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Iodine in PDB 8u04: Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo

Protein crystallography data

The structure of Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo, PDB code: 8u04 was solved by P.Daniel-Ivad, K.S.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.36 / 1.62
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.78, 186.72, 71.69, 90, 111.12, 90
R / Rfree (%) 16.4 / 20.8

Other elements in 8u04:

The structure of Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo (pdb code 8u04). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo, PDB code: 8u04:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 8u04

Go back to Iodine Binding Sites List in 8u04
Iodine binding site 1 out of 8 in the Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:41.6
occ:1.00
 NZ A:LYS4 3.5 28.8 1.0
NH1 A:ARG86 3.6 12.8 1.0
O A:HOH481 3.6 36.9 1.0
CD A:PRO60 3.9 15.3 1.0
N A:PRO60 3.9 16.6 1.0
C A:SER59 4.0 13.9 1.0
CE A:LYS4 4.1 26.4 1.0
O A:ALA57 4.1 22.3 1.0
N A:SER59 4.1 16.6 1.0
CA A:SER59 4.2 14.4 1.0
O A:ALA58 4.2 23.3 1.0
C A:ALA58 4.3 15.8 1.0
O A:SER59 4.4 15.6 1.0
O A:HOH436 4.4 30.6 1.0
O A:HOH676 4.6 39.0 1.0
CZ A:ARG86 4.6 14.6 1.0
O A:HOH656 4.6 19.2 1.0
CA A:PRO60 4.7 17.2 1.0
CG A:PRO60 4.7 19.2 1.0
CB A:PRO60 4.7 21.3 1.0
NH2 A:ARG86 4.8 20.5 1.0
C A:ALA57 4.9 20.6 1.0

Iodine binding site 2 out of 8 in 8u04

Go back to Iodine Binding Sites List in 8u04
Iodine binding site 2 out of 8 in the Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:62.0
occ:1.00
 N A:LYS4 3.5 18.6 1.0
CG A:PRO60 3.9 19.2 1.0
O A:HOH493 4.0 24.9 1.0
CA A:ALA3 4.1 15.7 1.0
CB A:LYS4 4.2 16.5 1.0
CG A:LYS4 4.3 20.7 1.0
C A:ALA3 4.3 19.4 1.0
CB A:ALA3 4.3 17.4 1.0
CD A:PRO60 4.3 15.3 1.0
CA A:LYS4 4.4 16.6 1.0
O A:LYS4 4.6 14.6 1.0
CE A:LYS4 4.7 26.4 1.0
O A:HOH609 4.7 42.3 1.0
O A:HOH682 4.8 35.0 1.0

Iodine binding site 3 out of 8 in 8u04

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Iodine binding site 3 out of 8 in the Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:71.2
occ:1.00
 O D:HOH594 3.2 29.4 1.0
NH2 D:ARG254 3.7 26.9 1.0
CD A:PRO96 4.0 14.0 1.0
CG A:PRO96 4.0 15.6 1.0
CB A:PRO96 4.1 12.6 1.0
CG1 A:VAL97 4.1 20.7 1.0
CD D:PRO194 4.2 20.5 1.0
N A:VAL97 4.3 19.6 1.0
CG D:PRO194 4.4 22.9 1.0
CB A:VAL97 4.5 17.7 1.0
N A:PRO96 4.7 17.2 1.0
CZ D:ARG254 4.7 22.9 1.0
CD1 D:LEU253 4.7 28.4 1.0
NE D:ARG254 4.8 30.6 1.0
CA A:PRO96 4.9 15.6 1.0
C A:PRO96 4.9 20.9 1.0
CA A:VAL97 4.9 16.7 1.0

Iodine binding site 4 out of 8 in 8u04

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Iodine binding site 4 out of 8 in the Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:43.0
occ:1.00
 O C:HOH655 3.5 33.1 1.0
N B:VAL97 3.9 14.4 1.0
CD B:PRO96 4.0 18.0 1.0
CB B:VAL97 4.0 18.3 1.0
CB B:PRO96 4.1 15.2 1.0
CG1 B:VAL97 4.1 19.9 1.0
CG C:PRO194 4.1 19.5 1.0
CG B:PRO96 4.2 18.2 1.0
O C:HOH629 4.5 32.0 1.0
N B:PRO96 4.5 16.7 1.0
CA B:VAL97 4.5 15.1 1.0
C B:PRO96 4.7 16.4 1.0
CA B:PRO96 4.7 16.3 1.0
O C:HOH524 4.7 40.2 1.0
O B:HOH735 4.8 38.3 1.0
CD C:PRO194 4.8 26.4 1.0
CD1 C:LEU253 4.8 31.3 1.0

