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Iodine in PDB 7cp6: Crystal Structure of Fqzb

Protein crystallography data

The structure of Crystal Structure of Fqzb, PDB code: 7cp6 was solved by K.Hara, H.Hashimoto, T.Matsushita, S.Kishimoto, K.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.64 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.893, 120.181, 68.048, 90, 94.11, 90
R / Rfree (%) 21.3 / 23.8

Other elements in 7cp6:

The structure of Crystal Structure of Fqzb also contains other interesting chemical elements:

Mercury (Hg) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Fqzb (pdb code 7cp6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of Fqzb, PDB code: 7cp6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 7cp6

Go back to Iodine Binding Sites List in 7cp6
Iodine binding site 1 out of 9 in the Crystal Structure of Fqzb


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 Fqzb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:41.3
occ:1.00
 N A:GLY331 3.5 24.8 1.0
C10 A:FAD501 3.7 35.2 1.0
N A:GLY329 3.7 36.2 1.0
N10 A:FAD501 3.7 35.2 1.0
CA A:PRO326 3.8 44.6 1.0
N A:GLN330 3.8 29.5 1.0
N1 A:FAD501 3.9 33.6 1.0
CG2 A:VAL328 3.9 41.2 1.0
C1' A:FAD501 4.0 34.2 1.0
CA A:GLY331 4.1 27.1 1.0
CA A:GLY329 4.1 36.1 1.0
C9A A:FAD501 4.2 36.5 1.0
O A:PHE325 4.2 45.2 1.0
C4X A:FAD501 4.2 34.9 1.0
CB A:TYR324 4.3 30.0 1.0
C A:GLY329 4.4 32.1 1.0
C A:PRO326 4.4 47.6 1.0
N A:VAL327 4.4 45.5 1.0
N A:VAL328 4.5 42.9 1.0
CB A:PRO326 4.5 48.9 1.0
C A:GLN330 4.5 29.7 1.0
C2 A:FAD501 4.6 39.0 1.0
N A:PRO326 4.6 43.7 1.0
CD2 A:TYR324 4.6 30.9 1.0
C A:VAL328 4.6 40.0 1.0
C5X A:FAD501 4.6 35.5 1.0
N5 A:FAD501 4.6 34.7 1.0
C A:PHE325 4.7 41.2 1.0
CA A:GLN330 4.7 28.5 1.0
C9 A:FAD501 4.8 36.3 1.0
C4 A:FAD501 4.8 35.3 1.0
CA A:VAL328 4.9 37.6 1.0
N3 A:FAD501 5.0 33.7 1.0

Iodine binding site 2 out of 9 in 7cp6

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Iodine binding site 2 out of 9 in the Crystal Structure of Fqzb


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 Fqzb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:182.1
occ:1.00
 CD1 A:TYR366 4.0 32.0 1.0
CE1 A:TYR366 4.1 35.0 1.0
CA A:PRO367 4.1 33.0 1.0
CB A:PRO367 4.2 37.2 1.0
CG A:PRO367 4.2 32.9 1.0
O A:HOH698 4.3 32.0 1.0
N A:PRO367 4.6 31.3 1.0
CD A:PRO367 5.0 29.9 1.0

Iodine binding site 3 out of 9 in 7cp6

Go back to Iodine Binding Sites List in 7cp6
Iodine binding site 3 out of 9 in the Crystal Structure of Fqzb


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 Fqzb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:44.0
occ:1.00
 NE2 A:HIS409 3.3 40.3 1.0
CB A:CYS411 3.5 31.2 1.0
NH1 A:ARG365 3.6 28.3 1.0
ND2 A:ASN436 3.6 37.1 1.0
CA A:CYS411 3.8 36.9 1.0
CD2 A:HIS409 4.0 38.5 1.0
CD A:ARG368 4.0 29.3 1.0
CG2 A:ILE364 4.1 27.8 1.0
CD A:ARG365 4.1 28.9 1.0
CG2 A:VAL341 4.2 27.9 1.0
CD2 A:TYR414 4.3 34.4 1.0
CE1 A:HIS409 4.4 43.9 1.0
CB A:ASN436 4.4 34.9 1.0
O A:CYS411 4.4 34.1 1.0
CG A:ASN436 4.5 37.2 1.0
NE A:ARG368 4.5 34.0 1.0
C A:CYS411 4.6 38.2 1.0
OE1 A:GLU337 4.7 32.5 1.0
CZ A:ARG365 4.7 26.4 1.0
O A:ILE364 4.8 31.4 1.0
NE A:ARG365 4.9 30.6 1.0
CE2 A:TYR414 4.9 34.8 1.0
N A:CYS411 4.9 35.6 1.0
CG A:TYR414 5.0 36.7 1.0
OG1 A:THR415 5.0 32.7 1.0

