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Nickel in PDB 1sum: Crystal Structure of A Hypothetical Protein at 2.0 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution, PDB code: 1sum was solved by J.Liu, Y.Lou, H.Yokota, P.D.Adams, R.Kim, S.H.Kim, Berkeley Structuralgenomics Center (Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.677, 90.677, 45.255, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 25.5

Other elements in 1sum:

The structure of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution also contains other interesting chemical elements:

Iron (Fe) 7 atoms
Calcium (Ca) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution (pdb code 1sum). 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 A Hypothetical Protein at 2.0 A Resolution, PDB code: 1sum:

Nickel binding site 1 out of 1 in 1sum

Go back to Nickel Binding Sites List in 1sum
Nickel binding site 1 out of 1 in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution


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 A Hypothetical Protein at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:71.6
occ:1.00
O B:HOH611 2.0 72.5 1.0
OD2 B:ASP53 2.3 22.8 1.0
OE2 B:GLU49 2.5 15.3 1.0
OE1 B:GLU49 2.5 15.1 1.0
OE1 B:GLU50 2.6 21.4 1.0
O B:HOH592 2.7 47.5 1.0
CD B:GLU49 2.9 14.7 1.0
O B:HOH646 3.2 63.4 1.0
O3 B:PO3569 3.5 69.2 1.0
CG B:ASP53 3.5 16.4 1.0
CD B:GLU50 3.5 19.8 1.0
OE2 B:GLU50 3.9 21.1 1.0
FE B:FE237 4.0 40.3 1.0
OD1 B:ASP53 4.1 18.5 1.0
CG B:GLU49 4.4 15.3 1.0
P B:PO3569 4.6 72.1 1.0
CA B:GLU50 4.6 16.5 1.0
CB B:ASP53 4.6 15.1 1.0
O2 B:PO3569 4.7 71.8 1.0
CG B:GLU50 4.8 18.2 1.0
N B:GLU50 4.8 15.9 1.0
CB B:GLU50 4.9 17.1 1.0
O B:HOH575 4.9 38.9 1.0
O B:GLU49 4.9 15.2 1.0
C B:GLU49 5.0 15.8 1.0

Reference:

J.Liu, Y.Lou, H.Yokota, P.D.Adams, R.Kim, S.H.Kim. Crystal Structure of A Phou Protein Homologue: A New Class of Metalloprotein Containing Multinuclear Iron Clusters. J.Biol.Chem. V. 280 15960 2005.
ISSN: ISSN 0021-9258
PubMed: 15716271
DOI: 10.1074/JBC.M414117200
Page generated: Wed Dec 16 01:15:12 2020

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