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Iodine in PDB 2x76: The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode

Protein crystallography data

The structure of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode, PDB code: 2x76 was solved by S.Wakadkar, S.Hermawan, D.Jendrossek, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.45
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 49.630, 140.580, 56.750, 90.00, 90.00, 90.00
R / Rfree (%) n/a / 17.8

Other elements in 2x76:

The structure of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Sodium (Na) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode (pdb code 2x76). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode, PDB code: 2x76:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 2x76

Go back to Iodine Binding Sites List in 2x76
Iodine binding site 1 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1360

b:19.6
occ:1.00
 O A:HOH2103 3.5 19.4 1.0
O A:HOH2107 3.7 27.1 1.0
O A:HOH2102 3.9 20.9 1.0
CA A:LYS40 4.0 5.8 0.5
CA A:LYS40 4.1 5.7 0.5
O A:THR39 4.1 8.4 1.0
CG A:LYS40 4.4 6.6 0.5
N A:LYS40 4.5 5.8 1.0
C A:THR39 4.5 7.1 1.0
CG2 A:THR39 4.5 8.8 1.0
CG A:LYS40 4.7 7.0 0.5
CB A:LYS40 4.7 5.1 0.5
CB A:LYS40 4.8 5.1 0.5
C A:LYS40 5.0 6.4 1.0
N A:THR41 5.0 6.8 1.0

Iodine binding site 2 out of 8 in 2x76

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Iodine binding site 2 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1343

b:21.6
occ:1.00
 NA A:NA1357 1.9 6.1 1.0
OG A:SER35 2.9 22.9 0.5
N A:SER35 3.6 11.2 1.0
N A:GLY20 3.8 8.5 1.0
CB A:SER35 3.9 15.4 0.5
C A:GLY34 3.9 8.9 1.0
CB A:SER35 4.0 13.9 0.5
CA A:GLY34 4.0 9.4 1.0
CA A:GLY20 4.0 8.7 1.0
CA A:SER35 4.2 13.3 0.5
CA A:SER35 4.2 13.1 0.5
O A:HOH2088 4.4 24.9 1.0
CB A:ALA19 4.5 8.4 1.0
O A:GLY34 4.7 11.5 1.0
C A:ALA19 4.9 7.8 1.0
O A:HOH2087 5.0 28.4 1.0

Iodine binding site 3 out of 8 in 2x76

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Iodine binding site 3 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1344

b:25.3
occ:1.00
 O A:HOH2358 2.3 37.7 1.0
O A:HOH2354 3.1 23.6 1.0
O A:HOH2273 3.4 23.2 1.0
CB A:ALA230 3.7 12.7 1.0
CA A:ARG228 3.9 9.5 1.0
N A:ALA230 3.9 9.2 1.0
C A:ARG228 3.9 8.9 1.0
CB A:ARG228 4.0 9.8 1.0
CG2 A:VAL231 4.1 8.6 1.0
N A:THR229 4.2 9.8 1.0
CA A:ALA230 4.3 10.1 1.0
O A:ARG228 4.3 9.0 1.0
CD A:ARG228 4.4 9.3 1.0
CB A:TRP152 4.4 8.7 1.0
N A:VAL231 4.4 7.2 1.0
C A:ALA230 4.6 9.2 1.0
O A:HOH2353 4.7 33.5 1.0
O A:TRP152 4.8 9.0 1.0
CG A:ARG228 4.8 8.6 1.0
O A:HOH2133 4.8 31.5 1.0
C A:TRP152 4.9 7.7 1.0
CG2 A:THR153 4.9 15.6 1.0
O A:HOH2182 4.9 45.8 1.0
O A:HOH2130 4.9 31.1 1.0

Iodine binding site 4 out of 8 in 2x76

Go back to Iodine Binding Sites List in 2x76
Iodine binding site 4 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1345

b:29.9
occ:1.00
 O A:HOH2022 3.2 34.4 1.0
N A:GLY25 3.5 12.1 1.0
CD A:PRO24 3.9 11.9 1.0
CA A:ALA23 4.0 10.5 1.0
C A:ALA23 4.0 11.8 1.0
CB A:ALA23 4.0 12.5 1.0
N A:PRO24 4.0 9.7 1.0
CA A:GLY25 4.0 15.5 1.0
CE2 A:TYR18 4.3 8.3 1.0
CD2 A:TYR18 4.3 7.0 1.0
CG A:PRO24 4.4 11.8 1.0
O A:ALA23 4.6 17.6 1.0
C A:PRO24 4.6 11.4 1.0
CA A:PRO24 4.9 9.9 1.0
O A:HOH2056 5.0 11.9 1.0

