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Terbium 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:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Terbium Binding Sites:

The binding sites of Terbium 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 Terbium atom.
In total 5 binding sites of Terbium where determined in the Structure of the Bacteriophage T5 Distal Tail Protein PB9 Co- Crystallized with 10MM Tb-XO4, PDB code: 6f2m:
Jump to Terbium binding site number: 1; 2; 3; 4; 5;

Terbium binding site 1 out of 5 in 6f2m

Go back to Terbium Binding Sites List in 6f2m
Terbium binding site 1 out of 5 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 Terbium with other atoms in the Tb 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:Tb301

b:36.1
occ:0.80
 TB A:7MT301 0.0 36.1 0.8
N06 A:7MT301 2.4 30.8 0.8
N17 A:7MT301 2.4 33.7 0.8
OE2 A:GLU18 2.4 38.9 1.0
OE1 A:GLU18 2.4 33.8 1.0
N23 A:7MT301 2.5 32.2 0.8
H061 A:7MT301 2.6 30.6 0.8
N02 A:7MT301 2.7 28.3 0.8
N09 A:7MT301 2.7 30.8 0.8
CD A:GLU18 2.7 38.2 1.0
O26 A:7MT301 2.8 33.9 0.8
O28 A:7MT301 2.8 32.6 0.8
C05 A:7MT301 3.2 35.8 0.8
C10 A:7MT301 3.3 32.5 0.8
H052 A:7MT301 3.3 36.2 0.8
C16 A:7MT301 3.3 36.4 0.8
C30 A:7MT301 3.3 30.7 0.8
C11 A:7MT301 3.4 34.3 0.8
C22 A:7MT301 3.4 33.6 0.8
C08 A:7MT301 3.4 30.1 0.8
C01 A:7MT301 3.4 30.4 0.8
C07 A:7MT301 3.5 29.1 0.8
C29 A:7MT301 3.5 31.2 0.8
H012 A:7MT301 3.5 29.2 0.8
H082 A:7MT301 3.5 30.6 0.8
C18 A:7MT301 3.5 36.6 0.8
C24 A:7MT301 3.5 35.4 0.8
H301 A:7MT301 3.5 30.5 0.8
C04 A:7MT301 3.5 32.3 0.8
C03 A:7MT301 3.6 32.3 0.8
H291 A:7MT301 3.6 30.8 0.8
H072 A:7MT301 4.1 29.2 0.8
H071 A:7MT301 4.2 29.3 0.8
H031 A:7MT301 4.2 32.1 0.8
H042 A:7MT301 4.2 32.2 0.8
H051 A:7MT301 4.2 36.1 0.8
CG A:GLU18 4.2 39.2 1.0
HA A:GLU18 4.3 33.6 1.0
H041 A:7MT301 4.3 32.2 0.8
HB3 A:PRO55 4.4 32.4 1.0
H302 A:7MT301 4.4 30.6 0.8
H081 A:7MT301 4.4 30.7 0.8
H011 A:7MT301 4.5 30.0 0.8
H292 A:7MT301 4.5 30.5 0.8
O A:HOH401 4.5 35.9 1.0
H032 A:7MT301 4.5 32.8 0.8
HG2 A:GLU18 4.5 39.1 1.0
C13 A:7MT301 4.6 32.0 0.8
C15 A:7MT301 4.6 36.0 0.8
C19 A:7MT301 4.7 33.8 0.8
O27 A:7MT301 4.7 39.3 0.8
O25 A:7MT301 4.7 36.6 0.8
C21 A:7MT301 4.7 30.9 0.8
HG3 A:GLU18 4.8 38.5 1.0
O A:HOH437 4.8 43.6 1.0

