Iodine in PDB 7cbf: Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis

Enzymatic activity of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis

All present enzymatic activity of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis:
2.3.1.220;

Protein crystallography data

The structure of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis, PDB code: 7cbf was solved by C.Songsiriritthigul, N.Nualkaew, C.-J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.35 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.810, 98.330, 112.024, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.5

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis (pdb code 7cbf). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis, PDB code: 7cbf:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 7cbf

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Iodine binding site 1 out of 10 in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:26.2
occ:1.00
 O A:HOH730 3.2 50.1 1.0
OG A:SER94 3.2 12.5 1.0
N A:GLY83 3.4 13.4 1.0
CA A:GLY83 3.8 13.4 1.0
C A:ASN81 3.8 15.5 1.0
CA A:ASN81 3.9 16.4 1.0
CB A:SER94 3.9 12.2 1.0
N A:PRO82 4.0 15.1 1.0
CD A:PRO82 4.1 14.8 1.0
O A:ASN81 4.2 15.8 1.0
CB A:ASN81 4.4 16.3 1.0
C A:PRO82 4.6 14.6 1.0
N A:ILE84 4.7 12.9 1.0
O B:HOH685 4.7 20.9 1.0
OD1 A:ASN81 4.7 15.6 1.0
C A:GLY83 4.7 13.5 1.0
CG A:PRO82 4.8 14.7 1.0
CA A:PRO82 4.9 14.6 1.0

Iodine binding site 2 out of 10 in 7cbf

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Iodine binding site 2 out of 10 in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:52.7
occ:1.00
 O A:HOH664 3.4 10.5 1.0
N A:ALA243 3.6 11.1 1.0
CA A:ALA242 3.6 11.8 1.0
CB A:ALA242 3.7 11.8 1.0
O A:HOH662 3.8 23.7 1.0
O A:ALA243 3.9 10.9 1.0
NZ A:LYS176 4.0 11.8 1.0
C A:ALA242 4.2 11.5 1.0
CE A:LYS176 4.3 11.7 1.0
NH1 B:ARG156 4.3 12.6 1.0
OD1 B:ASN182 4.5 10.8 1.0
C A:ALA243 4.6 11.1 1.0
CA A:ALA243 4.6 10.9 1.0
O A:VAL241 4.8 12.1 1.0
O B:HOH626 4.8 24.7 1.0
CE1 A:HIS244 4.8 15.1 1.0
N A:ALA242 4.9 12.2 1.0

Iodine binding site 3 out of 10 in 7cbf

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Iodine binding site 3 out of 10 in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:75.7
occ:1.00
 OE2 A:GLU204 3.0 36.7 1.0
OE1 A:GLU204 3.4 31.0 1.0
CD A:GLU204 3.5 28.4 1.0
N A:ASP52 3.7 21.4 1.0
CA A:LEU50 3.8 24.3 1.0
C A:LEU50 3.8 22.9 1.0
CB A:ASP52 3.8 26.8 1.0
N A:LEU53 3.8 21.1 1.0
CD2 A:LEU50 3.9 23.8 1.0
CG A:LEU53 4.0 22.3 1.0
N A:THR51 4.0 22.3 1.0
CB A:LEU50 4.1 23.6 1.0
O A:LEU50 4.1 21.4 1.0
CA A:ASP52 4.2 23.3 1.0
C A:ASP52 4.5 21.6 1.0
CB A:LEU53 4.5 22.0 1.0
CG A:LEU50 4.6 24.0 1.0
C A:THR51 4.7 21.5 1.0
CG A:ASP52 4.7 31.6 1.0
CD1 A:LEU53 4.8 22.9 1.0
CA A:LEU53 4.8 21.1 1.0
CD2 A:LEU53 4.8 23.3 1.0
CG A:GLU204 4.9 23.5 1.0
CA A:THR51 5.0 23.9 1.0

Iodine binding site 4 out of 10 in 7cbf

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Iodine binding site 4 out of 10 in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:65.7
occ:1.00
 N A:GLU75 3.5 19.0 1.0
ND2 A:ASN30 3.8 26.3 1.0
O A:HOH709 3.9 21.6 1.0
OD1 A:ASN30 3.9 26.6 1.0
CB A:GLU75 4.0 22.8 1.0
CA A:THR74 4.0 17.8 1.0
CB A:THR74 4.0 17.0 1.0
CE1 A:PHE40 4.1 18.3 1.0
CG A:ASN30 4.2 24.6 1.0
C A:THR74 4.2 18.3 1.0
CA A:GLU75 4.4 20.8 1.0
CG2 A:THR74 4.6 16.4 1.0
CD1 A:PHE40 4.8 17.9 1.0
CZ A:PHE40 4.9 17.9 1.0
CD1 A:ILE32 5.0 18.1 1.0

Iodine binding site 5 out of 10 in 7cbf

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Iodine binding site 5 out of 10 in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I506

b:66.0
occ:1.00
 O A:HOH706 3.4 30.2 1.0
N A:GLU35 3.8 17.5 1.0
CA A:GLU35 3.9 19.7 1.0
CB A:GLN34 4.0 14.0 1.0
C A:GLN34 4.1 15.7 1.0
CG A:GLN34 4.1 13.6 1.0
CA A:VAL62 4.2 27.5 1.0
CB A:GLU35 4.3 22.4 1.0
O A:CYS61 4.3 22.0 1.0
O A:GLN34 4.5 14.5 1.0
CG2 A:VAL62 4.5 27.9 1.0
O A:HOH692 4.6 20.8 1.0
N A:VAL62 4.7 24.1 1.0
C A:CYS61 4.7 21.7 1.0
O A:HOH646 4.8 20.4 1.0
CA A:GLN34 4.8 14.9 1.0
CB A:VAL62 4.9 29.0 1.0
O A:VAL62 5.0 34.4 1.0

