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Terbium in PDB 6hf6: Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4.

Enzymatic activity of Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4.

All present enzymatic activity of Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4.:
3.5.1.124;

Protein crystallography data

The structure of Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4., PDB code: 6hf6 was solved by S.Engilberge, T.Wagner, G.Santoni, C.Breyton, S.Shima, B.Franzetti, F.Riobe, O.Maury, E.Girard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 124.620, 124.620, 130.310, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.1

Terbium Binding Sites:

The binding sites of Terbium atom in the Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4. (pdb code 6hf6). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 7 binding sites of Terbium where determined in the Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4., PDB code: 6hf6:
Jump to Terbium binding site number: 1; 2; 3; 4; 5; 6; 7;

Terbium binding site 1 out of 7 in 6hf6

Go back to Terbium Binding Sites List in 6hf6
Terbium binding site 1 out of 7 in the Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii 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 Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb201

b:50.1
occ:0.80
 TB A:7MT201 0.0 50.1 0.8
H061 A:7MT201 1.7 40.5 0.8
O27 A:7MT201 2.5 39.2 0.8
N17 A:7MT201 2.6 49.1 0.8
N23 A:7MT201 2.6 46.1 0.8
O8 A:MLI202 2.6 38.0 0.8
O9 A:MLI202 2.6 47.5 0.8
O26 A:7MT201 2.6 29.9 0.8
N06 A:7MT201 2.7 39.6 0.8
N02 A:7MT201 2.8 41.6 0.8
N09 A:7MT201 2.9 51.4 0.8
C3 A:MLI202 2.9 49.2 0.8
C18 A:7MT201 3.3 45.7 0.8
C05 A:7MT201 3.4 42.5 0.8
C24 A:7MT201 3.4 34.3 0.8
H051 A:7MT201 3.4 41.0 0.8
C22 A:7MT201 3.4 41.5 0.8
C16 A:7MT201 3.4 47.1 0.8
C30 A:7MT201 3.4 40.6 0.8
C10 A:7MT201 3.5 43.9 0.8
HH11 A:ARG75 3.5 45.9 1.0
C08 A:7MT201 3.5 48.0 0.8
H301 A:7MT201 3.5 40.4 0.8
H081 A:7MT201 3.5 48.2 0.8
C01 A:7MT201 3.5 42.9 0.8
C11 A:7MT201 3.5 50.0 0.8
C29 A:7MT201 3.6 50.5 0.8
H012 A:7MT201 3.6 42.0 0.8
C04 A:7MT201 3.6 43.9 0.8
C07 A:7MT201 3.6 46.1 0.8
H291 A:7MT201 3.6 50.0 0.8
C03 A:7MT201 3.7 47.9 0.8
HH12 A:ARG75 3.9 46.4 1.0
NH1 A:ARG75 4.0 45.0 1.0
HD22 A:ASN9 4.1 36.7 1.0
H042 A:7MT201 4.3 43.6 0.8
H072 A:7MT201 4.3 47.3 0.8
H041 A:7MT201 4.4 44.4 0.8
H071 A:7MT201 4.4 47.4 0.8
H031 A:7MT201 4.4 48.4 0.8
H052 A:7MT201 4.4 42.3 0.8
C1 A:MLI202 4.4 57.3 0.8
H302 A:7MT201 4.5 40.2 0.8
O28 A:7MT201 4.5 49.4 0.8
H032 A:7MT201 4.5 48.7 0.8
HD3 A:ARG75 4.5 49.5 1.0
O25 A:7MT201 4.5 31.7 0.8
H011 A:7MT201 4.5 42.0 0.8
H082 A:7MT201 4.5 48.9 0.8
H292 A:7MT201 4.6 51.0 0.8
H12 A:MLI202 4.7 59.2 0.8
C13 A:7MT201 4.8 46.0 0.8
C15 A:7MT201 4.8 47.2 0.8
C21 A:7MT201 4.8 43.9 0.8
C19 A:7MT201 4.9 49.2 0.8
O7 A:MLI202 4.9 62.2 0.8

