Iodine in PDB 6f2h: Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.

Enzymatic activity of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.

All present enzymatic activity of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.:
3.5.1.124;

Protein crystallography data

The structure of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide., PDB code: 6f2h 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) 46.01 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.577, 84.698, 144.343, 90.00, 90.97, 90.00
R / Rfree (%) 15 / 19.3

Other elements in 6f2h:

The structure of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. also contains other interesting chemical elements:

Terbium (Tb) 18 atoms

Iodine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. (pdb code 6f2h). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide., PDB code: 6f2h:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 6f2h

Go back to Iodine Binding Sites List in 6f2h
Iodine binding site 1 out of 11 in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:0.5
occ:0.70
TB A:7MT201 2.7 62.0 0.7
HD22 A:ASN9 2.7 35.1 1.0
HH12 A:ARG75 3.2 53.8 1.0
N23 A:7MT201 3.3 35.0 0.7
H291 A:7MT201 3.4 34.5 0.7
ND2 A:ASN9 3.4 33.4 1.0
O28 A:7MT201 3.5 32.6 0.7
HD21 A:ASN9 3.5 37.2 1.0
H061 A:7MT201 3.7 35.9 0.7
H081 A:7MT201 3.8 33.6 0.7
C11 A:7MT201 3.8 38.7 0.7
C29 A:7MT201 3.9 35.4 0.7
O26 A:7MT201 3.9 17.9 0.7
NH1 A:ARG75 3.9 53.9 1.0
C22 A:7MT201 4.0 34.0 0.7
HH11 A:ARG75 4.0 53.3 1.0
N09 A:7MT201 4.0 34.9 0.7
C24 A:7MT201 4.2 24.9 0.7
C08 A:7MT201 4.4 33.3 0.7
HB2 A:ASN9 4.5 22.6 1.0
C18 A:7MT201 4.5 36.4 0.7
N06 A:7MT201 4.5 34.7 0.7
CG A:ASN9 4.6 39.1 1.0
N17 A:7MT201 4.8 41.4 0.7
H292 A:7MT201 4.8 34.9 0.7
C19 A:7MT201 4.9 40.5 0.7
HH22 A:ARG75 5.0 33.6 1.0
C21 A:7MT201 5.0 42.1 0.7

Iodine binding site 2 out of 11 in 6f2h

Go back to Iodine Binding Sites List in 6f2h
Iodine binding site 2 out of 11 in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I202

b:0.9
occ:0.60
HH12 B:ARG75 2.3 51.1 1.0
HD22 B:ASN9 2.4 30.3 1.0
TB B:7MT201 2.9 83.1 0.6
NH1 B:ARG75 3.2 50.6 1.0
ND2 B:ASN9 3.2 29.0 1.0
N23 B:7MT201 3.3 40.7 0.6
HH11 B:ARG75 3.4 50.4 1.0
HD21 B:ASN9 3.6 34.2 1.0
O28 B:7MT201 3.6 40.7 0.6
H291 B:7MT201 3.7 44.8 0.6
O26 B:7MT201 3.7 25.1 0.6
HB2 B:ASN9 3.9 33.9 1.0
C22 B:7MT201 3.9 32.2 0.6
C11 B:7MT201 4.0 44.2 0.6
C24 B:7MT201 4.1 30.2 0.6
HH22 B:ARG75 4.1 59.3 1.0
CG B:ASN9 4.3 30.5 1.0
C29 B:7MT201 4.3 45.7 0.6
CZ B:ARG75 4.3 66.9 1.0
CB B:ASN9 4.4 32.7 1.0
H061 B:7MT201 4.5 47.6 0.6
HB3 B:ASN9 4.5 31.8 1.0
C18 B:7MT201 4.6 40.6 0.6
NH2 B:ARG75 4.6 58.4 1.0
N09 B:7MT201 4.8 51.8 0.6
N17 B:7MT201 4.8 39.4 0.6
H081 B:7MT201 4.8 48.6 0.6
C21 B:7MT201 5.0 27.7 0.6

