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Terbium in PDB 6frm: Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4

Protein crystallography data

The structure of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4, PDB code: 6frm was solved by S.Engilberge, F.Riobe, T.Wagner, S.Di Pietro, 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) 48.69 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.170, 147.875, 146.059, 90.00, 90.40, 90.00
R / Rfree (%) 17.7 / 20.9

Other elements in 6frm:

The structure of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 17 atoms

Terbium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Terbium atom in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 (pdb code 6frm). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 16 binding sites of Terbium where determined in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4, PDB code: 6frm:
Jump to Terbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Terbium binding site 1 out of 16 in 6frm

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Terbium binding site 1 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb502

b:50.5
occ:1.00
TB A:7MT502 0.0 50.5 1.0
OE2 A:GLU113 2.4 55.2 1.0
N23 A:7MT502 2.5 44.6 1.0
N06 A:7MT502 2.5 56.8 1.0
N17 A:7MT502 2.6 37.4 1.0
N02 A:7MT502 2.7 49.0 1.0
O26 A:7MT502 2.7 42.1 1.0
OE1 A:GLU113 2.8 50.6 1.0
N09 A:7MT502 2.8 52.1 1.0
CD A:GLU113 2.9 60.7 1.0
O27 A:7MT502 3.0 49.7 1.0
C05 A:7MT502 3.1 47.6 1.0
C01 A:7MT502 3.3 52.5 1.0
C22 A:7MT502 3.3 46.0 1.0
C11 A:7MT502 3.4 46.5 1.0
C24 A:7MT502 3.4 46.9 1.0
C04 A:7MT502 3.4 45.4 1.0
C10 A:7MT502 3.4 43.7 1.0
C16 A:7MT502 3.5 43.1 1.0
C30 A:7MT502 3.5 45.0 1.0
C29 A:7MT502 3.5 47.2 1.0
C08 A:7MT502 3.5 53.9 1.0
C07 A:7MT502 3.6 57.1 1.0
C18 A:7MT502 3.6 48.9 1.0
C03 A:7MT502 3.6 51.9 1.0
CG A:GLU113 4.3 48.6 1.0
O25 A:7MT502 4.6 49.1 1.0
C21 A:7MT502 4.7 49.3 1.0
O A:HOH601 4.7 60.5 1.0
C19 A:7MT502 4.7 49.3 1.0
C13 A:7MT502 4.7 45.4 1.0
C15 A:7MT502 4.8 44.4 1.0
O28 A:7MT502 4.8 53.8 1.0
O A:HOH679 4.9 55.7 1.0
O A:HOH740 5.0 58.6 1.0

Terbium binding site 2 out of 16 in 6frm

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Terbium binding site 2 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb503

b:52.1
occ:1.00
OD1 A:ASP171 2.3 45.1 1.0
OD2 A:ASP88 2.4 50.2 1.0
NE2 A:HIS89 2.5 44.1 1.0
NE2 A:HIS234 2.7 35.6 1.0
O A:HOH649 2.8 43.4 1.0
OD2 A:ASP171 2.9 58.0 1.0
CG A:ASP171 2.9 49.7 1.0
O A:HOH735 3.1 42.3 1.0
CD2 A:HIS89 3.4 44.0 1.0
CG A:ASP88 3.4 49.5 1.0
CD2 A:HIS234 3.5 35.8 1.0
CE1 A:HIS89 3.5 44.7 1.0
OD1 A:ASP88 3.7 49.4 1.0
CE1 A:HIS234 3.7 35.7 1.0
CB A:ASP171 4.4 47.9 1.0
OG A:SER233 4.5 45.3 1.0
CG A:HIS89 4.5 42.7 1.0
ND1 A:HIS89 4.6 45.2 1.0
CG A:HIS234 4.7 37.3 1.0
OE1 A:GLU86 4.7 0.8 1.0
CB A:ASP88 4.8 41.2 1.0
ND1 A:HIS234 4.8 37.9 1.0
CE2 A:TYR25 4.9 51.1 1.0
OH A:TYR25 5.0 60.8 1.0
OD1 A:ASN170 5.0 66.3 1.0