Terbium binding site 2 out of 5 in 6f2m

Go back to Terbium Binding Sites List in 6f2m
Terbium binding site 2 out of 5 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 Terbium with other atoms in the Tb binding site number 2 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
B:Tb301

b:37.8
occ:0.30
 O B:HOH553 2.8 55.6 1.0
OE1 B:GLU18 3.0 99.5 1.0
HB3 B:GLU18 3.0 60.2 1.0
O B:HOH526 3.3 53.6 1.0
HB2 B:GLU18 3.9 60.4 1.0
CB B:GLU18 3.9 60.0 1.0
O B:HOH509 4.0 58.2 1.0
CD B:GLU18 4.1 0.8 1.0
HB3 B:PRO55 4.4 43.1 1.0
CG B:GLU18 4.6 73.9 1.0
HA B:GLU18 4.7 56.0 1.0

Terbium binding site 3 out of 5 in 6f2m

Go back to Terbium Binding Sites List in 6f2m
Terbium binding site 3 out of 5 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 Terbium with other atoms in the Tb binding site number 3 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
C:Tb301

b:35.9
occ:0.80
 TB C:7MT301 0.0 35.9 0.8
H061 C:7MT301 1.5 31.9 0.8
N17 C:7MT301 2.3 31.4 0.8
N06 C:7MT301 2.5 32.1 0.8
OE1 C:GLU18 2.5 31.6 1.0
OE2 C:GLU18 2.5 30.7 1.0
N23 C:7MT301 2.6 35.7 0.8
N02 C:7MT301 2.7 29.0 0.8
N09 C:7MT301 2.7 33.2 0.8
O28 C:7MT301 2.7 34.7 0.8
CD C:GLU18 2.8 24.6 1.0
O26 C:7MT301 2.9 32.9 0.8
C10 C:7MT301 3.2 30.3 0.8
H081 C:7MT301 3.2 30.7 0.8
C16 C:7MT301 3.2 34.2 0.8
H052 C:7MT301 3.3 34.4 0.8
C05 C:7MT301 3.3 34.8 0.8
C08 C:7MT301 3.3 31.1 0.8
C30 C:7MT301 3.3 29.5 0.8
C18 C:7MT301 3.4 36.9 0.8
C07 C:7MT301 3.4 31.3 0.8
H301 C:7MT301 3.4 29.8 0.8
C11 C:7MT301 3.4 34.5 0.8
C29 C:7MT301 3.5 32.6 0.8
C22 C:7MT301 3.5 35.0 0.8
C01 C:7MT301 3.6 33.2 0.8
C04 C:7MT301 3.6 32.4 0.8
C24 C:7MT301 3.6 36.1 0.8
H291 C:7MT301 3.6 32.8 0.8
H012 C:7MT301 3.7 33.0 0.8
C03 C:7MT301 3.7 35.3 0.8
H071 C:7MT301 4.0 31.6 0.8
H042 C:7MT301 4.2 32.5 0.8
H072 C:7MT301 4.2 31.2 0.8
H031 C:7MT301 4.2 35.4 0.8
H051 C:7MT301 4.3 35.5 0.8
CG C:GLU18 4.3 35.6 1.0
HA C:GLU18 4.3 31.9 1.0
H082 C:7MT301 4.3 31.1 0.8
H302 C:7MT301 4.3 30.1 0.8
H041 C:7MT301 4.4 32.5 0.8
HB3 C:PRO55 4.4 31.1 1.0
H292 C:7MT301 4.5 31.8 0.8
C13 C:7MT301 4.5 31.6 0.8
H032 C:7MT301 4.5 35.0 0.8
C15 C:7MT301 4.6 33.9 0.8
H011 C:7MT301 4.6 33.6 0.8
HG2 C:GLU18 4.6 35.6 1.0
O C:HOH401 4.6 33.6 1.0
O27 C:7MT301 4.6 39.4 0.8
O C:HOH430 4.7 54.3 1.0
C19 C:7MT301 4.8 34.8 0.8
HG3 C:GLU18 4.8 35.3 1.0
O C:HOH406 4.8 40.4 1.0
O25 C:7MT301 4.8 36.4 0.8
C21 C:7MT301 4.8 33.6 0.8