Iodine binding site 6 out of 10 in 7cbf

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Iodine binding site 6 out of 10 in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:27.6
occ:1.00
 N B:GLU323 3.8 17.6 1.0
CB B:GLU323 3.8 19.4 1.0
CB B:ASP321 4.0 19.2 1.0
CG B:ASP321 4.0 20.3 1.0
N B:GLU322 4.1 18.8 1.0
OD1 B:ASP321 4.2 21.3 1.0
CB B:GLU322 4.3 24.3 1.0
OD2 B:ASP321 4.3 21.7 1.0
CA B:GLU323 4.4 18.7 1.0
CA B:GLU322 4.6 20.3 1.0
C B:GLU322 4.7 18.5 1.0
C B:ASP321 4.8 17.4 1.0
CA B:ASP321 4.9 17.8 1.0

Iodine binding site 7 out of 10 in 7cbf

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Iodine binding site 7 out of 10 in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I503

b:46.5
occ:1.00
 NH1 B:ARG351 3.6 13.7 1.0
NH2 B:ARG235 3.7 45.5 1.0
CD B:ARG351 4.1 14.8 1.0
CG1 B:VAL237 4.1 12.6 1.0
CG2 B:THR362 4.3 12.7 1.0
CZ B:ARG235 4.3 46.4 1.0
NE B:ARG235 4.3 44.0 1.0
CG2 B:VAL237 4.4 12.6 1.0
CB B:ARG351 4.4 15.6 1.0
CZ B:ARG351 4.6 14.4 1.0
CG B:ARG351 4.6 14.9 1.0
CB B:VAL237 4.8 12.6 1.0
NE B:ARG351 4.8 15.1 1.0
O B:HOH659 5.0 17.6 1.0
OE2 B:GLU117 5.0 15.3 1.0

Iodine binding site 8 out of 10 in 7cbf

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Iodine binding site 8 out of 10 in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I504

b:51.0
occ:1.00
 O B:HOH680 3.5 14.5 1.0
N B:ALA243 3.5 12.5 1.0
CA B:ALA242 3.7 13.4 1.0
O B:HOH608 3.8 10.5 1.0
CB B:ALA242 3.9 13.1 1.0
O B:ALA243 3.9 13.1 1.0
NH1 A:ARG156 4.1 12.0 1.0
C B:ALA242 4.1 12.9 1.0
NZ B:LYS176 4.2 11.8 1.0
CE B:LYS176 4.4 11.7 1.0
OD1 A:ASN182 4.5 14.9 1.0
C B:ALA243 4.6 13.0 1.0
CA B:ALA243 4.6 12.7 1.0
O B:VAL241 4.7 14.1 1.0
N B:ALA242 4.9 14.1 1.0

Iodine binding site 9 out of 10 in 7cbf

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Iodine binding site 9 out of 10 in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I505

b:62.4
occ:1.00
 CE B:LYS317 4.0 25.4 1.0
CA B:PRO274 4.0 16.7 1.0
CA B:GLY313 4.0 18.6 1.0
CG2 B:ILE273 4.1 18.2 1.0
CA B:GLY277 4.1 18.1 1.0
O B:ILE273 4.1 15.8 1.0
O B:GLY313 4.2 19.8 1.0
N B:PRO274 4.3 17.0 1.0
C B:ILE273 4.4 16.8 1.0
CG B:LYS317 4.4 23.3 1.0
C B:GLY313 4.4 19.3 1.0
CB B:PRO274 4.6 16.7 1.0
N B:GLY277 4.8 17.4 1.0
CD B:LYS317 4.8 24.1 1.0
C B:GLY277 4.9 18.9 1.0

Iodine binding site 10 out of 10 in 7cbf

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Iodine binding site 10 out of 10 in the Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I506

b:48.7
occ:1.00
 N B:GLY83 3.3 17.3 1.0
OG B:SER94 3.4 17.2 1.0
CA B:GLY83 3.6 16.7 1.0
C B:ASN81 3.7 19.7 1.0
CA B:ASN81 3.9 21.8 1.0
O B:ASN81 3.9 17.5 1.0
N B:PRO82 4.0 19.8 1.0
CB B:SER94 4.1 15.1 1.0
O A:HOH666 4.1 22.1 1.0
CB B:ASN81 4.2 22.1 1.0
N B:ILE84 4.3 15.4 1.0
CD B:PRO82 4.3 19.7 1.0
C B:GLY83 4.4 16.4 1.0
C B:PRO82 4.4 18.0 1.0
O B:GLY90 4.5 17.7 1.0
OD1 B:ASN81 4.6 22.4 1.0
CA B:SER91 4.7 14.6 1.0
CB B:SER91 4.8 14.1 1.0
CA B:PRO82 4.8 19.0 1.0
CG B:PRO82 4.9 19.9 1.0
CG B:ASN81 5.0 23.6 1.0
CG1 B:ILE84 5.0 15.2 1.0

Reference:

C.Songsiriritthigul, N.Nualkaew, J.Ketudat-Cairnsb, C.-J.Chen. Crystal Structure of Benzophenone Synthase From Garcinia Mangostana L. Pericarps Reveals Basis For Substrate Specificity and Catalysis. Acta Crystallogr.,Sect.F V. 76 597 2020.
ISSN: ESSN 2053-230X
DOI: 10.1107/S2053230X20014818
Page generated: Sun Dec 13 19:58:00 2020

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