Iodine binding site 4 out of 9 in 7cp6

Go back to Iodine Binding Sites List in 7cp6
Iodine binding site 4 out of 9 in the Crystal Structure of Fqzb


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 Fqzb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:66.1
occ:1.00
 O B:HOH648 3.6 39.5 1.0
O B:LYS46 4.0 35.5 1.0
CD B:LYS46 4.1 35.5 1.0
CG B:LYS46 4.1 32.1 1.0
C B:LYS46 4.3 33.3 1.0
CE B:LYS46 4.4 37.6 1.0
CB B:LYS46 4.4 30.5 1.0
CA B:VAL47 4.5 32.7 1.0
N B:VAL47 4.5 30.9 1.0
CG1 B:VAL47 4.6 31.7 1.0
NZ B:LYS46 5.0 43.1 1.0

Iodine binding site 5 out of 9 in 7cp6

Go back to Iodine Binding Sites List in 7cp6
Iodine binding site 5 out of 9 in the Crystal Structure of Fqzb


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 Fqzb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I503

b:107.4
occ:1.00
 O B:ASP146 3.9 56.9 1.0
CA B:GLY147 3.9 47.8 1.0
C B:ASP146 4.0 52.3 1.0
N B:GLY147 4.0 49.8 1.0
CB B:ASP146 4.2 57.1 1.0
CA B:ASP146 4.7 50.0 1.0

Iodine binding site 6 out of 9 in 7cp6

Go back to Iodine Binding Sites List in 7cp6
Iodine binding site 6 out of 9 in the Crystal Structure of Fqzb


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 Fqzb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I504

b:68.3
occ:1.00
 NH1 B:ARG158 3.4 48.9 1.0
NH1 B:ARG148 3.5 45.2 1.0
CD B:ARG158 4.0 42.6 1.0
CG B:ARG158 4.1 36.7 1.0
CZ B:ARG148 4.2 57.8 1.0
NH2 B:ARG148 4.2 56.8 1.0
CB B:ALA160 4.4 35.5 1.0
CZ B:ARG158 4.4 47.1 1.0
CB B:ARG158 4.6 31.7 1.0
NE B:ARG158 4.6 42.5 1.0
O B:ARG158 4.7 30.6 1.0
CZ2 B:TRP143 4.7 37.8 1.0
CH2 B:TRP143 4.9 41.6 1.0
C B:ARG158 5.0 34.7 1.0

Iodine binding site 7 out of 9 in 7cp6

Go back to Iodine Binding Sites List in 7cp6
Iodine binding site 7 out of 9 in the Crystal Structure of Fqzb


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 Fqzb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I505

