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Terbium in PDB 5mf2: Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4

Protein crystallography data

The structure of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4, PDB code: 5mf2 was solved by S.Engilberge, F.Riobe, S.Di Pietro, L.Lassalle, C.-A.Arnaud, C.Breyton, D.Madern, N.Coquelle, O.Maury, E.Girard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.38 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.464, 95.502, 71.492, 90.00, 103.46, 90.00
R / Rfree (%) 21 / 23.6

Other elements in 5mf2:

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

Chlorine (Cl) 4 atoms

Terbium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Terbium atom in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 (pdb code 5mf2). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 15 binding sites of Terbium where determined in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4, PDB code: 5mf2:
Jump to Terbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Terbium binding site 1 out of 15 in 5mf2

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Terbium binding site 1 out of 15 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb301

b:66.9
occ:0.30
O A:HOH489 2.4 61.3 1.0
O A:HOH437 4.9 36.1 1.0

Terbium binding site 2 out of 15 in 5mf2

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Terbium binding site 2 out of 15 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb302

b:64.5
occ:0.20
OE1 A:GLU18 2.5 80.0 0.2
CD A:GLU18 3.1 80.9 0.2
OE2 A:GLU18 3.2 82.5 0.2
TB A:TB303 4.3 40.9 0.1
HA A:GLU18 4.5 88.7 1.0
CG A:GLU18 4.6 80.2 0.2
HB3 A:PRO55 4.6 54.0 1.0
HG3 A:GLU18 4.7 96.3 0.2

Terbium binding site 3 out of 15 in 5mf2

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Terbium binding site 3 out of 15 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb303

b:40.9
occ:0.10
OE2 A:GLU18 2.0 82.5 0.2
CD A:GLU18 3.2 80.9 0.2
HG2 A:GLU18 3.6 96.3 0.2
CG A:GLU18 4.0 80.2 0.2
OE1 A:GLU18 4.2 80.0 0.2
HG3 A:GLU18 4.3 96.3 0.2
TB A:TB302 4.3 64.5 0.2
HB3 A:PRO55 4.4 54.0 1.0

Terbium binding site 4 out of 15 in 5mf2

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Terbium binding site 4 out of 15 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 4 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb304

b:51.0
occ:0.70
TB A:7MT304 0.0 51.0 0.7
N23 A:7MT304 2.4 43.4 0.7
OE2 A:GLU71 2.5 51.0 0.7
N17 A:7MT304 2.5 44.5 0.7
OE1 A:GLU71 2.6 51.8 0.7
N06 A:7MT304 2.6 37.0 0.7
N09 A:7MT304 2.6 37.0 0.7
N02 A:7MT304 2.7 33.9 0.7
H061 A:7MT304 2.7 44.5 0.7
O26 A:7MT304 2.8 32.0 0.7
CD A:GLU71 2.8 49.4 0.7
O28 A:7MT304 2.9 44.5 0.7
H292 A:7MT304 3.1 45.6 0.7
C29 A:7MT304 3.2 38.0 0.7
C11 A:7MT304 3.2 41.9 0.7
H032 A:7MT304 3.3 41.1 0.7
C10 A:7MT304 3.3 38.8 0.7
C03 A:7MT304 3.3 34.2 0.7
C22 A:7MT304 3.4 42.5 0.7
C30 A:7MT304 3.4 35.5 0.7
C16 A:7MT304 3.5 46.2 0.7
H302 A:7MT304 3.5 42.7 0.7
C04 A:7MT304 3.5 32.2 0.7
C07 A:7MT304 3.5 40.3 0.7
C24 A:7MT304 3.5 38.4 0.7
H041 A:7MT304 3.5 38.7 0.7
H071 A:7MT304 3.6 48.5 0.7
C18 A:7MT304 3.6 47.9 0.7
C01 A:7MT304 3.6 37.6 0.7
C05 A:7MT304 3.6 33.5 0.7
C08 A:7MT304 3.7 39.8 0.7
H291 A:7MT304 4.1 45.6 0.7
H011 A:7MT304 4.1 45.1 0.7
H051 A:7MT304 4.2 40.3 0.7
H052 A:7MT304 4.2 40.3 0.7
H082 A:7MT304 4.2 47.8 0.7
H031 A:7MT304 4.3 41.1 0.7
H012 A:7MT304 4.3 45.1 0.7
H301 A:7MT304 4.3 42.7 0.7
CG A:GLU71 4.3 47.7 0.7
H081 A:7MT304 4.3 47.8 0.7
H072 A:7MT304 4.4 48.5 0.7
H042 A:7MT304 4.4 38.7 0.7
HG2 A:GLU71 4.4 57.2 0.7
C19 A:7MT304 4.5 42.5 0.7
C21 A:7MT304 4.7 44.9 0.7
C13 A:7MT304 4.7 43.6 0.7
O25 A:7MT304 4.7 38.8 0.7
C15 A:7MT304 4.8 44.6 0.7
HB2 A:GLU71 4.8 55.5 0.7
O27 A:7MT304 4.8 54.1 0.7
HG3 A:GLU71 4.8 57.2 0.7
HH11 A:ARG68 5.0 70.5 1.0