Terbium binding site 2 out of 7 in 6hf6

Go back to Terbium Binding Sites List in 6hf6
Terbium binding site 2 out of 7 in the Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii 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 Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb203

b:64.1
occ:0.25
 O A:HOH433 4.8 74.2 1.0

Terbium binding site 3 out of 7 in 6hf6

Go back to Terbium Binding Sites List in 6hf6
Terbium binding site 3 out of 7 in the Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii 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 Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb204

b:29.3
occ:0.30
 OE1 A:GLU10 2.3 78.2 1.0
HE A:ARG71 3.0 73.6 1.0
O A:HOH424 3.3 60.4 1.0
HH21 A:ARG71 3.3 58.3 1.0
HH21 A:ARG75 3.6 42.0 1.0
CD A:GLU10 3.6 76.2 1.0
HG3 A:GLU10 3.9 44.2 1.0
NE A:ARG71 3.9 72.6 1.0
NH2 A:ARG71 4.2 56.8 1.0
HH22 A:ARG75 4.2 43.3 1.0
NH2 A:ARG75 4.3 41.9 1.0
CG A:GLU10 4.4 42.9 1.0
OE2 A:GLU10 4.5 74.0 1.0
CZ A:ARG71 4.5 75.5 1.0
HD2 A:ARG71 4.5 62.9 1.0
O A:HOH503 4.7 84.4 1.0
CD A:ARG71 4.8 61.9 1.0
HH22 A:ARG71 5.0 58.0 1.0

Terbium binding site 4 out of 7 in 6hf6

Go back to Terbium Binding Sites List in 6hf6
Terbium binding site 4 out of 7 in the Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii 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 Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb201

b:58.6
occ:0.80
 TB B:7MT201 0.0 58.6 0.8
H061 B:7MT201 1.7 53.2 0.8
N17 B:7MT201 2.5 51.8 0.8
N23 B:7MT201 2.6 50.0 0.8
N06 B:7MT201 2.7 52.4 0.8
O8 B:MLI202 2.7 58.8 0.8
N09 B:7MT201 2.8 54.3 0.8
O9 B:MLI202 2.8 64.8 0.8
N02 B:7MT201 2.8 46.0 0.8
O27 B:7MT201 2.8 54.4 0.8
O26 B:7MT201 2.8 39.2 0.8
C3 B:MLI202 3.1 64.7 0.8
C10 B:7MT201 3.4 47.9 0.8
C30 B:7MT201 3.4 44.0 0.8
C08 B:7MT201 3.4 56.0 0.8
H081 B:7MT201 3.4 56.9 0.8
C29 B:7MT201 3.4 53.1 0.8
H301 B:7MT201 3.5 43.3 0.8
C05 B:7MT201 3.5 52.0 0.8
C16 B:7MT201 3.5 54.0 0.8
HH11 B:ARG75 3.5 44.1 1.0
H291 B:7MT201 3.5 54.2 0.8
C11 B:7MT201 3.5 52.4 0.8
H051 B:7MT201 3.5 51.4 0.8
C01 B:7MT201 3.5 45.5 0.8
C24 B:7MT201 3.5 40.8 0.8
C22 B:7MT201 3.5 46.6 0.8
C18 B:7MT201 3.5 55.5 0.8
H012 B:7MT201 3.6 43.2 0.8
C07 B:7MT201 3.6 55.3 0.8
C04 B:7MT201 3.7 52.3 0.8
C03 B:7MT201 3.7 51.1 0.8
HH12 B:ARG75 3.9 44.6 1.0
NH1 B:ARG75 4.0 43.3 1.0
HD22 B:ASN9 4.2 36.8 1.0
H071 B:7MT201 4.3 56.8 0.8
H072 B:7MT201 4.3 55.5 0.8
H031 B:7MT201 4.4 52.0 0.8
H042 B:7MT201 4.4 53.4 0.8
H041 B:7MT201 4.4 52.8 0.8
H082 B:7MT201 4.5 56.7 0.8
H302 B:7MT201 4.5 42.4 0.8
H052 B:7MT201 4.5 52.1 0.8
H292 B:7MT201 4.5 53.9 0.8
H032 B:7MT201 4.5 51.7 0.8
H011 B:7MT201 4.6 44.0 0.8
HD3 B:ARG75 4.6 53.6 1.0
C1 B:MLI202 4.7 68.9 0.8
C13 B:7MT201 4.7 49.2 0.8
O25 B:7MT201 4.7 38.1 0.8
O28 B:7MT201 4.7 58.5 0.8
C15 B:7MT201 4.8 53.5 0.8
C19 B:7MT201 4.8 52.1 0.8
C21 B:7MT201 4.9 47.5 0.8

