Atomistry » Terbium » PDB 1m9s-6xym » 6hf6
Atomistry »
  Terbium »
    PDB 1m9s-6xym »
      6hf6 »

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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy