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Calcium in PDB 5n0k: Rat Ceruloplasmin Orthorhombic Form

Protein crystallography data

The structure of Rat Ceruloplasmin Orthorhombic Form, PDB code: 5n0k was solved by V.R.Samygina, A.V.Sokolov, G.Bourenkov, V.B.Vasilyev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.98 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.360, 103.810, 172.811, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.6

Other elements in 5n0k:

The structure of Rat Ceruloplasmin Orthorhombic Form also contains other interesting chemical elements:

Copper (Cu) 9 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Rat Ceruloplasmin Orthorhombic Form (pdb code 5n0k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Rat Ceruloplasmin Orthorhombic Form, PDB code: 5n0k:

Calcium binding site 1 out of 1 in 5n0k

Go back to Calcium Binding Sites List in 5n0k
Calcium binding site 1 out of 1 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1111

b:44.9
occ:1.00
O A:HOH1335 1.9 28.3 1.0
O A:LYS109 2.3 49.7 1.0
O A:GLN124 2.4 69.1 1.0
OD2 A:ASP127 2.4 51.3 1.0
OD1 A:ASP128 2.4 46.8 1.0
OD2 A:ASP128 2.6 48.3 1.0
OD1 A:ASP127 2.6 55.7 1.0
O A:HOH1249 2.6 41.1 1.0
CG A:ASP128 2.8 48.5 1.0
CG A:ASP127 2.9 53.8 1.0
C A:LYS109 3.5 48.3 1.0
C A:GLN124 3.6 70.2 1.0
CA A:ALA110 4.2 50.4 1.0
CA A:ARG125 4.3 61.3 1.0
N A:ALA110 4.3 49.2 1.0
CB A:ASP128 4.3 49.7 1.0
N A:ARG125 4.3 65.3 1.0
CB A:ASP127 4.4 55.0 1.0
O A:ALA114 4.4 46.6 1.0
O A:HOH1293 4.5 50.1 1.0
C A:ALA110 4.5 49.4 1.0
CA A:GLN124 4.6 74.9 1.0
CB A:GLU112 4.6 43.5 1.0
CA A:LYS109 4.6 44.9 1.0
N A:ASP128 4.7 52.9 1.0
OD2 A:ASP118 4.8 46.4 1.0
OE1 A:GLU112 4.8 45.2 1.0
N A:GLU112 4.8 44.5 1.0
N A:GLY113 4.9 43.0 1.0
N A:ASN111 4.9 47.2 1.0
CB A:LYS109 4.9 45.7 1.0
OG1 A:THR120 4.9 53.1 1.0
C A:ARG125 5.0 60.2 1.0
O A:ALA110 5.0 49.6 1.0
CA A:ASP128 5.0 51.4 1.0
CB A:GLN124 5.0 74.0 1.0

Reference:

V.R.Samygina, A.V.Sokolov, G.Bourenkov, T.R.Schneider, V.A.Anashkin, S.O.Kozlov, N.N.Kolmakov, V.B.Vasilyev. Rat Ceruloplasmin: A New Labile Copper Binding Site and Zinc/Copper Mosaic. Metallomics V. 9 1828 2017.
ISSN: ESSN 1756-591X
PubMed: 29177316
DOI: 10.1039/C7MT00157F
Page generated: Sat Dec 12 05:39:12 2020

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