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Nickel in PDB 5c4v: Ski-Like Protein

Protein crystallography data

The structure of Ski-Like Protein, PDB code: 5c4v was solved by K.Wallden, T.Nyman, B.M.Hallberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.30 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 213.540, 122.830, 51.570, 90.00, 90.72, 90.00
R / Rfree (%) 20.8 / 24.2

Other elements in 5c4v:

The structure of Ski-Like Protein also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Ski-Like Protein (pdb code 5c4v). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Ski-Like Protein, PDB code: 5c4v:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5c4v

Go back to Nickel Binding Sites List in 5c4v
Nickel binding site 1 out of 2 in the Ski-Like Protein


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ski-Like Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni402

b:86.9
occ:1.00
ND1 B:HIS308 3.2 27.4 1.0
CE1 B:HIS308 3.5 26.9 1.0
O B:SER307 4.1 37.0 1.0
CE1 B:HIS306 4.1 17.1 1.0
CG B:HIS308 4.1 30.1 1.0
NI B:NI403 4.2 98.5 1.0
CA B:HIS308 4.5 35.7 1.0
NE2 B:HIS308 4.5 29.9 1.0
ND1 B:HIS306 4.6 18.6 1.0
C B:SER307 4.7 30.3 1.0
CB B:HIS308 4.8 32.1 1.0
ZN B:ZN401 4.8 48.4 1.0
N B:HIS308 4.9 32.9 1.0
CD2 B:HIS308 4.9 32.0 1.0

Nickel binding site 2 out of 2 in 5c4v

Go back to Nickel Binding Sites List in 5c4v
Nickel binding site 2 out of 2 in the Ski-Like Protein


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ski-Like Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni403

b:98.5
occ:1.00
ND1 B:HIS306 3.3 18.6 1.0
N B:SER307 3.5 28.5 1.0
O B:SER307 3.6 37.0 1.0
CA B:HIS306 3.7 22.5 1.0
O B:MET305 3.9 37.8 1.0
C B:HIS306 4.1 26.8 1.0
CG B:HIS306 4.2 19.1 1.0
CE1 B:HIS306 4.2 17.1 1.0
NI B:NI402 4.2 86.9 1.0
CB B:HIS306 4.3 20.1 1.0
C B:SER307 4.4 30.3 1.0
CA B:SER307 4.6 29.5 1.0
N B:HIS306 4.7 26.5 1.0
C B:MET305 4.7 30.3 1.0

Reference:

K.Wallden, T.Nyman, B.M.Hallberg. Snon Stabilizes the SMAD3/SMAD4 Protein Complex. Sci Rep V. 7 46370 2017.
ISSN: ESSN 2045-2322
PubMed: 28397834
DOI: 10.1038/SREP46370
Page generated: Wed Dec 16 01:40:17 2020

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