Atomistry » Sodium » PDB 8tb2-8u2z » 8u07
Atomistry »
  Sodium »
    PDB 8tb2-8u2z »
      8u07 »

Sodium 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:

Iodine (I) 7 atoms
Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site), PDB code: 8u07:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8u07

Go back to Sodium Binding Sites List in 8u07
Sodium binding site 1 out of 2 in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na305

b:25.6
occ:1.00
O A:THR92 2.4 25.9 1.0
O A:HOH612 2.4 25.9 1.0
OD1 A:ASP115 2.4 21.6 1.0
O A:GLY116 2.4 21.2 1.0
OH A:TYR69 2.6 26.9 1.0
O A:ASN90 3.2 20.6 1.0
CG A:ASP115 3.4 22.6 1.0
C A:GLY116 3.6 21.7 1.0
C A:THR92 3.6 28.7 1.0
OD2 A:ASP115 3.8 25.2 1.0
CZ A:TYR69 3.8 27.2 1.0
N A:GLY116 3.8 20.9 1.0
CE1 A:TYR69 4.1 26.9 1.0
O A:HOH458 4.1 30.9 1.0
C A:LEU91 4.1 24.0 1.0
N A:THR92 4.1 22.5 1.0
CG1 A:VAL117 4.2 21.6 1.0
C A:ASN90 4.2 21.1 1.0
CA A:GLY116 4.3 23.1 1.0
CA A:LEU91 4.3 19.4 1.0
CA A:THR92 4.4 25.6 1.0
O A:LEU91 4.5 30.3 1.0
N A:SER93 4.5 25.7 1.0
O A:HOH585 4.6 27.4 1.0
N A:VAL117 4.6 19.8 1.0
O A:HOH513 4.6 22.2 1.0
CB A:ASP115 4.6 25.4 1.0
CA A:SER93 4.6 26.7 1.0
C A:ASP115 4.7 21.5 1.0
N A:LEU91 4.7 20.8 1.0
CA A:VAL117 4.9 24.9 1.0
CA A:ASP115 4.9 18.6 1.0
N A:GLY94 5.0 27.5 1.0
CE2 A:TYR69 5.0 19.3 1.0

Sodium binding site 2 out of 2 in 8u07

Go back to Sodium Binding Sites List in 8u07
Sodium binding site 2 out of 2 in the Imine Reductase Rede Bound with Nadp+ and Arcyriaflavin A (Secondary Site)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
B:Na305

b:26.1
occ:1.00
O B:THR92 2.3 25.4 1.0
OD1 B:ASP115 2.4 21.7 1.0
O B:HOH573 2.5 29.1 1.0
O B:GLY116 2.5 21.3 1.0
OH B:TYR69 2.6 27.6 1.0
O B:ASN90 3.2 23.3 1.0
CG B:ASP115 3.4 29.2 1.0
C B:THR92 3.5 28.1 1.0
C B:GLY116 3.6 19.8 1.0
OD2 B:ASP115 3.7 25.3 1.0
CZ B:TYR69 3.8 28.1 1.0
N B:GLY116 3.8 21.1 1.0
N B:THR92 4.0 28.1 1.0
CE1 B:TYR69 4.1 23.7 1.0
O B:HOH466 4.1 29.5 1.0
C B:LEU91 4.1 29.3 1.0
C B:ASN90 4.2 24.2 1.0
CG1 B:VAL117 4.3 19.4 1.0
CA B:GLY116 4.3 21.4 1.0
CA B:LEU91 4.3 23.8 1.0
CA B:THR92 4.4 27.4 1.0
N B:SER93 4.5 26.3 1.0
O B:LEU91 4.5 28.0 1.0
O B:HOH552 4.6 29.4 1.0
CA B:SER93 4.6 24.8 1.0
O B:HOH506 4.6 23.0 1.0
CB B:ASP115 4.6 22.0 1.0
N B:VAL117 4.6 18.4 1.0
N B:LEU91 4.7 24.2 1.0
C B:ASP115 4.7 21.8 1.0
CA B:VAL117 4.9 21.7 1.0
N B:GLY94 4.9 24.6 1.0
CA B:ASP115 4.9 19.7 1.0
CE2 B:TYR69 5.0 31.9 1.0
C B:SER93 5.0 25.4 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: Wed Oct 9 13:45:14 2024

Last articles

Zn in 9FS1
Zn in 9FS3
Zn in 9FS2
Zn in 9H3H
Zn in 9F29
Zn in 9F2A
Zn in 9EY2
Zn in 9F26
Zn in 9E8J
Zn in 9E8N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy