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Iodine in PDB 1qi9: X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution

Enzymatic activity of X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution

All present enzymatic activity of X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution:
1.11.1.10;

Protein crystallography data

The structure of X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution, PDB code: 1qi9 was solved by M.Weyand, H.-J.Hecht, M.Kiess, M.F.Liaud, H.Vilter, D.Schomburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.00 / 2.05
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.190, 113.190, 272.300, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 21.9

Other elements in 1qi9:

The structure of X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution also contains other interesting chemical elements:

Vanadium (V) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution (pdb code 1qi9). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution, PDB code: 1qi9:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 1qi9

Go back to Iodine Binding Sites List in 1qi9
Iodine binding site 1 out of 5 in the X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I601

b:11.6
occ:0.10
 CE1 A:TYR398 2.1 11.6 1.0
NZ A:LYS362 2.9 30.4 1.0
CD1 A:TYR398 3.0 10.6 1.0
CZ A:TYR398 3.0 11.7 1.0
OH A:TYR398 3.2 12.9 1.0
O A:HOH1327 3.5 29.3 1.0
CG A:LYS362 3.6 22.1 1.0
CD A:LYS362 3.8 27.2 1.0
CE A:LYS362 3.9 28.6 1.0
CG2 A:ILE361 4.1 9.0 1.0
CG1 A:VAL396 4.1 13.5 1.0
CG A:TYR398 4.3 7.6 1.0
CE2 A:TYR398 4.3 10.8 1.0
CA A:LYS362 4.8 15.8 1.0
N A:LYS362 4.8 14.0 1.0
CB A:LYS362 4.8 17.9 1.0
CD2 A:TYR398 4.8 9.8 1.0
CB A:ILE361 4.8 9.6 1.0
O A:VAL396 4.9 11.1 1.0
CE1 A:HIS358 4.9 9.1 1.0
C A:ILE361 4.9 13.2 1.0
ND1 A:HIS358 4.9 7.6 1.0
O A:ILE361 5.0 13.3 1.0

Iodine binding site 2 out of 5 in 1qi9

Go back to Iodine Binding Sites List in 1qi9
Iodine binding site 2 out of 5 in the X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I602

b:18.6
occ:0.50
 CE1 A:TYR447 2.1 18.8 1.0
CZ A:TYR447 3.0 19.7 1.0
CD1 A:TYR447 3.0 17.0 1.0
OH A:TYR447 3.1 19.9 1.0
CG A:MET153 3.6 15.1 1.0
O A:PRO448 3.9 9.9 1.0
OD1 A:ASP450 4.0 12.7 1.0
O A:HOH1042 4.0 19.9 1.0
CA A:ASP449 4.0 7.7 1.0
CB A:MET153 4.1 12.9 1.0
CG1 A:ILE456 4.2 11.8 1.0
CE2 A:TYR447 4.3 20.0 1.0
O A:HOH1316 4.3 35.3 1.0
CG A:TYR447 4.3 15.9 1.0
O A:HOH1111 4.4 25.9 1.0
C A:PRO448 4.6 8.8 1.0
N A:ASP450 4.6 6.0 1.0
C A:ASP449 4.7 6.9 1.0
SD A:MET153 4.7 22.7 1.0
CB A:ASP449 4.7 9.0 1.0
N A:ASP449 4.8 7.8 1.0
CB A:ILE456 4.8 11.2 1.0
O A:HOH1409 4.8 45.1 1.0
CD2 A:TYR447 4.8 18.4 1.0
CE A:MET153 4.9 9.8 1.0
CG A:ASP450 4.9 10.9 1.0
O A:HOH773 5.0 9.1 1.0

