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Zinc 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:

Nickel (Ni) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Ski-Like Protein (pdb code 5c4v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Ski-Like Protein, PDB code: 5c4v:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5c4v

Go back to Zinc Binding Sites List in 5c4v
Zinc binding site 1 out of 3 in the Ski-Like Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ski-Like Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:48.4
occ:1.00
SG B:CYS291 1.6 31.5 1.0
NE2 B:HIS306 1.9 15.8 1.0
SG B:CYS294 2.0 33.3 1.0
NE2 B:HIS308 2.0 29.9 1.0
CE1 B:HIS306 2.5 17.1 1.0
CE1 B:HIS308 2.6 26.9 1.0
CB B:CYS294 3.0 30.6 1.0
CD2 B:HIS308 3.1 32.0 1.0
CB B:CYS291 3.2 37.0 1.0
CD2 B:HIS306 3.2 16.8 1.0
ND1 B:HIS308 3.7 27.4 1.0
ND1 B:HIS306 3.7 18.6 1.0
N B:CYS294 3.8 35.8 1.0
CG B:HIS308 3.9 30.1 1.0
CA B:CYS294 4.0 31.1 1.0
CG B:HIS306 4.1 19.1 1.0
CB B:GLU293 4.5 33.1 1.0
CA B:CYS291 4.7 40.3 1.0
CZ B:PHE298 4.8 31.0 1.0
CE1 B:PHE298 4.8 33.2 1.0
C B:GLU293 4.8 44.1 1.0
NI B:NI402 4.8 86.9 1.0
C B:CYS294 4.9 35.3 1.0

Zinc binding site 2 out of 3 in 5c4v

Go back to Zinc Binding Sites List in 5c4v
Zinc binding site 2 out of 3 in the Ski-Like Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ski-Like Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:57.9
occ:1.00
NE2 D:HIS306 2.2 46.2 1.0
SG D:CYS294 2.2 52.4 1.0
NE2 D:HIS308 2.2 68.2 1.0
SG D:CYS291 2.3 51.3 1.0
CE1 D:HIS308 2.6 70.9 1.0
CE1 D:HIS306 2.9 50.2 1.0
CB D:CYS291 3.1 64.2 1.0
CB D:CYS294 3.2 52.9 1.0
CD2 D:HIS308 3.2 67.0 1.0
CD2 D:HIS306 3.3 54.1 1.0
N D:CYS294 3.5 56.6 1.0
ND1 D:HIS308 3.6 69.8 1.0
CA D:CYS294 3.9 51.3 1.0
CG D:HIS308 4.0 64.8 1.0
ND1 D:HIS306 4.1 52.0 1.0
CB D:GLU293 4.1 59.8 1.0
CG D:HIS306 4.3 50.8 1.0
C D:GLU293 4.5 56.6 1.0
CA D:CYS291 4.6 65.6 1.0
CA D:GLU293 4.7 56.5 1.0
N D:GLU293 4.7 56.5 1.0
SG D:CYS272 4.7 74.4 1.0
C D:CYS294 4.8 54.3 1.0
CE1 D:PHE298 4.8 57.3 1.0
C D:CYS291 4.9 58.8 1.0
CZ D:PHE298 4.9 52.0 1.0

Zinc binding site 3 out of 3 in 5c4v

Go back to Zinc Binding Sites List in 5c4v
Zinc binding site 3 out of 3 in the Ski-Like Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ski-Like Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:41.7
occ:1.00
NE2 F:HIS308 1.5 36.4 1.0
CE1 F:HIS308 1.9 39.0 1.0
NE2 F:HIS306 1.9 27.1 1.0
SG F:CYS294 2.0 40.7 1.0
SG F:CYS291 2.2 31.0 1.0
CB F:CYS291 2.8 30.1 1.0
CD2 F:HIS308 2.8 39.6 1.0
CE1 F:HIS306 2.8 27.7 1.0
CD2 F:HIS306 3.0 25.5 1.0
ND1 F:HIS308 3.1 35.4 1.0
CB F:CYS294 3.2 40.8 1.0
N F:CYS294 3.5 44.8 1.0
CG F:HIS308 3.5 37.5 1.0
CA F:CYS294 3.9 44.5 1.0
ND1 F:HIS306 4.0 28.5 1.0
CG F:HIS306 4.1 28.6 1.0
CA F:CYS291 4.2 33.1 1.0
CE1 F:PHE298 4.4 30.9 1.0
CB F:GLU293 4.5 52.6 1.0
CZ F:PHE298 4.6 36.7 1.0
C F:GLU293 4.6 51.9 1.0
C F:CYS294 4.7 45.5 1.0
C F:CYS291 4.7 35.2 1.0
SG F:CYS272 4.7 35.7 1.0
O F:CYS291 4.8 38.6 1.0
N F:GLU293 4.8 47.9 1.0
N F:CYS295 4.8 46.0 1.0
CA F:GLU293 4.9 48.6 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 06:05:57 2020

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