Iodine binding site 3 out of 11 in 6f2h

Go back to Iodine Binding Sites List in 6f2h
Iodine binding site 3 out of 11 in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I202

b:0.0
occ:0.45
HD22 C:ASN9 2.6 34.3 1.0
HH22 C:ARG75 2.7 61.4 1.0
HH21 C:ARG75 3.0 60.0 1.0
TB C:TB201 3.0 70.7 0.5
NH2 C:ARG75 3.2 61.3 1.0
ND2 C:ASN9 3.3 32.4 1.0
HD21 C:ASN9 3.6 35.4 1.0
HB2 C:ASN9 4.0 19.4 1.0
CG C:ASN9 4.3 42.4 1.0
O C:HOH356 4.3 48.7 1.0
O C:HOH370 4.4 60.3 1.0
CZ C:ARG75 4.5 91.1 1.0
O C:HOH362 4.6 55.8 1.0
CB C:ASN9 4.6 26.6 1.0
HB3 C:ASN9 4.7 26.4 1.0
HH12 C:ARG75 4.9 56.0 1.0

Iodine binding site 4 out of 11 in 6f2h

Go back to Iodine Binding Sites List in 6f2h
Iodine binding site 4 out of 11 in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I204

b:0.2
occ:0.70
TB E:7MT203 2.6 62.0 0.7
HD22 E:ASN9 2.8 36.6 1.0
HH12 E:ARG75 3.0 51.3 1.0
O28 E:7MT203 3.0 20.6 0.7
H081 E:7MT203 3.4 35.5 0.7
H291 E:7MT203 3.5 46.0 0.7
ND2 E:ASN9 3.6 37.7 1.0
H061 E:7MT203 3.6 38.1 0.7
N23 E:7MT203 3.7 41.9 0.7
HD21 E:ASN9 3.7 39.8 1.0
NH1 E:ARG75 3.8 51.0 1.0
O26 E:7MT203 3.9 25.5 0.7
HH11 E:ARG75 4.0 50.1 1.0
N09 E:7MT203 4.0 43.0 0.7
C29 E:7MT203 4.1 47.0 0.7
C08 E:7MT203 4.1 36.8 0.7
C18 E:7MT203 4.2 32.0 0.7
C11 E:7MT203 4.2 47.9 0.7
N06 E:7MT203 4.4 34.3 0.7
C22 E:7MT203 4.5 36.6 0.7
HB2 E:ASN9 4.5 22.9 1.0
C24 E:7MT203 4.5 28.5 0.7
N17 E:7MT203 4.7 22.0 0.7
HH22 E:ARG75 4.7 58.2 1.0
CG E:ASN9 4.7 43.6 1.0
H082 E:7MT203 4.8 39.1 0.7
C07 E:7MT203 4.9 30.8 0.7
O27 E:7MT203 4.9 44.8 0.7
C16 E:7MT203 5.0 30.8 0.7
CZ E:ARG75 5.0 59.5 1.0
H292 E:7MT203 5.0 46.3 0.7

Iodine binding site 5 out of 11 in 6f2h

Go back to Iodine Binding Sites List in 6f2h
Iodine binding site 5 out of 11 in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I204

b:0.8
occ:0.80
TB F:7MT203 2.9 66.2 0.8
HD22 F:ASN9 2.9 39.2 1.0
O28 F:7MT203 3.3 30.5 0.8
HH12 F:ARG75 3.5 52.2 1.0
H291 F:7MT203 3.6 45.8 0.8
ND2 F:ASN9 3.6 36.2 1.0
HD21 F:ASN9 3.6 39.8 1.0
N23 F:7MT203 3.7 33.0 0.8
H081 F:7MT203 3.7 36.4 0.8
H061 F:7MT203 3.9 42.4 0.8
C29 F:7MT203 4.2 47.1 0.8
C11 F:7MT203 4.2 44.0 0.8
O26 F:7MT203 4.3 30.5 0.8
NH1 F:ARG75 4.3 51.4 1.0
N09 F:7MT203 4.3 43.9 0.8
C22 F:7MT203 4.3 31.9 0.8
HH11 F:ARG75 4.4 50.5 1.0
C08 F:7MT203 4.4 38.8 0.8
N06 F:7MT203 4.5 40.3 0.8
C18 F:7MT203 4.5 36.6 0.8
C24 F:7MT203 4.6 34.7 0.8
HB2 F:ASN9 4.8 20.4 1.0
CG F:ASN9 4.8 41.0 1.0

