Atomistry » Silicon » PDB 7zpz-8uas » 8uas
Atomistry »
  Silicon »
    PDB 7zpz-8uas »
      8uas »

Silicon in PDB 8uas: Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A

Protein crystallography data

The structure of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A, PDB code: 8uas was solved by L.A.Wilson, L.W.Guddat, G.Schenk, C.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.22 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.144, 157.745, 272.429, 90, 91.06, 90
R / Rfree (%) 18.2 / 21

Other elements in 8uas:

The structure of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A also contains other interesting chemical elements:

Sodium (Na) 4 atoms
Zinc (Zn) 26 atoms

Silicon Binding Sites:

The binding sites of Silicon atom in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A (pdb code 8uas). This binding sites where shown within 5.0 Angstroms radius around Silicon atom.
In total 10 binding sites of Silicon where determined in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A, PDB code: 8uas:
Jump to Silicon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silicon binding site 1 out of 10 in 8uas

Go back to Silicon Binding Sites List in 8uas
Silicon binding site 1 out of 10 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Si404

b:72.8
occ:1.00
SI05 C:W3O404 0.0 72.8 1.0
O08 C:W3O404 1.7 64.3 1.0
C07 C:W3O404 1.9 60.1 1.0
C06 C:W3O404 1.9 57.0 1.0
C02 C:W3O404 1.9 65.1 1.0
C09 C:W3O404 2.8 51.8 1.0
C03 C:W3O404 2.8 59.0 1.0
C04 C:W3O404 2.9 73.9 1.0
C01 C:W3O404 2.9 53.9 1.0
HB3 C:SER40 3.1 57.5 1.0
C10 C:W3O404 3.9 47.5 1.0
CB C:SER40 4.0 47.9 1.0
HG C:SER40 4.1 67.4 1.0
OG C:SER40 4.2 56.1 1.0
C11 C:W3O404 4.3 49.8 1.0
N12 C:W3O404 4.3 48.0 1.0
C20 C:W3O404 4.3 49.7 1.0
HG21 C:ILE271 4.4 70.7 1.0
HB2 C:SER40 4.5 57.5 1.0
HD13 C:ILE271 4.5 76.6 1.0
HA C:SER40 4.7 56.8 1.0
C13 C:W3O404 4.8 49.0 1.0
HE1 C:TYR294 4.8 45.9 1.0
C16 C:W3O404 4.9 51.0 1.0
CA C:SER40 5.0 47.3 1.0

Silicon binding site 2 out of 10 in 8uas

Go back to Silicon Binding Sites List in 8uas
Silicon binding site 2 out of 10 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 2 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Si405

b:53.1
occ:1.00
SI05 D:W3O405 0.0 53.1 1.0
O08 D:W3O405 1.7 43.4 1.0
C07 D:W3O405 1.9 44.6 1.0
C06 D:W3O405 1.9 46.8 1.0
C02 D:W3O405 1.9 48.0 1.0
C09 D:W3O405 2.8 36.6 1.0
C03 D:W3O405 2.8 46.4 1.0
C01 D:W3O405 2.8 46.5 1.0
C04 D:W3O405 2.9 44.8 1.0
HB3 D:SER40 4.0 42.7 1.0
C10 D:W3O405 4.1 34.5 1.0
C20 D:W3O405 4.1 34.8 1.0
HG D:SER40 4.2 46.6 1.0
N12 D:W3O405 4.3 37.8 1.0
C16 D:W3O405 4.3 34.6 1.0
HE1 D:TYR294 4.5 38.4 1.0
C13 D:W3O405 4.6 34.4 1.0
OG D:SER40 4.6 38.8 1.0
HG21 D:ILE271 4.6 55.4 1.0
C15 D:W3O405 4.6 35.1 1.0
CB D:SER40 4.7 35.5 1.0
C14 D:W3O405 4.7 35.5 1.0
C11 D:W3O405 4.8 36.6 1.0
HD13 D:ILE271 4.8 57.7 1.0
C17 D:W3O405 4.9 34.4 1.0

