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Terbium in PDB 6f2f: Crystal Structure of Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate.

Enzymatic activity of Crystal Structure of Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate.

All present enzymatic activity of Crystal Structure of Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate.:
3.5.1.124;

Protein crystallography data

The structure of Crystal Structure of Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate., PDB code: 6f2f was solved by S.Engilberge, F.Riobe, S.Di Pietro, B.Franzetti, 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) 44.77 / 1.65
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 124.588, 124.588, 128.866, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 17

Terbium Binding Sites:

The binding sites of Terbium atom in the Crystal Structure of Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate. (pdb code 6f2f). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 4 binding sites of Terbium where determined in the Crystal Structure of Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate., PDB code: 6f2f:
Jump to Terbium binding site number: 1; 2; 3; 4;

Terbium binding site 1 out of 4 in 6f2f

Go back to Terbium Binding Sites List in 6f2f
Terbium binding site 1 out of 4 in the Crystal Structure of Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate.


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 Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb201

b:34.0
occ:0.80
 TB A:7MT201 0.0 34.0 0.8
H061 A:7MT201 1.6 39.1 0.8
O28 A:7MT201 1.9 30.1 0.8
O26 A:7MT201 2.4 29.1 0.8
O1 A:SO4202 2.4 29.3 0.8
O4 A:SO4202 2.4 38.8 0.8
N23 A:7MT201 2.5 38.2 0.8
N06 A:7MT201 2.6 34.8 0.8
N17 A:7MT201 2.6 39.2 0.8
N02 A:7MT201 2.6 33.3 0.8
N09 A:7MT201 2.8 40.0 0.8
S A:SO4202 3.0 44.5 0.8
C18 A:7MT201 3.0 40.6 0.8
C24 A:7MT201 3.2 31.0 0.8
C22 A:7MT201 3.3 36.6 0.8
C01 A:7MT201 3.3 37.2 0.8
C05 A:7MT201 3.3 40.3 0.8
H012 A:7MT201 3.3 37.6 0.8
C16 A:7MT201 3.4 37.9 0.8
H051 A:7MT201 3.4 40.2 0.8
C11 A:7MT201 3.4 39.8 0.8
C30 A:7MT201 3.4 31.0 0.8
HH11 A:ARG75 3.5 32.3 1.0
C10 A:7MT201 3.5 33.4 0.8
C29 A:7MT201 3.5 41.2 0.8
C04 A:7MT201 3.5 40.9 0.8
C08 A:7MT201 3.5 40.5 0.8
C07 A:7MT201 3.6 39.2 0.8
H301 A:7MT201 3.6 31.5 0.8
C03 A:7MT201 3.6 39.4 0.8
H291 A:7MT201 3.7 41.2 0.8
H081 A:7MT201 3.7 40.9 0.8
HH12 A:ARG75 3.8 35.0 1.0
O2 A:SO4202 4.0 46.3 0.8
NH1 A:ARG75 4.0 32.9 1.0
O3 A:SO4202 4.1 41.8 0.8
HD22 A:ASN9 4.1 30.7 1.0
O27 A:7MT201 4.2 38.3 0.8
H042 A:7MT201 4.2 40.2 0.8
H031 A:7MT201 4.2 39.2 0.8
H071 A:7MT201 4.2 39.8 0.8
H072 A:7MT201 4.3 39.3 0.8
H041 A:7MT201 4.3 40.3 0.8
H011 A:7MT201 4.3 36.9 0.8
H052 A:7MT201 4.3 39.5 0.8
H032 A:7MT201 4.4 39.6 0.8
O25 A:7MT201 4.4 27.6 0.8
H302 A:7MT201 4.5 32.0 0.8
H292 A:7MT201 4.5 41.5 0.8
H082 A:7MT201 4.5 40.1 0.8
HD3 A:ARG75 4.6 33.4 1.0
C21 A:7MT201 4.6 37.8 0.8
C15 A:7MT201 4.7 38.1 0.8
C19 A:7MT201 4.7 38.5 0.8
C13 A:7MT201 4.8 34.3 0.8
ND2 A:ASN9 5.0 30.1 1.0

Terbium binding site 2 out of 4 in 6f2f

Go back to Terbium Binding Sites List in 6f2f
Terbium binding site 2 out of 4 in the Crystal Structure of Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate.


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 Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb204

b:32.2
occ:0.25
 O A:HOH501 4.2 52.6 1.0
O A:HOH433 4.4 88.4 1.0

Terbium binding site 3 out of 4 in 6f2f

Go back to Terbium Binding Sites List in 6f2f
Terbium binding site 3 out of 4 in the Crystal Structure of Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate.


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 Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb201

