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Sodium in PDB 6frn: Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride

Protein crystallography data

The structure of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride, PDB code: 6frn was solved by S.Engilberge, F.Riobe, S.Di Pietro, T.Wagner, S.Shima, E.Girard, E.Dumont, O.Maury, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.48 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.660, 144.970, 74.210, 90.00, 91.78, 90.00
R / Rfree (%) 16.4 / 18.9

Other elements in 6frn:

The structure of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride also contains other interesting chemical elements:

Terbium (Tb) 8 atoms
Calcium (Ca) 15 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride (pdb code 6frn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride, PDB code: 6frn:

Sodium binding site 1 out of 1 in 6frn

Go back to Sodium Binding Sites List in 6frn
Sodium binding site 1 out of 1 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na514

b:35.5
occ:1.00
H D:SER121 2.3 31.3 1.0
HG D:SER121 2.6 36.3 1.0
HB3 D:PHE119 2.8 31.8 1.0
HA D:PHE119 2.9 30.5 1.0
HB3 D:SER121 2.9 35.2 1.0
OG D:SER121 3.0 35.4 1.0
HD2 D:PRO120 3.0 36.9 1.0
N D:SER121 3.3 31.9 1.0
CB D:SER121 3.4 35.5 1.0
CA D:PHE119 3.5 30.4 1.0
HB3 D:PRO94 3.6 30.0 1.0
C D:PHE119 3.6 34.0 1.0
CB D:PHE119 3.6 31.2 1.0
N D:PRO120 3.7 33.6 1.0
HD1 D:PHE119 3.8 35.7 1.0
CD D:PRO120 3.8 36.2 1.0
CA D:SER121 4.0 32.0 1.0
HG3 D:PRO94 4.0 32.8 1.0
HG2 D:PRO94 4.2 33.1 1.0
O D:PHE119 4.2 30.9 1.0
HB2 D:SER121 4.4 35.8 1.0
HD3 D:PRO120 4.4 35.6 1.0
C D:PRO120 4.4 36.0 1.0
HB2 D:PHE119 4.4 29.9 1.0
CB D:PRO94 4.4 29.8 1.0
CG D:PRO94 4.4 33.0 1.0
H D:LEU122 4.4 29.5 1.0
CA D:PRO120 4.5 35.1 1.0
CD1 D:PHE119 4.5 35.1 1.0
CG D:PHE119 4.6 31.7 1.0
HG D:LEU122 4.7 35.6 1.0
HA D:SER121 4.8 31.3 1.0
HB2 D:PRO94 4.8 29.8 1.0
HB2 D:PRO120 4.8 37.0 1.0
N D:PHE119 4.9 31.4 1.0
C D:SER121 4.9 35.9 1.0
CG D:PRO120 4.9 41.0 1.0
N D:LEU122 5.0 31.1 1.0

Reference:

S.Engilberge, F.Riobe, T.Wagner, S.Di Pietro, C.Breyton, B.Franzetti, S.Shima, E.Girard, E.Dumont, O.Maury. Unveiling the Binding Modes of the Crystallophore, A Terbium-Based Nucleating and Phasing Molecular Agent For Protein Crystallography. Chemistry V. 24 9739 2018.
ISSN: ISSN 1521-3765
PubMed: 29806881
DOI: 10.1002/CHEM.201802172
Page generated: Tue Dec 15 12:15:43 2020

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