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Zinc in PDB 3kfu: Crystal Structure of the Transamidosome

Protein crystallography data

The structure of Crystal Structure of the Transamidosome, PDB code: 3kfu was solved by M.Blaise, M.Bailly, M.Frechin, S.Thirup, H.D.Becker, D.Kern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.19 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 115.920, 214.000, 127.840, 90.00, 93.36, 90.00
R / Rfree (%) 19.9 / 25.2

Other elements in 3kfu:

The structure of Crystal Structure of the Transamidosome also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Transamidosome (pdb code 3kfu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Transamidosome, PDB code: 3kfu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3kfu

Go back to Zinc Binding Sites List in 3kfu
Zinc binding site 1 out of 2 in the Crystal Structure of the Transamidosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Transamidosome within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn673

b:0.4
occ:1.00
SG F:CYS41 2.0 80.2 1.0
SG F:CYS24 2.1 0.0 1.0
SG F:CYS38 2.2 46.1 1.0
SG F:CYS22 2.2 68.5 1.0
CB F:CYS24 3.1 29.2 1.0
CB F:CYS22 3.2 20.7 1.0
CB F:CYS38 3.3 62.5 1.0
N F:CYS38 3.6 66.5 1.0
N F:CYS24 3.8 56.1 1.0
CB F:CYS41 3.8 21.3 1.0
CA F:CYS38 4.0 57.1 1.0
CA F:CYS24 4.0 43.1 1.0
N F:CYS41 4.1 50.4 1.0
C F:THR37 4.3 59.9 1.0
CD F:LYS19 4.4 51.0 1.0
N F:GLY23 4.5 16.0 1.0
CA F:CYS22 4.5 30.0 1.0
CA F:CYS41 4.6 50.3 1.0
CA F:THR37 4.6 25.5 1.0
C F:CYS22 4.6 39.3 1.0
C F:CYS38 4.7 56.0 1.0
NZ F:LYS19 4.7 23.4 1.0
O F:CYS38 4.7 67.5 1.0
CB F:VAL40 4.7 32.7 1.0
CE F:LYS19 4.8 58.8 1.0
C F:GLY23 5.0 29.2 1.0

Zinc binding site 2 out of 2 in 3kfu

Go back to Zinc Binding Sites List in 3kfu
Zinc binding site 2 out of 2 in the Crystal Structure of the Transamidosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Transamidosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn467

b:0.1
occ:1.00
SG I:CYS41 2.0 51.2 1.0
SG I:CYS24 2.1 53.2 1.0
SG I:CYS22 2.1 51.8 1.0
SG I:CYS38 2.2 26.9 1.0
CB I:CYS24 3.1 12.6 1.0
CB I:CYS22 3.2 36.3 1.0
CB I:CYS38 3.4 72.8 1.0
N I:CYS38 3.7 48.7 1.0
N I:CYS24 3.8 44.6 1.0
CB I:CYS41 3.8 10.0 1.0
CA I:CYS24 4.0 27.2 1.0
CA I:CYS38 4.1 28.9 1.0
N I:CYS41 4.1 56.4 1.0
C I:THR37 4.3 54.8 1.0
CD I:LYS19 4.4 42.9 1.0
N I:GLY23 4.5 16.3 1.0
CA I:CYS22 4.5 31.6 1.0
CA I:CYS41 4.6 68.4 1.0
C I:CYS22 4.6 44.4 1.0
CA I:THR37 4.6 26.1 1.0
NZ I:LYS19 4.6 20.4 1.0
C I:CYS38 4.7 37.8 1.0
CE I:LYS19 4.7 41.0 1.0
O I:CYS38 4.8 47.6 1.0
CB I:VAL40 4.8 29.9 1.0
C I:GLY23 4.9 16.1 1.0

Reference:

M.Blaise, M.Bailly, M.Frechin, M.A.Behrens, F.Fischer, C.L.Oliveira, H.D.Becker, J.S.Pedersen, S.Thirup, D.Kern. Crystal Structure of A Transfer-Ribonucleoprotein Particle That Promotes Asparagine Formation. Embo J. V. 29 3118 2010.
ISSN: ISSN 0261-4189
PubMed: 20717102
DOI: 10.1038/EMBOJ.2010.192
Page generated: Wed Dec 16 04:30:11 2020

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