b:46.2
occ:1.00
 N B:GLY329 3.5 47.2 1.0
O B:HOH675 3.5 44.4 1.0
N10 B:FAD501 3.6 34.4 1.0
C10 B:FAD501 3.7 33.4 1.0
CA B:PRO326 3.8 44.2 1.0
N B:GLY331 3.8 31.3 1.0
N B:GLN330 3.9 36.3 1.0
CG2 B:VAL328 3.9 44.1 1.0
CA B:GLY329 3.9 44.0 1.0
C1' B:FAD501 3.9 36.0 1.0
C9A B:FAD501 4.0 33.2 1.0
N1 B:FAD501 4.0 32.2 1.0
O B:PHE325 4.1 46.9 1.0
C4X B:FAD501 4.1 35.6 1.0
CB B:TYR324 4.3 37.5 1.0
N B:VAL328 4.3 43.3 1.0
C B:PRO326 4.4 49.6 1.0
N B:VAL327 4.4 45.9 1.0
C B:GLY329 4.4 38.3 1.0
CA B:GLY331 4.4 34.8 1.0
C5X B:FAD501 4.4 35.9 1.0
C B:VAL328 4.5 39.6 1.0
N5 B:FAD501 4.5 33.1 1.0
CD2 B:TYR324 4.5 35.4 1.0
CB B:PRO326 4.5 44.3 1.0
C9 B:FAD501 4.6 35.5 1.0
N B:PRO326 4.6 53.1 1.0
C B:PHE325 4.6 48.9 1.0
C2 B:FAD501 4.7 38.3 1.0
CA B:VAL328 4.8 45.7 1.0
C B:GLN330 4.8 31.6 1.0
C4 B:FAD501 4.9 34.1 1.0
CA B:GLN330 4.9 37.3 1.0
CG B:TYR324 4.9 28.0 1.0
CB B:VAL328 5.0 47.8 1.0
O B:HOH610 5.0 38.4 1.0

Iodine binding site 8 out of 9 in 7cp6

Go back to Iodine Binding Sites List in 7cp6
Iodine binding site 8 out of 9 in the Crystal Structure of Fqzb


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 Fqzb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I506

b:53.6
occ:1.00
 N B:ARG262 3.9 42.9 1.0
C B:ARG262 4.1 34.4 1.0
CB B:ALA263 4.2 35.5 1.0
C B:GLY261 4.2 37.3 1.0
N B:ALA263 4.3 34.2 1.0
CA B:ARG262 4.3 35.0 1.0
O B:ARG262 4.4 36.5 1.0
CA B:GLY261 4.5 36.9 1.0
CA B:VAL294 4.6 36.9 1.0
N B:ASP295 4.6 41.0 1.0
O B:GLY261 4.7 38.0 1.0
O B:LEU293 4.8 37.8 1.0
CB B:VAL294 4.8 42.6 1.0
CG1 B:VAL294 4.9 41.6 1.0
CA B:ALA263 4.9 32.8 1.0

Iodine binding site 9 out of 9 in 7cp6

Go back to Iodine Binding Sites List in 7cp6
Iodine binding site 9 out of 9 in the Crystal Structure of Fqzb


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 Fqzb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I507

b:53.8
occ:1.00
 NE2 B:HIS409 3.4 61.0 1.0
CB B:CYS411 3.5 51.4 1.0
ND2 B:ASN436 3.7 58.0 1.0
NH1 B:ARG365 3.7 42.3 1.0
CA B:CYS411 4.0 57.1 1.0
CD2 B:HIS409 4.1 62.6 1.0
CD B:ARG368 4.1 40.9 1.0
CD B:ARG365 4.1 40.3 1.0
CG2 B:ILE364 4.1 56.6 1.0
CG2 B:VAL341 4.2 41.6 1.0
CD2 B:TYR414 4.3 61.1 1.0
CE1 B:HIS409 4.5 65.1 1.0
O B:CYS411 4.5 54.4 1.0
NE B:ARG368 4.6 52.6 1.0
CB B:ASN436 4.6 61.0 1.0
CG B:ASN436 4.6 61.8 1.0
O B:ILE364 4.7 51.9 1.0
C B:CYS411 4.8 53.2 1.0
CZ B:ARG365 4.8 33.7 1.0
OE1 B:GLU337 4.8 47.0 1.0
CE2 B:TYR414 4.8 61.2 1.0
NE B:ARG365 4.9 35.5 1.0
OG1 B:THR415 5.0 54.0 1.0

Reference:

T.Matsushita, S.Kishimoto, K.Hara, H.Hashimoto, K.Watanabe. Structural and Functional Analyses of A Spiro-Carbon-Forming, Highly Promiscuous Epoxidase From Fungal Natural Product Biosynthesis. Biochemistry V. 59 4787 2020.
ISSN: ISSN 0006-2960
PubMed: 33332106
DOI: 10.1021/ACS.BIOCHEM.0C00896
Page generated: Mon Aug 12 00:55:06 2024

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