Iodine binding site 6 out of 11 in 6f2h

Go back to Iodine Binding Sites List in 6f2h
Iodine binding site 6 out of 11 in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:I202

b:0.1
occ:0.60
TB G:7MT201 2.5 56.7 0.6
HD22 G:ASN9 2.9 37.7 1.0
O28 G:7MT201 3.0 21.4 0.6
H291 G:7MT201 3.3 31.6 0.6
N23 G:7MT201 3.3 35.0 0.6
HH12 G:ARG75 3.4 55.0 1.0
H081 G:7MT201 3.6 31.0 0.6
H061 G:7MT201 3.6 36.9 0.6
ND2 G:ASN9 3.7 35.3 1.0
HD21 G:ASN9 3.7 37.7 1.0
C29 G:7MT201 3.8 32.6 0.6
C11 G:7MT201 3.8 35.4 0.6
O26 G:7MT201 3.9 24.9 0.6
N09 G:7MT201 3.9 35.5 0.6
C22 G:7MT201 4.1 30.7 0.6
C18 G:7MT201 4.1 29.0 0.6
NH1 G:ARG75 4.1 54.2 1.0
HH11 G:ARG75 4.1 52.2 1.0
C08 G:7MT201 4.2 32.2 0.6
C24 G:7MT201 4.3 27.7 0.6
N06 G:7MT201 4.4 35.2 0.6
N17 G:7MT201 4.6 31.8 0.6
HB2 G:ASN9 4.7 33.6 1.0
H292 G:7MT201 4.7 32.0 0.6
O27 G:7MT201 4.8 32.7 0.6
CG G:ASN9 4.8 31.6 1.0
C16 G:7MT201 4.9 30.2 0.6
C07 G:7MT201 4.9 34.8 0.6
C19 G:7MT201 4.9 37.4 0.6

Iodine binding site 7 out of 11 in 6f2h

Go back to Iodine Binding Sites List in 6f2h
Iodine binding site 7 out of 11 in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I202

b:0.3
occ:0.50
TB H:TB201 2.6 75.2 0.5
HD22 H:ASN9 2.8 38.6 1.0
HH12 H:ARG75 2.8 83.5 1.0
NH1 H:ARG75 3.6 83.7 1.0
HH11 H:ARG75 3.6 83.6 1.0
ND2 H:ASN9 3.7 38.3 1.0
O H:HOH327 3.7 46.8 1.0
HD21 H:ASN9 3.9 39.6 1.0
O H:HOH330 4.1 39.8 1.0
HB2 H:ASN9 4.4 32.4 1.0
HH22 H:ARG75 4.7 65.9 1.0
CZ H:ARG75 4.8 91.5 1.0
CG H:ASN9 4.8 40.0 1.0

Iodine binding site 8 out of 11 in 6f2h

Go back to Iodine Binding Sites List in 6f2h
Iodine binding site 8 out of 11 in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:I202

b:0.2
occ:0.60
HD22 I:ASN9 2.4 35.3 1.0
HH12 I:ARG75 2.6 62.0 1.0
TB I:7MT201 3.1 72.5 0.6
ND2 I:ASN9 3.2 32.2 1.0
O28 I:7MT201 3.3 37.6 0.6
NH1 I:ARG75 3.4 61.3 1.0
HD21 I:ASN9 3.5 33.2 1.0
HH11 I:ARG75 3.6 60.9 1.0
N23 I:7MT201 3.7 43.0 0.6
O26 I:7MT201 3.7 41.6 0.6
H291 I:7MT201 3.9 44.0 0.6
HB2 I:ASN9 4.0 33.2 1.0
H061 I:7MT201 4.2 55.5 0.6
C24 I:7MT201 4.2 39.0 0.6
C22 I:7MT201 4.3 39.9 0.6
CG I:ASN9 4.3 54.0 1.0
HH22 I:ARG75 4.4 85.7 1.0
C11 I:7MT201 4.4 48.5 0.6
C18 I:7MT201 4.4 43.7 0.6
C29 I:7MT201 4.5 44.1 0.6
H081 I:7MT201 4.5 51.6 0.6
CZ I:ARG75 4.6 83.3 1.0
CB I:ASN9 4.6 31.7 1.0
N09 I:7MT201 4.7 50.3 0.6
HB3 I:ASN9 4.7 32.9 1.0
N17 I:7MT201 4.8 43.5 0.6
N06 I:7MT201 4.9 54.3 0.6
NH2 I:ARG75 4.9 85.7 1.0