Terbium binding site 5 out of 7 in 6hf6

Go back to Terbium Binding Sites List in 6hf6
Terbium binding site 5 out of 7 in the Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii 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 Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb203

b:43.1
occ:0.30
 O B:HOH450 2.9 71.7 1.0
O B:HOH397 2.9 57.1 1.0
HH11 B:ARG71 3.2 60.6 1.0
HG3 B:GLU10 3.4 43.0 1.0
HH21 B:ARG75 3.6 49.2 1.0
O C:HOH367 3.6 70.5 1.0
HD3 B:ARG71 3.6 54.1 1.0
O C:HOH363 3.7 66.3 1.0
NH1 B:ARG71 4.0 61.6 1.0
HZ1 C:LYS43 4.0 65.5 1.0
HD2 B:ARG71 4.1 54.1 1.0
HH22 C:ARG71 4.2 53.1 1.0
HE3 C:LYS43 4.3 56.5 1.0
HH12 B:ARG71 4.3 62.1 1.0
CD B:ARG71 4.3 54.2 1.0
HH22 B:ARG75 4.4 50.3 1.0
NH2 B:ARG75 4.4 48.6 1.0
CG B:GLU10 4.4 43.0 1.0
HH21 C:ARG71 4.6 52.0 1.0
CD B:GLU10 4.6 71.7 1.0
OE2 B:GLU10 4.7 60.9 1.0
NH2 C:ARG71 4.7 53.2 1.0
HZ2 C:LYS43 4.8 65.2 1.0
NZ C:LYS43 4.8 65.7 1.0
CZ B:ARG71 4.9 82.3 1.0
HG2 B:GLU10 5.0 42.8 1.0

Terbium binding site 6 out of 7 in 6hf6

Go back to Terbium Binding Sites List in 6hf6
Terbium binding site 6 out of 7 in the Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii 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 Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tb201

