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Nickel in PDB 3ny0: Crystal Structure of Uree From Helicobacter Pylori (NI2+ Bound Form)

Protein crystallography data

The structure of Crystal Structure of Uree From Helicobacter Pylori (NI2+ Bound Form), PDB code: 3ny0 was solved by R.Shi, C.Munger, A.Assinas, A.Matte, M.Cygler, Montreal-Kingston Bacterialstructural Genomics Initiative (Bsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.63 / 3.09
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.057, 91.057, 202.823, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 29.9

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Uree From Helicobacter Pylori (NI2+ Bound Form) (pdb code 3ny0). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Uree From Helicobacter Pylori (NI2+ Bound Form), PDB code: 3ny0:

Nickel binding site 1 out of 1 in 3ny0

Go back to Nickel Binding Sites List in 3ny0
Nickel binding site 1 out of 1 in the Crystal Structure of Uree From Helicobacter Pylori (NI2+ Bound Form)


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 Uree From Helicobacter Pylori (NI2+ Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni171

b:63.9
occ:1.00
NE2 D:HIS102 1.9 55.3 1.0
NE2 C:HIS102 2.0 59.7 1.0
NE2 B:HIS102 2.1 59.5 1.0
NE2 A:HIS102 2.1 55.9 1.0
NE2 B:HIS152 2.3 77.4 1.0
CD2 D:HIS102 2.8 55.5 1.0
CE1 A:HIS102 2.8 54.7 1.0
CD2 B:HIS102 2.9 59.1 1.0
CE1 C:HIS102 2.9 59.2 1.0
CE1 D:HIS102 3.0 54.4 1.0
CD2 C:HIS102 3.1 58.9 1.0
CE1 B:HIS102 3.2 59.0 1.0
CD2 B:HIS152 3.3 80.0 1.0
CD2 A:HIS102 3.3 53.5 1.0
CE1 B:HIS152 3.3 79.9 1.0
CG D:HIS102 4.0 53.5 1.0
ND1 D:HIS102 4.0 52.0 1.0
ND1 A:HIS102 4.0 51.3 1.0
ND1 C:HIS102 4.1 57.2 1.0
CG B:HIS102 4.1 56.3 1.0
CG C:HIS102 4.2 55.9 1.0
ND1 B:HIS102 4.2 56.1 1.0
CG A:HIS102 4.3 50.0 1.0
ND1 B:HIS152 4.4 81.8 1.0
CG B:HIS152 4.4 83.6 1.0
O B:ASN100 4.6 54.1 1.0
O D:ASN100 4.8 60.0 1.0
O A:ASN100 4.9 52.0 1.0

Reference:

R.Shi, C.Munger, A.Asinas, S.L.Benoit, E.Miller, A.Matte, R.J.Maier, M.Cygler. Crystal Structures of Apo and Metal-Bound Forms of the Uree Protein From Helicobacter Pylori: Role of Multiple Metal Binding Sites Biochemistry V. 49 7080 2010.
ISSN: ISSN 0006-2960
PubMed: 20681615
DOI: 10.1021/BI100372H
Page generated: Fri Sep 25 08:31:03 2020
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