Iodine binding site 5 out of 8 in 8u04

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Iodine binding site 5 out of 8 in the Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I303

b:31.9
occ:0.74
 CD B:PRO60 3.8 18.9 1.0
O B:ALA58 3.8 23.2 1.0
NH1 B:ARG86 3.9 25.7 1.0
O A:HOH507 4.0 39.2 1.0
N B:PRO60 4.0 17.4 1.0
O B:ALA57 4.0 22.4 1.0
CB A:ARG33 4.0 28.5 1.0
CG2 A:THR34 4.0 24.3 1.0
C B:SER59 4.1 15.2 1.0
CA B:SER59 4.2 16.2 1.0
C B:ALA58 4.2 19.1 1.0
N B:SER59 4.2 19.2 1.0
CD A:ARG33 4.3 28.1 1.0
NH1 A:ARG33 4.5 27.7 1.0
NE A:ARG33 4.6 27.8 1.0
CG B:PRO60 4.7 22.2 1.0
CZ A:ARG33 4.7 28.8 1.0
O B:SER59 4.7 15.9 1.0
CE B:LYS4 4.7 25.2 1.0
CA B:PRO60 4.7 19.3 1.0
CG A:ARG33 4.8 29.3 1.0
CB B:PRO60 4.8 22.4 1.0
NH2 B:ARG86 4.8 30.2 1.0
CZ B:ARG86 4.8 24.3 1.0
O A:HOH578 4.9 33.9 1.0
C A:ARG33 5.0 28.0 1.0
O A:ARG33 5.0 35.4 1.0

Iodine binding site 6 out of 8 in 8u04

Go back to Iodine Binding Sites List in 8u04
Iodine binding site 6 out of 8 in the Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I301

b:41.7
occ:1.00
 O B:HOH700 3.3 48.0 1.0
CG1 C:VAL97 3.6 27.8 1.0
O B:HOH688 3.8 39.0 1.0
CD C:PRO96 3.8 22.2 1.0
CG2 C:VAL97 3.9 22.3 1.0
N C:VAL97 3.9 15.9 1.0
O B:HOH679 3.9 42.8 1.0
CG B:PRO194 4.0 20.8 1.0
CB C:PRO96 4.0 16.2 1.0
CG C:PRO96 4.1 16.7 1.0
CB C:VAL97 4.2 20.1 1.0
N C:PRO96 4.4 23.5 1.0
O B:HOH648 4.6 54.2 1.0
CA C:PRO96 4.7 15.9 1.0
CA C:VAL97 4.7 18.9 1.0
O B:HOH633 4.7 37.7 1.0
C C:PRO96 4.7 15.0 1.0
CD B:PRO194 4.7 19.8 1.0
CB C:SER95 5.0 17.2 1.0

Iodine binding site 7 out of 8 in 8u04

Go back to Iodine Binding Sites List in 8u04
Iodine binding site 7 out of 8 in the Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I302

b:93.7
occ:1.00
 O C:ALA58 3.4 21.5 1.0
NH1 C:ARG86 3.5 23.3 1.0
C C:ALA58 3.6 23.7 1.0
N C:SER59 3.8 25.4 1.0
CD C:PRO60 3.8 23.6 1.0
O C:ALA57 3.8 29.4 1.0
C C:SER59 3.8 22.2 1.0
CA C:SER59 3.9 22.8 1.0
N C:PRO60 3.9 18.7 1.0
NZ C:LYS4 4.4 23.8 1.0
O C:SER59 4.4 25.0 1.0
CA C:ALA58 4.5 23.3 1.0
C C:ALA57 4.6 26.3 1.0
O C:HOH628 4.6 53.7 1.0
CZ C:ARG86 4.6 25.7 1.0
CA C:PRO60 4.7 19.0 1.0
CE C:LYS4 4.7 27.3 1.0
CG C:PRO60 4.8 27.1 1.0
CB C:PRO60 4.8 25.9 1.0
NH2 C:ARG86 4.9 29.8 1.0
N C:ALA58 4.9 24.0 1.0

Iodine binding site 8 out of 8 in 8u04

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Iodine binding site 8 out of 8 in the Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Reductasporine Biosynthetic Pathway Imine Reductase Rede, Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I301

b:42.5
occ:1.00
 NH2 A:ARG254 3.5 39.4 1.0
O A:HOH413 3.8 37.0 1.0
N D:VAL97 3.8 18.6 1.0
CD D:PRO96 3.8 22.2 1.0
CG A:PRO194 3.9 25.7 1.0
O D:HOH598 3.9 39.1 1.0
CB D:PRO96 4.0 18.4 1.0
CB D:VAL97 4.0 22.4 1.0
CG D:PRO96 4.0 19.1 1.0
CG1 D:VAL97 4.1 23.1 1.0
N D:PRO96 4.3 20.0 1.0
CZ A:ARG254 4.4 37.2 1.0
CD A:PRO194 4.5 25.7 1.0
CA D:VAL97 4.5 20.4 1.0
CA D:PRO96 4.6 13.7 1.0
NH1 A:ARG254 4.6 37.0 1.0
C D:PRO96 4.6 14.9 1.0
CD1 A:LEU253 4.8 31.7 1.0
CB D:SER95 4.9 20.2 1.0

Reference:

P.Daniel-Ivad, K.S.Ryan. An Imine Reductase That Captures Reactive Intermediates in the Biosynthesis of the Indolocarbazole Reductasporine. J.Biol.Chem. V. 300 05642 2024.
ISSN: ESSN 1083-351X
PubMed: 38199566
DOI: 10.1016/J.JBC.2024.105642
Page generated: Sat Aug 9 00:29:56 2025

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