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Sodium in PDB 5n4l: Rat Ceruloplasmin Trigonal Form

Protein crystallography data

The structure of Rat Ceruloplasmin Trigonal Form, PDB code: 5n4l 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) 14.99 / 3.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.230, 128.230, 407.660, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 26.5

Other elements in 5n4l:

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

Copper (Cu) 11 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Rat Ceruloplasmin Trigonal Form (pdb code 5n4l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Rat Ceruloplasmin Trigonal Form, PDB code: 5n4l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5n4l

Go back to Sodium Binding Sites List in 5n4l
Sodium binding site 1 out of 2 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1107

b:0.5
occ:1.00
O A:SER236 2.2 0.3 1.0
O A:TYR36 2.5 0.5 1.0
O A:GLY45 2.8 0.3 1.0
OH A:TYR48 2.8 91.3 1.0
C A:SER236 3.3 0.8 1.0
OG A:SER236 3.4 0.3 1.0
N A:GLY45 3.4 0.6 1.0
C A:TYR36 3.6 0.8 1.0
C A:GLY45 3.6 0.3 1.0
CA A:GLY45 3.6 0.9 1.0
CB A:SER236 3.9 0.0 1.0
CZ A:TYR48 3.9 0.0 1.0
OD1 A:ASN237 4.1 0.4 1.0
CA A:SER236 4.1 0.2 1.0
CA A:TYR36 4.1 0.8 1.0
N A:ASN237 4.2 0.7 1.0
CE1 A:TYR48 4.4 0.3 1.0
CA A:ASN237 4.4 0.5 1.0
N A:ILE44 4.5 0.5 1.0
O A:ARG38 4.5 0.1 1.0
C A:ILE44 4.6 0.1 1.0
SD A:MET239 4.6 1.0 1.0
N A:LEU37 4.7 0.2 1.0
O A:PHE35 4.7 0.7 1.0
N A:ARG46 4.9 0.2 1.0
CA A:ILE44 4.9 0.2 1.0
CB A:TYR36 5.0 0.3 1.0

Sodium binding site 2 out of 2 in 5n4l

Go back to Sodium Binding Sites List in 5n4l
Sodium binding site 2 out of 2 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1108

b:95.7
occ:1.00
O B:SER236 2.7 0.1 1.0
OH B:TYR48 2.8 0.7 1.0
O B:TYR36 2.9 0.6 1.0
O B:GLY45 3.0 0.6 1.0
C B:SER236 3.4 0.6 1.0
C B:TYR36 3.6 0.5 1.0
N B:GLY45 3.6 0.7 1.0
CB B:SER236 3.7 0.7 1.0
C B:GLY45 3.8 0.6 1.0
OG B:SER236 3.9 0.2 1.0
CA B:GLY45 3.9 0.6 1.0
OD1 B:ASN237 4.0 0.7 1.0
CA B:SER236 4.0 0.8 1.0
O B:PHE35 4.0 0.9 1.0
CA B:TYR36 4.1 0.8 1.0
CZ B:TYR48 4.1 0.7 1.0
N B:ILE44 4.2 0.6 1.0
N B:ASN237 4.3 0.2 1.0
N B:LEU37 4.4 98.4 1.0
C B:ILE44 4.5 0.8 1.0
CB B:ARG43 4.7 0.4 1.0
CE1 B:TYR48 4.7 0.5 1.0
CA B:ASN237 4.7 0.7 1.0
N B:ARG38 4.8 0.1 1.0
CA B:ILE44 4.8 1.0 1.0
C B:PHE35 4.8 0.2 1.0
SD B:MET239 4.9 0.9 1.0
N B:TYR36 4.9 0.3 1.0
CA B:LEU37 4.9 0.4 1.0
C B:ARG43 4.9 1.0 1.0
CD B:ARG43 4.9 0.7 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: Tue Dec 15 11:19:56 2020

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