Iodine binding site 3 out of 5 in 1qi9

Go back to Iodine Binding Sites List in 1qi9
Iodine binding site 3 out of 5 in the X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I603

b:24.5
occ:0.50
 CE2 A:TYR447 2.1 20.0 1.0
O A:HOH995 3.0 30.3 1.0
CZ A:TYR447 3.0 19.7 1.0
CD2 A:TYR447 3.0 18.4 1.0
OH A:TYR447 3.2 19.9 1.0
O A:ASP457 3.4 15.2 1.0
CA A:PHE458 3.6 14.8 1.0
O A:HOH1315 3.6 40.2 1.0
CD1 A:PHE458 3.9 11.9 1.0
C A:ASP457 4.1 14.2 1.0
CB A:PHE458 4.2 13.6 1.0
N A:ARG459 4.2 21.2 1.0
N A:PHE458 4.2 13.5 1.0
CE1 A:TYR447 4.3 18.8 1.0
CG A:TYR447 4.3 15.9 1.0
O A:HOH1341 4.3 27.9 1.0
CG2 A:ILE456 4.4 10.5 1.0
C A:PHE458 4.5 17.8 1.0
CG A:PHE458 4.5 11.9 1.0
CD1 A:TYR447 4.8 17.0 1.0
CE1 A:PHE458 4.9 11.4 1.0
O A:ILE456 4.9 9.8 1.0

Iodine binding site 4 out of 5 in 1qi9

Go back to Iodine Binding Sites List in 1qi9
Iodine binding site 4 out of 5 in the X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I601

b:18.2
occ:0.50
 CE1 B:TYR447 2.1 18.3 1.0
CZ B:TYR447 3.0 19.0 1.0
CD1 B:TYR447 3.0 16.6 1.0
OH B:TYR447 3.1 19.9 1.0
O B:HOH1282 3.4 28.0 1.0
O B:HOH1000 3.6 12.3 1.0
CG B:MET153 3.6 11.7 1.0
O B:HOH1001 3.7 30.7 1.0
CA B:ASP449 4.0 9.9 1.0
O B:PRO448 4.0 6.8 1.0
CB B:MET153 4.2 9.5 1.0
OD1 B:ASP450 4.2 12.0 1.0
CE2 B:TYR447 4.3 18.7 1.0
CG1 B:ILE456 4.3 11.0 1.0
CG B:TYR447 4.3 14.9 1.0
O B:HOH1369 4.5 28.8 1.0
N B:ASP450 4.6 7.6 1.0
O B:HOH1467 4.6 60.9 1.0
C B:ASP449 4.6 9.9 1.0
O B:HOH1465 4.6 51.6 1.0
CB B:ASP449 4.7 10.1 1.0
C B:PRO448 4.7 8.8 1.0
N B:ASP449 4.7 9.8 1.0
CD2 B:TYR447 4.8 17.7 1.0
CB B:ILE456 4.8 10.0 1.0
SD B:MET153 5.0 16.8 1.0

Iodine binding site 5 out of 5 in 1qi9

Go back to Iodine Binding Sites List in 1qi9
Iodine binding site 5 out of 5 in the X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of X-Ray Siras Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I602

b:21.4
occ:0.50
 CE2 B:TYR447 2.1 18.7 1.0
O B:HOH878 3.0 12.2 1.0
CZ B:TYR447 3.0 19.0 1.0
CD2 B:TYR447 3.0 17.7 1.0
OH B:TYR447 3.2 19.9 1.0
O B:ASP457 3.3 7.7 1.0
O B:HOH1006 3.5 20.1 1.0
CA B:PHE458 3.8 7.2 1.0
C B:ASP457 4.1 7.8 1.0
CD1 B:PHE458 4.2 7.0 1.0
CE1 B:TYR447 4.3 18.3 1.0
CG B:TYR447 4.3 14.9 1.0
O B:HOH1465 4.3 51.6 1.0
CG2 B:ILE456 4.4 9.6 1.0
CB B:PHE458 4.4 7.0 1.0
N B:PHE458 4.4 8.0 1.0
N B:ARG459 4.6 4.5 1.0
C B:PHE458 4.7 5.6 1.0
CD1 B:TYR447 4.8 16.6 1.0
O B:HOH1082 4.8 23.4 1.0
CG B:PHE458 4.8 6.3 1.0
O B:ILE456 4.8 4.7 1.0

Reference:

M.Weyand, H.Hecht, M.Kiess, M.Liaud, H.Vilter, D.Schomburg. X-Ray Structure Determination of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum at 2.0 A Resolution. J.Mol.Biol. V. 293 595 1999.
ISSN: ISSN 0022-2836
PubMed: 10543953
DOI: 10.1006/JMBI.1999.3179
Page generated: Sun Aug 11 12:45:01 2024

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