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Sodium in PDB 6f2m: Structure of the Bacteriophage T5 Distal Tail Protein PB9 Co- Crystallized with 10MM Tb-XO4

Protein crystallography data

The structure of Structure of the Bacteriophage T5 Distal Tail Protein PB9 Co- Crystallized with 10MM Tb-XO4, PDB code: 6f2m was solved by S.Engilberge, F.Riobe, S.Di Pietro, C.Breyton, 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) 48.16 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.400, 95.240, 71.584, 90.00, 102.66, 90.00
R / Rfree (%) 17.8 / 20.3

Other elements in 6f2m:

The structure of Structure of the Bacteriophage T5 Distal Tail Protein PB9 Co- Crystallized with 10MM Tb-XO4 also contains other interesting chemical elements:

Terbium (Tb) 5 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Bacteriophage T5 Distal Tail Protein PB9 Co- Crystallized with 10MM Tb-XO4 (pdb code 6f2m). 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 the Bacteriophage T5 Distal Tail Protein PB9 Co- Crystallized with 10MM Tb-XO4, PDB code: 6f2m:

Sodium binding site 1 out of 1 in 6f2m

Go back to Sodium Binding Sites List in 6f2m
Sodium binding site 1 out of 1 in the Structure of the Bacteriophage T5 Distal Tail Protein PB9 Co- Crystallized with 10MM Tb-XO4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Bacteriophage T5 Distal Tail Protein PB9 Co- Crystallized with 10MM Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:39.4
occ:1.00
HH A:TYR54 1.9 32.9 1.0
HE1 A:PHE17 2.4 30.6 1.0
O A:PRO4 2.5 30.8 1.0
HE1 A:TYR54 2.6 30.3 1.0
HB3 A:LEU15 2.6 30.1 1.0
O A:LEU15 2.8 29.1 1.0
OH A:TYR54 2.8 32.4 1.0
HA A:ASP5 3.0 30.1 1.0
HG A:LEU3 3.2 32.5 1.0
HB3 A:ASP5 3.2 31.1 1.0
CE1 A:PHE17 3.3 30.6 1.0
CE1 A:TYR54 3.4 29.3 1.0
CZ A:TYR54 3.5 34.3 1.0
HD21 A:LEU3 3.6 32.8 1.0
C A:PRO4 3.6 33.4 1.0
HD22 A:LEU15 3.6 40.0 1.0
CB A:LEU15 3.7 29.9 1.0
CA A:ASP5 3.8 30.0 1.0
C A:LEU15 3.8 30.9 1.0
HA A:LEU15 3.8 29.9 1.0
HD23 A:LEU3 3.8 32.3 1.0
CB A:ASP5 3.9 30.5 1.0
CA A:LEU15 4.0 29.1 1.0
HB2 A:ASP5 4.0 29.0 1.0
CD2 A:LEU3 4.0 33.0 1.0
HZ A:PHE17 4.0 29.5 1.0
HD13 A:LEU15 4.1 36.9 1.0
HD1 A:PHE17 4.1 29.7 1.0
CG A:LEU3 4.1 32.1 1.0
CZ A:PHE17 4.1 29.8 1.0
N A:ASP5 4.1 30.6 1.0
CD1 A:PHE17 4.2 30.2 1.0
HD3 A:PRO6 4.3 30.1 1.0
HB2 A:LEU15 4.3 29.9 1.0
HD11 A:LEU3 4.3 30.5 1.0
HD13 A:LEU65 4.3 32.9 1.0
HG2 A:PRO4 4.4 33.6 1.0
CD2 A:LEU15 4.5 40.2 1.0
CG A:LEU15 4.5 36.1 1.0
O A:HOH535 4.6 28.1 1.0
CD1 A:TYR54 4.7 29.5 1.0
CD1 A:LEU15 4.8 36.8 1.0
CD1 A:LEU3 4.8 31.8 1.0
CA A:PRO4 4.9 29.7 1.0
CE2 A:TYR54 4.9 31.4 1.0
HD11 A:LEU65 5.0 32.4 1.0
N A:PRO4 5.0 28.2 1.0
HD22 A:LEU65 5.0 31.7 1.0
HD23 A:LEU15 5.0 39.2 1.0
O A:LEU3 5.0 28.2 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 12:14:24 2020

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