Iodine binding site 5 out of 8 in 2x76

Go back to Iodine Binding Sites List in 2x76
Iodine binding site 5 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1346

b:43.8
occ:1.00
 O A:HOH2064 3.2 37.4 1.0
N A:GLY27 3.3 11.2 1.0
O A:HOH2030 3.5 26.0 1.0
O A:HOH2111 3.5 18.8 1.0
CA A:VAL26 3.9 10.0 1.0
CG1 A:ILE113 4.0 9.1 1.0
CB A:VAL26 4.1 12.1 1.0
C A:VAL26 4.1 10.4 1.0
CA A:GLY27 4.3 9.4 1.0
CD1 A:ILE113 4.3 10.2 1.0
CG1 A:VAL26 4.5 12.1 1.0
O A:HOH2225 4.5 16.7 1.0
O A:GLY27 4.6 10.9 1.0
C A:GLY27 4.8 8.6 1.0
O A:HOH2069 4.9 28.1 1.0

Iodine binding site 6 out of 8 in 2x76

Go back to Iodine Binding Sites List in 2x76
Iodine binding site 6 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1347

b:19.8
occ:1.00
 N A:ALA341 3.6 9.0 1.0
CB A:ALA340 3.9 12.6 1.0
CA A:ALA340 4.0 9.4 1.0
C A:ALA340 4.3 9.7 1.0
CB A:ALA341 4.4 12.2 1.0
CA A:ALA341 4.6 10.7 1.0
O A:HOH2460 4.8 12.0 1.0
CD1 A:LEU328 4.9 19.4 1.0

Iodine binding site 7 out of 8 in 2x76

Go back to Iodine Binding Sites List in 2x76
Iodine binding site 7 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1348

b:29.2
occ:1.00
 O A:HOH2011 2.4 22.8 1.0
ND2 A:ASN6 3.5 10.8 1.0
SG A:CYS3 3.7 8.0 1.0
O A:HOH2007 3.8 47.6 1.0
O A:HOH2015 3.8 11.6 1.0
CB A:CYS3 3.9 6.7 1.0
CA A:THR5 3.9 8.0 1.0
O A:GLY4 4.0 12.8 1.0
C A:THR5 4.0 6.3 1.0
C A:GLY4 4.1 10.0 1.0
N A:THR5 4.1 9.3 1.0
CG A:PRO59 4.2 14.3 1.0
N A:ASN6 4.2 6.6 1.0
CD A:PRO59 4.3 7.3 1.0
N A:GLY4 4.3 7.4 1.0
CG A:ASN6 4.4 8.0 1.0
CB A:ASN6 4.5 8.1 1.0
O A:THR5 4.5 8.2 1.0
O A:HOH2013 4.6 35.3 1.0
C A:CYS3 4.7 7.2 1.0
O A:HOH2124 4.8 17.6 1.0
CA A:GLY4 4.8 9.3 1.0
CA A:CYS3 4.9 5.9 1.0

Iodine binding site 8 out of 8 in 2x76

Go back to Iodine Binding Sites List in 2x76
Iodine binding site 8 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1359

b:28.5
occ:1.00
 O A:HOH2446 2.7 17.5 1.0
N A:ASP329 4.0 7.2 1.0
CB A:ASP329 4.0 8.0 1.0
CA A:ASP329 4.2 7.1 1.0
OD1 A:ASP329 4.6 12.6 1.0
C A:LEU328 4.6 6.8 1.0
CB A:LEU328 4.7 9.6 1.0
CG A:ASP329 4.8 9.4 1.0

Reference:

S.Wakadkar, S.Hermawan, D.Jendrossek, A.C.Papageorgiou. The Structure of PHAZ7 at Atomic (1.2 A) Resolution Reveals Details of the Active Site and Suggests A Substrate-Binding Mode. Acta Crystallogr. Sect. F V. 66 648 2010STRUCT. Biol. Cryst. Commun..
ISSN: ESSN 1744-3091
PubMed: 20516591
DOI: 10.1107/S174430911001434X
Page generated: Sun Aug 11 14:28:59 2024

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