Terbium binding site 4 out of 5 in 6f2m

Go back to Terbium Binding Sites List in 6f2m
Terbium binding site 4 out of 5 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 Terbium with other atoms in the Tb binding site number 4 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
D:Tb301

b:42.5
occ:0.20
 OE1 D:GLU18 2.6 61.8 0.7
CD D:GLU18 3.6 75.3 0.7
O D:HOH532 3.9 65.6 1.0
HA D:GLU18 4.1 43.4 1.0
OE2 D:GLU18 4.2 65.3 0.7
HB3 D:PRO55 4.5 36.6 1.0
HG3 D:GLU18 4.7 56.0 0.7
CG D:GLU18 4.8 55.8 0.7

Terbium binding site 5 out of 5 in 6f2m

Go back to Terbium Binding Sites List in 6f2m
Terbium binding site 5 out of 5 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 Terbium with other atoms in the Tb binding site number 5 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
D:Tb302

b:35.0
occ:0.80
 TB D:7MT302 0.0 35.0 0.8
OE1 D:GLU71 2.3 37.0 1.0
O28 D:7MT302 2.4 39.0 0.8
OE2 D:GLU71 2.4 28.9 1.0
O26 D:7MT302 2.5 22.0 0.8
N23 D:7MT302 2.5 33.4 0.8
N06 D:7MT302 2.6 30.7 0.8
N17 D:7MT302 2.6 31.8 0.8
N02 D:7MT302 2.6 29.1 0.8
N09 D:7MT302 2.7 33.2 0.8
CD D:GLU71 2.7 37.9 1.0
H061 D:7MT302 2.9 29.7 0.8
C03 D:7MT302 3.3 33.5 0.8
H032 D:7MT302 3.3 33.6 0.8
C18 D:7MT302 3.3 40.9 0.8
C24 D:7MT302 3.3 25.4 0.8
C07 D:7MT302 3.4 33.7 0.8
C29 D:7MT302 3.4 35.6 0.8
C22 D:7MT302 3.4 31.3 0.8
C30 D:7MT302 3.4 32.8 0.8
C04 D:7MT302 3.4 29.6 0.8
C11 D:7MT302 3.4 37.0 0.8
H292 D:7MT302 3.4 34.8 0.8
C16 D:7MT302 3.4 35.5 0.8
C10 D:7MT302 3.5 33.2 0.8
H302 D:7MT302 3.5 32.5 0.8
C01 D:7MT302 3.5 32.1 0.8
H071 D:7MT302 3.5 33.7 0.8
C05 D:7MT302 3.5 32.1 0.8
C08 D:7MT302 3.5 32.4 0.8
H041 D:7MT302 3.6 28.5 0.8
HH22 D:ARG68 4.1 64.9 1.0
H011 D:7MT302 4.2 33.1 0.8
CG D:GLU71 4.2 38.4 1.0
H082 D:7MT302 4.2 32.1 0.8
H051 D:7MT302 4.2 30.9 0.8
H052 D:7MT302 4.3 32.8 0.8
H012 D:7MT302 4.3 31.8 0.8
H031 D:7MT302 4.3 34.4 0.8
H081 D:7MT302 4.3 32.1 0.8
H072 D:7MT302 4.4 33.3 0.8
H291 D:7MT302 4.4 34.4 0.8
H042 D:7MT302 4.4 29.8 0.8
H301 D:7MT302 4.4 33.3 0.8
HG2 D:GLU71 4.5 37.8 1.0
O27 D:7MT302 4.5 45.2 0.8
O25 D:7MT302 4.5 28.8 0.8
HB2 D:GLU71 4.7 32.5 1.0
C21 D:7MT302 4.7 34.0 0.8
HG3 D:GLU71 4.7 39.2 1.0
C19 D:7MT302 4.8 36.2 0.8
O D:HOH509 4.8 57.6 1.0
C15 D:7MT302 4.8 36.4 0.8
C13 D:7MT302 4.8 34.7 0.8
HA D:GLU71 4.9 32.3 1.0
HG23 D:THR75 4.9 49.1 1.0
NH2 D:ARG68 5.0 64.1 1.0
CB D:GLU71 5.0 32.5 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: Fri Oct 11 08:28:33 2024

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