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Iodine in PDB 8u07: Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site)

Protein crystallography data

The structure of Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site), PDB code: 8u07 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) 36.60 / 1.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.588, 111.529, 67.695, 90, 108.47, 90
R / Rfree (%) 19.4 / 22.1

Other elements in 8u07:

The structure of Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site) also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 7 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site) (pdb code 8u07). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site), PDB code: 8u07:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 8u07

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Iodine binding site 1 out of 7 in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:46.3
occ:0.40
 O A:HOH695 3.2 59.2 1.0
N A:LYS4 3.5 28.1 1.0
O A:HOH506 4.0 43.3 1.0
CG A:PRO60 4.1 47.2 1.0
CA A:ALA3 4.1 32.6 1.0
CB A:LYS4 4.1 32.1 1.0
C A:ALA3 4.3 34.4 1.0
CA A:LYS4 4.4 32.3 1.0
CG A:LYS4 4.4 27.9 1.0
CD A:PRO60 4.5 27.9 1.0
CB A:ALA3 4.5 38.6 1.0
O A:LYS4 4.7 32.6 1.0
CD A:LYS4 4.9 32.2 1.0

Iodine binding site 2 out of 7 in 8u07

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Iodine binding site 2 out of 7 in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:48.4
occ:0.49
 NH1 A:ARG86 3.6 38.9 1.0
CD A:PRO60 3.8 27.9 1.0
N A:PRO60 3.8 27.1 1.0
C A:SER59 3.9 26.5 1.0
O A:HOH473 3.9 44.3 1.0
O A:ALA57 4.0 31.4 1.0
O A:ALA58 4.1 32.8 1.0
CA A:SER59 4.1 25.8 1.0
N A:SER59 4.2 29.9 1.0
C A:ALA58 4.2 27.4 1.0
O A:HOH695 4.2 59.2 1.0
O A:HOH627 4.4 69.0 1.0
CA A:PRO60 4.5 27.9 1.0
O A:SER59 4.5 28.9 1.0
CG A:PRO60 4.6 47.2 1.0
CB A:PRO60 4.6 39.5 1.0
CZ A:ARG86 4.7 50.3 1.0
NH2 A:ARG86 4.9 35.1 1.0
C A:ALA57 5.0 41.7 1.0

Iodine binding site 3 out of 7 in 8u07

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Iodine binding site 3 out of 7 in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:45.8
occ:0.63
 O A:HOH686 3.7 40.6 1.0
CA A:LEU239 3.9 21.8 1.0
N A:LEU239 4.0 25.4 1.0
C A:HIS238 4.1 25.2 1.0
O A:HIS238 4.1 26.2 1.0
CD1 A:LEU239 4.2 29.7 1.0
CD A:ARG242 4.2 33.7 1.0
CB A:HIS238 4.3 25.1 1.0
CB A:LEU239 4.3 21.1 1.0
CB A:ARG242 4.5 24.2 1.0
O A:HOH542 4.6 43.5 1.0
CA A:HIS238 4.8 26.4 1.0
CG A:LEU239 4.9 26.6 1.0
CG A:ARG242 5.0 26.6 1.0

Iodine binding site 4 out of 7 in 8u07

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Iodine binding site 4 out of 7 in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:66.0
occ:0.57
 NH2 B:ARG254 3.4 33.5 1.0
CG1 A:VAL97 3.5 39.9 1.0
CG2 A:VAL97 3.8 61.2 1.0
C19 A:A7F302 4.1 23.1 0.6
N A:VAL97 4.1 20.4 1.0
O B:HOH576 4.1 52.8 1.0
CB A:VAL97 4.1 23.9 1.0
CD A:PRO96 4.2 19.3 1.0
CB A:PRO96 4.2 24.3 1.0
O02 A:A7F302 4.3 32.4 0.6
CG A:PRO96 4.3 23.3 1.0
C23 A:A7F302 4.4 25.1 0.6
CZ B:ARG254 4.5 39.9 1.0
CD B:PRO194 4.6 33.2 1.0
CA A:VAL97 4.7 21.4 1.0
NE B:ARG254 4.7 32.6 1.0
CG B:PRO194 4.7 45.2 1.0
N A:PRO96 4.7 23.7 1.0
C A:PRO96 4.9 25.2 1.0
CA A:PRO96 4.9 22.2 1.0
CD1 B:LEU253 4.9 37.2 1.0

Iodine binding site 5 out of 7 in 8u07

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Iodine binding site 5 out of 7 in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I306

b:34.4
occ:0.52
 O A:HOH589 3.2 56.4 1.0
NH2 A:ARG254 3.6 31.5 1.0
N B:VAL97 3.8 23.2 1.0
CB B:VAL97 3.8 24.8 1.0
CD B:PRO96 3.9 27.1 1.0
CG1 B:VAL97 4.0 32.1 1.0
CB B:PRO96 4.2 23.2 1.0
C18 B:A7F302 4.2 21.2 0.6
CG B:PRO96 4.2 24.6 1.0
CA B:VAL97 4.4 26.9 1.0
O01 B:A7F302 4.4 27.1 0.6
N B:PRO96 4.5 22.5 1.0
C22 B:A7F302 4.5 21.3 0.6
CD A:PRO194 4.6 30.9 1.0
C B:PRO96 4.6 23.8 1.0
CZ A:ARG254 4.7 27.9 1.0
CG A:PRO194 4.7 45.4 1.0
CA B:PRO96 4.7 21.4 1.0
O A:HOH642 5.0 55.0 1.0
NE A:ARG254 5.0 61.9 1.0

Iodine binding site 6 out of 7 in 8u07

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Iodine binding site 6 out of 7 in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I307

b:60.9
occ:0.55
 CD B:PRO60 3.7 49.3 1.0
NH1 B:ARG86 3.7 39.9 1.0
N B:PRO60 3.8 34.4 1.0
C B:SER59 4.0 28.6 1.0
O B:HOH425 4.2 57.2 1.0
O B:ALA57 4.2 36.6 1.0
O B:ALA58 4.2 40.7 1.0
CA B:SER59 4.2 31.7 1.0
O B:HOH628 4.3 53.5 1.0
N B:SER59 4.3 34.6 1.0
C B:ALA58 4.4 44.3 1.0
CA B:PRO60 4.5 35.3 1.0
CB B:PRO60 4.5 48.9 1.0
O B:SER59 4.5 36.6 1.0
CG B:PRO60 4.5 57.9 1.0
CZ B:ARG86 4.8 45.1 1.0
NH2 B:ARG86 5.0 42.1 1.0

Iodine binding site 7 out of 7 in 8u07

Go back to Iodine Binding Sites List in 8u07
Iodine binding site 7 out of 7 in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I308

b:59.6
occ:0.44
 N B:LYS4 3.5 47.2 1.0
O B:HOH501 3.9 39.2 1.0
CB B:LYS4 4.0 37.5 1.0
CG B:PRO60 4.1 57.9 1.0
CG B:LYS4 4.2 48.1 1.0
CA B:ALA3 4.2 62.6 1.0
CB B:ALA3 4.3 45.1 1.0
CA B:LYS4 4.4 33.4 1.0
O B:HOH522 4.4 53.3 1.0
C B:ALA3 4.4 66.0 1.0
CD B:PRO60 4.6 49.3 1.0
O B:LYS4 4.7 42.6 1.0

Reference:

P.Daniel-Ivad, K.S.Ryan. An Imine Reductase That Captures Reactive Intermediates in the Biosynthesis of the Indolocarbazole Reductasporine To Be Published.
Page generated: Sat Sep 28 22:03:43 2024

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