b:64.4
occ:0.80
 TB C:7MT201 0.0 64.4 0.8
H061 C:7MT201 1.9 62.1 0.8
N23 C:7MT201 2.5 55.2 0.8
O7 C:MLI202 2.6 61.2 0.8
O27 C:7MT201 2.6 57.4 0.8
N17 C:7MT201 2.7 60.0 0.8
O26 C:7MT201 2.7 38.0 0.8
N09 C:7MT201 2.9 61.8 0.8
N06 C:7MT201 3.0 61.5 0.8
N02 C:7MT201 3.0 64.4 0.8
C2 C:MLI202 3.0 68.5 0.8
O6 C:MLI202 3.0 66.8 0.8
C22 C:7MT201 3.3 52.8 0.8
C24 C:7MT201 3.4 44.5 0.8
C11 C:7MT201 3.4 59.0 0.8
HH21 C:ARG75 3.4 43.1 1.0
H081 C:7MT201 3.4 59.8 0.8
C18 C:7MT201 3.4 57.1 0.8
C29 C:7MT201 3.5 59.7 0.8
C16 C:7MT201 3.5 58.1 0.8
C08 C:7MT201 3.5 60.6 0.8
H291 C:7MT201 3.5 59.6 0.8
C10 C:7MT201 3.5 60.0 0.8
H301 C:7MT201 3.5 62.0 0.8
C30 C:7MT201 3.5 62.0 0.8
H012 C:7MT201 3.6 66.0 0.8
C01 C:7MT201 3.6 65.2 0.8
C05 C:7MT201 3.7 63.9 0.8
C07 C:7MT201 3.8 60.9 0.8
H051 C:7MT201 3.8 63.2 0.8
C03 C:7MT201 3.8 64.2 0.8
HH22 C:ARG75 3.8 46.0 1.0
C04 C:7MT201 3.9 66.1 0.8
NH2 C:ARG75 4.0 44.6 1.0
HD22 C:ASN9 4.1 45.2 1.0
C1 C:MLI202 4.3 74.8 0.8
H11 C:MLI202 4.3 75.4 0.8
H071 C:7MT201 4.5 60.6 0.8
O25 C:7MT201 4.5 42.7 0.8
H292 C:7MT201 4.5 60.4 0.8
H072 C:7MT201 4.5 62.0 0.8
H031 C:7MT201 4.5 64.8 0.8
HD3 C:ARG75 4.5 53.8 1.0
H082 C:7MT201 4.5 61.8 0.8
H032 C:7MT201 4.6 64.8 0.8
H042 C:7MT201 4.6 67.5 0.8
H302 C:7MT201 4.6 62.5 0.8
O28 C:7MT201 4.6 57.0 0.8
C21 C:7MT201 4.7 58.2 0.8
C19 C:7MT201 4.7 60.7 0.8
H041 C:7MT201 4.7 67.3 0.8
H011 C:7MT201 4.7 66.4 0.8
H052 C:7MT201 4.8 64.2 0.8
C15 C:7MT201 4.8 57.9 0.8
C13 C:7MT201 4.9 60.5 0.8
H12 C:MLI202 4.9 75.4 0.8

Terbium binding site 7 out of 7 in 6hf6

Go back to Terbium Binding Sites List in 6hf6
Terbium binding site 7 out of 7 in the Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii 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 Crystal Structure of the Protease 1 (E29A,E60A,E80A) From Pyrococcus Horikoshii Co-Crystallized with Tb-XO4. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tb203

b:45.8
occ:0.30
 O C:HOH364 2.7 73.1 1.0
O C:HOH373 2.8 73.9 1.0
HE C:ARG71 3.0 72.6 1.0
O B:HOH417 3.1 74.3 1.0
HH11 C:ARG71 3.3 59.5 1.0
HG3 C:GLU10 3.3 48.2 1.0
HH21 B:ARG71 3.4 85.1 1.0
HH11 C:ARG75 3.6 60.4 1.0
NE C:ARG71 3.9 72.8 1.0
HZ1 B:LYS43 4.1 69.3 1.0
OE2 C:GLU10 4.1 90.7 1.0
NH1 C:ARG71 4.2 59.4 1.0
HH12 C:ARG75 4.2 62.0 1.0
NH2 B:ARG71 4.3 84.4 1.0
NH1 C:ARG75 4.3 60.7 1.0
CG C:GLU10 4.3 47.8 1.0
HH22 B:ARG71 4.4 85.2 1.0
HE3 B:LYS43 4.4 59.6 1.0
HD2 C:ARG71 4.5 69.3 1.0
CZ C:ARG71 4.5 77.3 1.0
CD C:GLU10 4.5 86.6 1.0
HZ2 B:LYS43 4.8 68.4 1.0
NZ B:LYS43 4.8 68.4 1.0
CD C:ARG71 4.9 68.9 1.0
HG2 C:GLU10 4.9 47.5 1.0
HH12 C:ARG71 5.0 59.8 1.0

Reference:

S.Engilberge, T.Wagner, G.Santoni, C.Breyton, S.Shima, B.Franzetti, F.Riobe, O.Maury, E.Girard. Protein Crystal Structure Determination with the Crystallophore, A Nucleating and Phasing Agent. J.Appl.Crystallogr. V. 52 722 2019.
ISSN: ISSN 0021-8898
PubMed: 31396026
DOI: 10.1107/S1600576719006381
Page generated: Wed Dec 16 02:27:19 2020

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