Terbium binding site 3 out of 16 in 6frm

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Terbium binding site 3 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb502

b:50.7
occ:1.00
OD2 B:ASP88 2.4 53.4 1.0
OD1 B:ASP171 2.5 44.6 1.0
O B:HOH723 2.6 46.4 1.0
NE2 B:HIS89 2.6 46.8 1.0
NE2 B:HIS234 2.7 36.9 1.0
OD2 B:ASP171 2.9 58.6 1.0
OE2 B:GLU86 3.0 53.0 1.0
CG B:ASP171 3.1 47.3 1.0
CD2 B:HIS234 3.4 37.6 1.0
CD2 B:HIS89 3.5 46.5 1.0
CG B:ASP88 3.5 51.1 1.0
CE1 B:HIS89 3.6 46.1 1.0
O B:HOH716 3.9 49.6 1.0
CE1 B:HIS234 3.9 37.2 1.0
OD1 B:ASP88 3.9 53.1 1.0
CD B:GLU86 3.9 83.0 1.0
OE1 B:GLU86 4.3 82.3 1.0
OG B:SER233 4.5 60.0 1.0
CB B:ASP171 4.5 43.6 1.0
CG B:HIS89 4.6 44.5 1.0
CG B:HIS234 4.6 37.7 1.0
ND1 B:HIS89 4.7 46.3 1.0
CB B:ASP88 4.8 37.6 1.0
ND1 B:HIS234 4.9 38.5 1.0
CE2 B:TYR25 4.9 48.0 1.0
OH B:TYR25 5.0 65.3 1.0

Terbium binding site 4 out of 16 in 6frm

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Terbium binding site 4 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 4 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tb502

b:62.4
occ:0.50
OE2 C:GLU113 2.6 58.2 1.0
OE1 C:GLU113 2.6 84.5 1.0
CD C:GLU113 2.9 84.7 1.0
O C:HOH786 3.0 65.4 1.0
O C:HOH788 3.4 60.9 1.0
O C:HOH769 3.5 75.0 1.0
CG C:GLU113 4.4 74.5 1.0

Terbium binding site 5 out of 16 in 6frm

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Terbium binding site 5 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 5 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tb503

b:61.0
occ:1.00
OD1 C:ASP171 2.2 39.4 1.0
NE2 C:HIS234 2.6 37.6 1.0
NE2 C:HIS89 2.6 38.1 1.0
OD2 C:ASP88 2.7 49.1 1.0
OD2 C:ASP171 2.8 53.9 1.0
CG C:ASP171 2.9 44.9 1.0
FE C:FE504 3.0 53.2 0.6
O C:HOH696 3.4 52.1 1.0
CD2 C:HIS89 3.4 38.7 1.0
CG C:ASP88 3.5 44.3 1.0
CD2 C:HIS234 3.5 38.0 1.0
OD1 C:ASP88 3.5 47.2 1.0
CE1 C:HIS89 3.6 38.6 1.0
CE1 C:HIS234 3.6 36.5 1.0
CB C:ASP171 4.3 42.5 1.0
OE2 C:GLU86 4.3 54.0 1.0
OG C:SER233 4.4 46.9 1.0
CG C:HIS89 4.6 39.9 1.0
CG C:HIS234 4.6 37.3 1.0
ND1 C:HIS89 4.7 41.0 1.0
ND1 C:HIS234 4.7 37.5 1.0
NE2 C:HIS152 4.8 78.4 1.0
CG C:GLU86 4.8 59.3 1.0
CE2 C:TYR25 4.8 54.0 1.0
CB C:ASP88 4.9 37.6 1.0
CD C:GLU86 4.9 75.7 1.0
CD2 C:HIS84 4.9 58.5 1.0
OH C:TYR25 5.0 71.1 1.0

Terbium binding site 6 out of 16 in 6frm

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Terbium binding site 6 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 6 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Tb502

b:71.2
occ:0.50
OE1 D:GLU113 2.5 0.9 1.0
OE2 D:GLU113 2.5 0.2 1.0
O D:HOH1597 2.5 74.0 1.0
CD D:GLU113 2.8 0.0 1.0
O D:HOH1612 2.9 66.5 1.0
O D:HOH1656 3.0 70.0 1.0
CG D:GLU113 4.3 77.7 1.0

Terbium binding site 7 out of 16 in 6frm

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Terbium binding site 7 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 7 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Tb503

b:63.9
occ:0.30
OD1 D:ASP321 2.8 63.8 1.0
OD2 D:ASP321 2.9 76.0 1.0
O D:HOH1652 3.0 65.1 1.0
CG D:ASP321 3.1 63.3 1.0
ND2 D:ASN357 4.3 55.8 1.0
CB D:ASP321 4.5 47.3 1.0
O D:HOH1504 4.6 35.2 1.0
O D:HOH1613 4.8 55.5 1.0

