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Sodium in PDB 5fje: Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B

Protein crystallography data

The structure of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B, PDB code: 5fje was solved by N.Vita, S.Platsaki, A.Basle, S.J.Allen, N.G.Paterson, A.T.Crombie, J.C.Murrell, K.J.Waldron, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.06 / 1.90
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 44.410, 41.420, 53.130, 90.00, 92.96, 90.00
R / Rfree (%) 19.819 / 23.166

Other elements in 5fje:

The structure of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B also contains other interesting chemical elements:

Copper (Cu) 26 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B (pdb code 5fje). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B, PDB code: 5fje:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5fje

Go back to Sodium Binding Sites List in 5fje
Sodium binding site 1 out of 2 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1136

b:40.9
occ:1.00
O A:HOH2027 2.2 50.5 1.0
OD1 A:ASN44 2.4 68.4 1.0
O A:HOH2029 2.5 70.3 1.0
O A:HOH2028 2.7 50.1 1.0
O A:HOH2072 2.8 52.6 1.0
O A:HOH2073 3.2 44.3 1.0
CG A:ASN44 3.6 64.5 1.0
ND2 A:ASN44 4.1 84.4 1.0
O A:LEU41 4.5 51.7 1.0
CB A:ASN44 4.8 58.8 1.0

Sodium binding site 2 out of 2 in 5fje

Go back to Sodium Binding Sites List in 5fje
Sodium binding site 2 out of 2 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1137

b:52.5
occ:1.00
O A:HOH2032 2.3 41.6 1.0
O A:HOH2074 2.5 55.3 1.0
O A:ALA46 2.5 41.1 1.0
O A:HOH2075 2.7 46.9 1.0
O A:HOH2033 2.8 34.1 1.0
C A:ALA46 3.7 37.9 1.0
O A:HOH2036 4.0 44.5 1.0
CA A:SER47 4.1 42.1 1.0
C A:SER47 4.3 38.5 1.0
N A:GLY49 4.3 34.1 1.0
N A:SER47 4.4 41.8 1.0
O A:SER47 4.4 42.0 1.0
CA A:GLY49 4.6 31.4 1.0
CB A:ALA46 4.7 38.9 1.0
N A:MET48 4.8 42.0 1.0
CA A:ALA46 4.8 38.5 1.0

Reference:

N.Vita, S.Platsaki, A.Basle, S.J.Allen, N.G.Paterson, A.T.Crombie, J.C.Murrell, K.J.Waldron, C.Dennison. A Four-Helix Bundle Stores Copper For Methane Oxidation. Nature V. 525 140 2015.
ISSN: ISSN 0028-0836
PubMed: 26308900
DOI: 10.1038/NATURE14854
Page generated: Tue Dec 15 10:59:07 2020

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