulgidus.

Protein crystallography data

The structure of The Structure of A Piwi Protein From Archaeoglobus Fulgidus., PDB code: 1w9h was solved by J.S.Parker, S.M.Roe, D.Barford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.01 / 1.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.090, 137.863, 51.663, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.7

Other elements in 1w9h:

The structure of The Structure of A Piwi Protein From Archaeoglobus Fulgidus. also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms
Chlorine (Cl) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus. (pdb code 1w9h). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus., PDB code: 1w9h:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 1w9h

Go back to Nickel Binding Sites List in 1w9h
Nickel binding site 1 out of 5 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1430

b:13.1
occ:1.00
O A:HOH2037 1.5 17.0 1.0
OD2 A:ASP73 2.3 24.2 1.0
OD1 A:ASP73 2.8 21.4 1.0
CG A:ASP73 2.9 19.0 1.0
ND1 A:HIS79 4.2 19.4 1.0
CB A:ASP73 4.4 14.0 1.0
O A:HOH2038 4.5 19.5 1.0
CE1 A:HIS79 4.8 18.9 1.0

Nickel binding site 2 out of 5 in 1w9h

Go back to Nickel Binding Sites List in 1w9h
Nickel binding site 2 out of 5 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1431

b:39.5
occ:1.00
OD1 A:ASP284 2.4 21.6 1.0
OD2 A:ASP284 2.8 28.9 1.0
CG A:ASP284 2.9 24.6 1.0
OE1 A:GLU247 2.9 25.4 1.0
OE2 A:GLU247 3.2 25.1 1.0
CD A:GLU247 3.4 21.4 1.0
OG A:SER282 3.9 19.7 1.0
CB A:ASP284 4.3 21.9 1.0
CB A:SER282 4.4 15.3 1.0
O A:HOH2163 4.5 32.5 1.0
O A:HOH2164 4.8 30.4 1.0
CG A:GLU247 4.9 13.7 1.0
N A:ASP284 4.9 18.3 1.0

Nickel binding site 3 out of 5 in 1w9h

Go back to Nickel Binding Sites List in 1w9h
Nickel binding site 3 out of 5 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1432

b:26.4
occ:1.00
O A:HOH2168 2.0 18.8 1.0
ND1 A:HIS291 2.4 7.2 1.0
O A:HOH2189 2.5 10.2 1.0
O A:HOH2190 2.9 26.4 1.0
CG A:HIS291 3.4 6.1 1.0
OE1 A:GLU349 3.4 25.3 1.0
CE1 A:HIS291 3.4 8.1 1.0
CB A:HIS291 3.6 4.1 1.0
OD1 A:ASN293 3.9 20.5 1.0
O A:HOH2063 4.3 29.7 1.0
NE2 A:HIS291 4.5 9.8 1.0
CD2 A:HIS291 4.5 7.3 1.0
O A:HOH2151 4.5 9.3 1.0
CD A:GLU349 4.6 15.1 1.0
O A:HOH2156 4.7 35.4 1.0
O A:HOH2188 4.8 7.9 1.0
NH2 A:ARG257 4.9 10.1 1.0
CG A:ASN293 5.0 16.4 1.0

Nickel binding site 4 out of 5 in 1w9h

Go back to Nickel Binding Sites List in 1w9h
Nickel binding site 4 out of 5 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1433

b:35.2
occ:1.00
NE2 A:HIS365 2.2 20.5 1.0
CE1 A:HIS365 2.4 4.7 1.0
OD2 A:ASP369 2.4 14.2 1.0
O A:HOH2177 2.4 34.3 1.0
O A:HOH2205 2.7 27.4 1.0
OD1 A:ASP369 2.8 10.2 1.0
CG A:ASP369 2.9 9.2 1.0
CD2 A:HIS365 3.6 23.3 1.0
ND1 A:HIS365 3.7 20.4 1.0
CG A:HIS365 4.3 19.7 1.0
CB A:ASP369 4.3 3.9 1.0
NZ A:LYS315 4.5 27.3 1.0
OH A:TYR373 4.6 17.9 1.0
CE A:LYS315 4.9 25.7 1.0

Nickel binding site 5 out of 5 in 1w9h

Go back to Nickel Binding Sites List in 1w9h
Nickel binding site 5 out of 5 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1434

b:27.9
occ:1.00
OD1 A:ASP105 2.5 20.2 1.0
OD2 A:ASP105 2.6 19.2 1.0
CG A:ASP105 2.9 16.9 1.0
O A:HOH2065 4.4 23.9 1.0
CB A:ASP105 4.4 15.0 1.0
O A:ASP101 4.7 9.7 1.0

Reference:

J.S.Parker, S.M.Roe, D.Barford. Crystal Structure of A Piwi Protein Suggests Mechanisms For Sirna Recognition and Slicer Activity Embo J. V. 23 4727 2004.
ISSN: ISSN 0261-4189
PubMed: 15565169
DOI: 10.1038/SJ.EMBOJ.7600488
Page generated: Thu Oct 29 06:16:01 2020
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