Terbium binding site 5 out of 15 in 5mf2

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Terbium binding site 5 out of 15 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 5 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb301

b:82.5
occ:0.30
O B:HOH461 2.3 72.6 1.0
O B:HOH458 2.5 61.3 1.0
OE2 B:GLU18 2.8 93.2 0.3
CD B:GLU18 3.7 90.1 0.3
OE1 B:GLU18 4.1 88.7 0.3
HB2 B:GLU18 4.4 0.9 0.3
HB3 B:PRO55 4.4 93.1 1.0
CG B:GLU18 4.9 87.7 0.3

Terbium binding site 6 out of 15 in 5mf2

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Terbium binding site 6 out of 15 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 6 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb302

b:51.5
occ:0.20
O B:HOH433 3.9 57.9 1.0
HB3 B:ARG92 4.0 48.4 1.0
H B:GLY93 4.3 54.6 1.0
HA2 B:GLY93 4.5 58.0 1.0
HD3 B:ARG92 4.5 50.6 1.0
N B:GLY93 4.8 45.5 1.0
CB B:ARG92 5.0 40.3 1.0

Terbium binding site 7 out of 15 in 5mf2

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Terbium binding site 7 out of 15 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 7 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb303

b:57.7
occ:0.20
O B:HOH463 2.5 63.1 1.0
O B:HOH462 3.0 78.0 1.0
O B:HOH435 4.8 35.6 1.0
HE2 B:LYS105 4.8 70.7 1.0

Terbium binding site 8 out of 15 in 5mf2

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Terbium binding site 8 out of 15 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 8 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb304

b:72.0
occ:0.20
O B:HOH461 3.5 72.6 1.0

Terbium binding site 9 out of 15 in 5mf2

Go back to Terbium Binding Sites List in 5mf2
Terbium binding site 9 out of 15 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 9 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb305

b:53.4
occ:0.10
HH21 B:ARG68 3.3 90.2 1.0
NH2 B:ARG68 3.6 75.1 1.0
HH22 B:ARG68 3.6 90.2 1.0
CZ B:ARG68 4.3 74.5 1.0
HE B:ARG68 4.5 87.0 1.0
HG2 B:GLU71 4.6 89.8 1.0
HE2 B:MET1 4.6 86.5 1.0
NE B:ARG68 4.7 72.5 1.0

Terbium binding site 10 out of 15 in 5mf2

Go back to Terbium Binding Sites List in 5mf2
Terbium binding site 10 out of 15 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 10 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tb301

b:61.8
occ:0.20
O C:HOH471 2.6 69.4 1.0
HH22 C:ARG90 3.9 82.0 1.0
HH12 C:ARG90 4.6 78.3 1.0
NH2 C:ARG90 4.8 68.3 1.0
O C:HOH420 4.9 55.5 1.0

Reference:

S.Engilberge, F.Riobe, S.Di Pietro, L.Lassalle, N.Coquelle, C.A.Arnaud, D.Pitrat, J.C.Mulatier, D.Madern, C.Breyton, O.Maury, E.Girard. Crystallophore: A Versatile Lanthanide Complex For Protein Crystallography Combining Nucleating Effects, Phasing Properties, and Luminescence. Chem Sci V. 8 5909 2017.
ISSN: ISSN 2041-6520
PubMed: 29619195
DOI: 10.1039/C7SC00758B
Page generated: Wed Dec 16 02:26:47 2020

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