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Nickel in PDB 5mkc: Crystal Structure of the Rrga Jo.in Complex

Protein crystallography data

The structure of Crystal Structure of the Rrga Jo.in Complex, PDB code: 5mkc was solved by J.Bonnet, J.Cartannaz, G.Tourcier, C.Contreras-Martel, J.P.Kleman, D.Fenel, G.Schoehn, C.Morlot, T.Vernet, A.M.Di Guilmi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 132.541, 134.571, 144.474, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.3

Other elements in 5mkc:

The structure of Crystal Structure of the Rrga Jo.in Complex also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Rrga Jo.in Complex (pdb code 5mkc). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of the Rrga Jo.in Complex, PDB code: 5mkc:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 5mkc

Go back to Nickel Binding Sites List in 5mkc
Nickel binding site 1 out of 3 in the Crystal Structure of the Rrga Jo.in Complex


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 the Rrga Jo.in Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni804

b:0.6
occ:1.00
O4 A:SO4801 2.2 53.8 1.0
NH2 A:ARG630 3.4 39.0 1.0
S A:SO4801 3.4 63.0 1.0
O2 A:SO4801 3.6 68.8 1.0
NH1 A:ARG630 3.6 42.1 1.0
CG A:GLU632 3.7 40.1 1.0
CZ A:ARG630 4.0 40.3 1.0
OE2 A:GLU632 4.0 49.0 1.0
CD A:GLU632 4.2 44.8 1.0
O3 A:SO4801 4.3 50.3 1.0
O1 A:SO4801 4.4 57.7 1.0
CB A:GLU632 4.7 37.8 1.0

Nickel binding site 2 out of 3 in 5mkc

Go back to Nickel Binding Sites List in 5mkc
Nickel binding site 2 out of 3 in the Crystal Structure of the Rrga Jo.in Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Rrga Jo.in Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni804

b:97.8
occ:1.00
O1 D:SO4801 2.1 64.5 1.0
NH2 D:ARG630 3.4 33.9 1.0
S D:SO4801 3.4 0.7 1.0
O2 D:SO4801 3.6 84.4 1.0
CG D:GLU632 3.6 39.2 1.0
NH1 D:ARG630 3.7 33.1 1.0
CZ D:ARG630 4.0 33.0 1.0
OE2 D:GLU632 4.1 49.9 1.0
CD D:GLU632 4.2 47.8 1.0
O3 D:SO4801 4.3 73.2 1.0
O4 D:SO4801 4.4 45.0 1.0
CB D:GLU632 4.7 38.7 1.0

Nickel binding site 3 out of 3 in 5mkc

Go back to Nickel Binding Sites List in 5mkc
Nickel binding site 3 out of 3 in the Crystal Structure of the Rrga Jo.in Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Rrga Jo.in Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni804

b:0.6
occ:1.00
O4 F:SO4801 2.0 76.1 1.0
O A:HOH902 3.2 37.9 1.0
O A:HOH946 3.2 51.8 1.0
NH2 F:ARG630 3.4 46.2 1.0
S F:SO4801 3.4 0.3 1.0
NH1 F:ARG630 3.5 43.9 1.0
CG F:GLU632 3.6 53.5 1.0
O2 F:SO4801 3.7 0.4 1.0
CZ F:ARG630 3.9 45.7 1.0
CD1 A:LEU610 4.1 47.3 1.0
O A:HOH979 4.2 48.2 1.0
OE1 F:GLU632 4.2 66.2 1.0
O1 F:SO4801 4.2 77.6 1.0
O3 F:SO4801 4.3 79.4 1.0
CD F:GLU632 4.3 60.9 1.0
O A:HOH1001 4.6 43.1 1.0
CE A:LYS659 4.6 63.4 1.0
CB F:GLU632 4.6 50.6 1.0
O A:THR656 4.9 44.7 1.0
CA F:GLU632 4.9 47.7 1.0

Reference:

J.Bonnet, J.Cartannaz, G.Tourcier, C.Contreras-Martel, J.P.Kleman, C.Morlot, T.Vernet, A.M.Di Guilmi. Autocatalytic Association of Proteins By Covalent Bond Formation: A Bio Molecular Welding Toolbox Derived From A Bacterial Adhesin. Sci Rep V. 7 43564 2017.
ISSN: ESSN 2045-2322
PubMed: 28252635
DOI: 10.1038/SREP43564
Page generated: Wed Dec 16 01:41:43 2020

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