Terbium binding site 8 out of 16 in 6frm

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Terbium binding site 8 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 8 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Tb504

b:63.9
occ:1.00
OD1 D:ASP171 2.3 55.1 1.0
FE D:FE505 2.5 54.6 0.4
NE2 D:HIS89 2.6 44.7 1.0
NE2 D:HIS234 2.6 48.2 1.0
OD2 D:ASP88 2.7 52.2 1.0
OD2 D:ASP171 2.9 68.2 1.0
CG D:ASP171 3.0 55.0 1.0
O D:HOH1578 3.3 46.0 1.0
CD2 D:HIS89 3.4 45.5 1.0
CD2 D:HIS234 3.4 48.4 1.0
CG D:ASP88 3.4 46.8 1.0
OD1 D:ASP88 3.5 50.6 1.0
CE1 D:HIS89 3.5 44.9 1.0
CE1 D:HIS234 3.7 47.3 1.0
OE2 D:GLU86 4.1 81.9 1.0
OG D:SER233 4.4 58.7 1.0
CB D:ASP171 4.4 46.8 1.0
CG D:HIS89 4.5 46.0 1.0
ND1 D:HIS89 4.6 47.4 1.0
CG D:HIS234 4.6 47.0 1.0
ND1 D:HIS234 4.8 47.7 1.0
CB D:ASP88 4.9 40.8 1.0
CE2 D:TYR25 4.9 56.1 1.0
OH D:TYR25 5.0 69.0 1.0
CB D:GLU86 5.0 53.5 1.0
CD D:GLU86 5.0 95.5 1.0

Terbium binding site 9 out of 16 in 6frm

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Terbium binding site 9 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 9 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Tb502

b:51.9
occ:1.00
OD2 E:ASP88 2.3 39.8 1.0
OD1 E:ASP171 2.3 44.6 1.0
NE2 E:HIS89 2.6 44.8 1.0
OD2 E:ASP171 2.8 51.4 1.0
NE2 E:HIS234 2.8 39.4 1.0
CG E:ASP171 2.9 47.8 1.0
OE2 E:GLU86 3.0 55.9 1.0
O E:HOH748 3.1 44.8 1.0
CG E:ASP88 3.3 47.3 1.0
CD2 E:HIS234 3.3 39.5 1.0
CD2 E:HIS89 3.4 44.6 1.0
CE1 E:HIS89 3.6 44.3 1.0
OD1 E:ASP88 3.7 50.5 1.0
CE1 E:HIS234 4.0 39.8 1.0
CD E:GLU86 4.1 86.6 1.0
CB E:ASP171 4.4 43.0 1.0
OG E:SER233 4.5 51.7 1.0
CG E:HIS89 4.6 43.9 1.0
CB E:ASP88 4.6 42.1 1.0
CG E:HIS234 4.6 40.7 1.0
OE1 E:GLU86 4.7 93.9 1.0
ND1 E:HIS89 4.7 44.8 1.0
CE2 E:TYR25 4.9 53.5 1.0
ND1 E:HIS234 4.9 41.9 1.0

Terbium binding site 10 out of 16 in 6frm

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Terbium binding site 10 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 10 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Tb501

b:55.1
occ:1.00
TB F:7MT501 0.0 55.1 1.0
OE2 F:GLU113 2.4 69.6 1.0
N23 F:7MT501 2.5 48.3 1.0
N17 F:7MT501 2.6 43.8 1.0
N06 F:7MT501 2.7 51.6 1.0
N09 F:7MT501 2.8 53.2 1.0
N02 F:7MT501 2.8 50.7 1.0
O26 F:7MT501 2.8 49.5 1.0
CD F:GLU113 2.9 67.8 1.0
O27 F:7MT501 2.9 49.2 1.0
OE1 F:GLU113 2.9 56.8 1.0
C11 F:7MT501 3.4 49.3 1.0
C22 F:7MT501 3.4 48.6 1.0
C10 F:7MT501 3.4 46.6 1.0
C01 F:7MT501 3.4 52.0 1.0
C16 F:7MT501 3.4 46.6 1.0
C29 F:7MT501 3.4 51.4 1.0
C08 F:7MT501 3.5 52.3 1.0
C05 F:7MT501 3.5 49.1 1.0
C24 F:7MT501 3.5 49.5 1.0
C30 F:7MT501 3.5 47.7 1.0
C18 F:7MT501 3.6 51.6 1.0
C03 F:7MT501 3.7 51.5 1.0
C07 F:7MT501 3.7 53.4 1.0
C04 F:7MT501 3.7 49.3 1.0
CG F:GLU113 4.3 57.9 1.0
O F:HOH777 4.6 59.5 1.0
C13 F:7MT501 4.7 50.8 1.0
C19 F:7MT501 4.7 50.0 1.0
C15 F:7MT501 4.7 47.2 1.0
C21 F:7MT501 4.7 48.1 1.0
O25 F:7MT501 4.7 51.3 1.0
O28 F:7MT501 4.8 56.0 1.0
NH1 C:ARG399 4.9 61.7 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: Wed Dec 16 02:27:13 2020

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