b:34.5
occ:0.80
 TB B:7MT201 0.0 34.5 0.8
H061 B:7MT201 1.6 39.7 0.8
O28 B:7MT201 2.0 33.3 0.8
O26 B:7MT201 2.3 26.6 0.8
O1 B:SO4204 2.4 32.2 0.8
O3 B:SO4204 2.4 36.0 0.8
N23 B:7MT201 2.5 42.1 0.8
N17 B:7MT201 2.5 40.1 0.8
N06 B:7MT201 2.6 36.0 0.8
N02 B:7MT201 2.7 38.1 0.8
N09 B:7MT201 2.8 44.1 0.8
C18 B:7MT201 3.0 41.5 0.8
S B:SO4204 3.0 45.4 0.8
C24 B:7MT201 3.1 33.7 0.8
C22 B:7MT201 3.2 39.8 0.8
C16 B:7MT201 3.2 41.6 0.8
C05 B:7MT201 3.3 41.4 0.8
H051 B:7MT201 3.4 40.9 0.8
C10 B:7MT201 3.4 40.9 0.8
C01 B:7MT201 3.4 40.4 0.8
C30 B:7MT201 3.5 39.7 0.8
C11 B:7MT201 3.5 45.9 0.8
HH11 B:ARG75 3.5 34.0 1.0
H012 B:7MT201 3.5 40.3 0.8
H301 B:7MT201 3.5 40.5 0.8
C29 B:7MT201 3.5 45.8 0.8
C04 B:7MT201 3.6 41.9 0.8
C08 B:7MT201 3.6 47.0 0.8
C07 B:7MT201 3.6 41.9 0.8
C03 B:7MT201 3.6 43.5 0.8
H291 B:7MT201 3.7 46.6 0.8
H081 B:7MT201 3.8 46.7 0.8
HH12 B:ARG75 3.9 34.8 1.0
O2 B:SO4204 4.0 47.3 0.8
NH1 B:ARG75 4.1 33.9 1.0
O4 B:SO4204 4.1 48.3 0.8
HD22 B:ASN9 4.1 29.4 1.0
O27 B:7MT201 4.2 40.4 0.8
O25 B:7MT201 4.2 28.9 0.8
H042 B:7MT201 4.3 41.6 0.8
H071 B:7MT201 4.3 41.5 0.8
H072 B:7MT201 4.3 41.6 0.8
H031 B:7MT201 4.3 44.2 0.8
H052 B:7MT201 4.3 41.0 0.8
H041 B:7MT201 4.3 41.4 0.8
H032 B:7MT201 4.4 43.6 0.8
H011 B:7MT201 4.5 40.2 0.8
H302 B:7MT201 4.5 39.8 0.8
H292 B:7MT201 4.6 45.6 0.8
H082 B:7MT201 4.6 46.9 0.8
C15 B:7MT201 4.6 42.5 0.8
O B:HOH369 4.6 57.2 1.0
C21 B:7MT201 4.6 41.7 0.8
HD3 B:ARG75 4.6 34.3 1.0
C13 B:7MT201 4.7 40.2 0.8
C19 B:7MT201 4.8 42.8 0.8
ND2 B:ASN9 5.0 29.6 1.0

Terbium binding site 4 out of 4 in 6f2f

Go back to Terbium Binding Sites List in 6f2f
Terbium binding site 4 out of 4 in the Crystal Structure of Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate.


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 Protease 1 From Pyrococcus Horikoshii Co- Cystallized in Presence of 10 Mm Tb-XO4 and Ammonium Sulfate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tb201

b:38.2
occ:0.80
 TB C:7MT201 0.0 38.2 0.8
O28 C:7MT201 1.5 22.8 0.8
H061 C:7MT201 1.8 47.6 0.8
O26 C:7MT201 2.3 25.7 0.8
N23 C:7MT201 2.3 36.0 0.8
O2 C:SO4204 2.4 39.5 0.8
O1 C:SO4204 2.5 37.8 0.8
N17 C:7MT201 2.5 42.4 0.8
C18 C:7MT201 2.6 39.8 0.8
N09 C:7MT201 2.7 44.0 0.8
N06 C:7MT201 2.8 46.1 0.8
N02 C:7MT201 2.9 49.0 0.8
S C:SO4204 3.0 48.3 0.8
C24 C:7MT201 3.1 30.1 0.8
C16 C:7MT201 3.1 40.1 0.8
C22 C:7MT201 3.2 36.0 0.8
C11 C:7MT201 3.3 43.0 0.8
H012 C:7MT201 3.4 48.4 0.8
C29 C:7MT201 3.4 44.3 0.8
C01 C:7MT201 3.4 47.9 0.8
HH21 C:ARG75 3.5 36.6 1.0
C08 C:7MT201 3.5 47.9 0.8
H291 C:7MT201 3.5 44.4 0.8
C05 C:7MT201 3.5 49.0 0.8
C03 C:7MT201 3.6 45.9 0.8
C10 C:7MT201 3.6 43.3 0.8
H051 C:7MT201 3.6 48.4 0.8
C30 C:7MT201 3.7 48.3 0.8
H081 C:7MT201 3.7 47.9 0.8
C07 C:7MT201 3.7 47.3 0.8
O27 C:7MT201 3.7 46.6 0.8
H301 C:7MT201 3.7 49.2 0.8
C04 C:7MT201 3.8 50.7 0.8
HH22 C:ARG75 3.9 37.7 1.0
O4 C:SO4204 4.0 48.0 0.8
NH2 C:ARG75 4.1 36.3 1.0
HD22 C:ASN9 4.1 28.5 1.0
O3 C:SO4204 4.1 46.1 0.8
O25 C:7MT201 4.2 28.2 0.8
H031 C:7MT201 4.3 45.9 0.8
H032 C:7MT201 4.3 46.2 0.8
H071 C:7MT201 4.4 46.7 0.8
H042 C:7MT201 4.4 50.6 0.8
H292 C:7MT201 4.4 45.0 0.8
H072 C:7MT201 4.4 47.6 0.8
H011 C:7MT201 4.5 48.3 0.8
C15 C:7MT201 4.5 39.2 0.8
C21 C:7MT201 4.5 40.5 0.8
H082 C:7MT201 4.5 48.0 0.8
H041 C:7MT201 4.6 50.3 0.8
H052 C:7MT201 4.6 48.8 0.8
C19 C:7MT201 4.6 42.8 0.8
HD3 C:ARG75 4.6 36.7 1.0
H302 C:7MT201 4.7 48.4 0.8
O C:HOH384 4.8 69.1 1.0
C13 C:7MT201 4.8 42.3 0.8

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 08:23:58 2024

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