Iodine binding site 9 out of 11 in 6f2h

Go back to Iodine Binding Sites List in 6f2h
Iodine binding site 9 out of 11 in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:I203

b:0.4
occ:0.80
TB J:7MT202 2.7 56.1 0.8
HD22 J:ASN9 2.7 33.0 1.0
HH12 J:ARG75 3.2 43.9 1.0
O28 J:7MT202 3.3 23.4 0.8
N23 J:7MT202 3.4 35.1 0.8
H291 J:7MT202 3.4 35.5 0.8
ND2 J:ASN9 3.5 32.5 1.0
HD21 J:ASN9 3.6 34.4 1.0
O J:HOH333 3.6 45.3 1.0
H061 J:7MT202 3.7 24.9 0.8
O26 J:7MT202 3.7 35.9 0.8
C11 J:7MT202 3.9 38.3 0.8
C29 J:7MT202 4.0 37.2 0.8
C22 J:7MT202 4.0 38.7 0.8
NH1 J:ARG75 4.0 44.5 1.0
HH11 J:ARG75 4.1 44.2 1.0
H081 J:7MT202 4.1 35.3 0.8
C24 J:7MT202 4.1 35.8 0.8
N09 J:7MT202 4.2 38.6 0.8
C18 J:7MT202 4.3 30.1 0.8
N06 J:7MT202 4.6 21.5 0.8
HB2 J:ASN9 4.6 41.9 1.0
C08 J:7MT202 4.6 34.2 0.8
CG J:ASN9 4.7 48.1 1.0
H292 J:7MT202 4.9 36.2 0.8
N17 J:7MT202 4.9 31.6 0.8
C19 J:7MT202 5.0 39.2 0.8

Iodine binding site 10 out of 11 in 6f2h

Go back to Iodine Binding Sites List in 6f2h
Iodine binding site 10 out of 11 in the Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Protease 1 From Pyrococcus Horikoshii Co-Crystallized in Presence of 10 Mm Tb-XO4 and Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:I203

b:0.7
occ:0.60
TB K:7MT202 3.1 73.2 0.6
HD22 K:ASN9 3.1 37.2 1.0
H291 K:7MT202 3.2 45.8 0.6
O28 K:7MT202 3.4 39.8 0.6
H081 K:7MT202 3.5 39.0 0.6
N23 K:7MT202 3.6 35.0 0.6
HD21 K:ASN9 3.6 40.7 1.0
ND2 K:ASN9 3.7 37.9 1.0
C29 K:7MT202 3.9 45.3 0.6
C11 K:7MT202 3.9 39.6 0.6
H061 K:7MT202 4.1 43.9 0.6
N09 K:7MT202 4.2 44.1 0.6
C08 K:7MT202 4.3 41.0 0.6
C22 K:7MT202 4.4 36.8 0.6
C18 K:7MT202 4.5 44.1 0.6
O K:HOH335 4.6 62.2 1.0
O26 K:7MT202 4.7 28.1 0.6
H292 K:7MT202 4.7 45.2 0.6
N06 K:7MT202 4.7 42.8 0.6
HH21 K:ARG75 4.8 56.9 1.0
C24 K:7MT202 4.8 29.6 0.6
C19 K:7MT202 4.8 38.7 0.6
H082 K:7MT202 5.0 40.3 0.6
CG K:ASN9 5.0 48.7 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: Sun Dec 13 19:43:55 2020

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