Silicon binding site 3 out of 10 in 8uas

Go back to Silicon Binding Sites List in 8uas
Silicon binding site 3 out of 10 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 3 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Si503

b:58.8
occ:1.00
SI05 E:W3O503 0.0 58.8 1.0
O08 E:W3O503 1.7 52.4 1.0
C07 E:W3O503 1.9 50.9 1.0
C06 E:W3O503 1.9 54.1 1.0
C02 E:W3O503 1.9 59.4 1.0
C09 E:W3O503 2.8 39.6 1.0
C03 E:W3O503 2.8 53.7 1.0
C01 E:W3O503 2.8 47.9 1.0
C04 E:W3O503 2.9 61.5 1.0
HB3 E:SER40 3.7 43.3 1.0
C10 E:W3O503 4.0 42.6 1.0
HE1 E:TYR294 4.5 41.6 1.0
CB E:SER40 4.6 36.0 1.0
N12 E:W3O503 4.6 44.6 1.0
C20 E:W3O503 4.6 40.3 1.0
HD13 E:LEU119 4.6 36.3 1.0
OG E:SER40 4.7 40.6 1.0
C11 E:W3O503 4.8 38.9 1.0
HG E:SER40 4.8 48.8 1.0
HD13 E:ILE271 4.9 65.8 1.0
C13 E:W3O503 5.0 42.0 1.0

Silicon binding site 4 out of 10 in 8uas

Go back to Silicon Binding Sites List in 8uas
Silicon binding site 4 out of 10 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 4 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Si404

b:72.0
occ:1.00
SI05 F:W3O404 0.0 72.0 1.0
O08 F:W3O404 1.7 55.3 0.5
C07 F:W3O404 1.9 51.8 1.0
C06 F:W3O404 1.9 51.1 1.0
C02 F:W3O404 1.9 64.9 1.0
C09 F:W3O404 2.8 51.2 1.0
C03 F:W3O404 2.8 64.7 1.0
C01 F:W3O404 2.9 61.3 1.0
C04 F:W3O404 2.9 57.2 0.2
C10 F:W3O404 3.6 48.2 1.0
HG F:SER40 3.7 69.6 1.0
HE1 F:TYR294 3.9 41.0 1.0
OG F:SER40 4.1 57.9 1.0
HB3 F:SER40 4.2 60.4 1.0
N12 F:W3O404 4.5 49.5 1.0
C11 F:W3O404 4.6 40.6 1.0
C20 F:W3O404 4.7 45.6 1.0
HZ A:PHE282 4.7 70.0 1.0
HZ A:PHE286 4.7 45.1 1.0
CB F:SER40 4.7 50.3 1.0
HD1 F:TYR294 4.7 31.4 1.0
CE1 F:TYR294 4.8 34.1 1.0
C13 F:W3O404 4.8 52.3 0.8
HD11 F:LEU119 5.0 47.7 1.0

Silicon binding site 5 out of 10 in 8uas

Go back to Silicon Binding Sites List in 8uas
Silicon binding site 5 out of 10 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 5 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Si404

b:62.3
occ:1.00
SI05 G:W3O404 0.0 62.3 1.0
O08 G:W3O404 1.7 53.8 1.0
C07 G:W3O404 1.9 56.6 1.0
C06 G:W3O404 1.9 55.4 1.0
C02 G:W3O404 1.9 62.3 1.0
C09 G:W3O404 2.8 49.1 1.0
C03 G:W3O404 2.8 60.0 1.0
C01 G:W3O404 2.8 56.8 1.0
C04 G:W3O404 2.9 62.5 1.0
HB3 G:SER40 3.6 55.5 1.0
C10 G:W3O404 4.0 49.1 1.0
C20 G:W3O404 4.5 48.3 1.0
HG21 G:ILE271 4.5 68.8 1.0
CB G:SER40 4.6 46.2 1.0
N12 G:W3O404 4.6 52.8 1.0
HE1 G:TYR294 4.6 44.0 1.0
HD13 G:ILE271 4.7 71.1 1.0
C16 G:W3O404 4.8 47.0 1.0
C11 G:W3O404 4.8 48.6 1.0
HD22 G:LEU119 4.9 50.0 1.0
HG23 G:VAL44 4.9 64.4 1.0
HB2 G:SER40 5.0 55.5 1.0
OG G:SER40 5.0 51.4 1.0

Silicon binding site 6 out of 10 in 8uas

Go back to Silicon Binding Sites List in 8uas
Silicon binding site 6 out of 10 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 6 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Si503

b:72.8
occ:1.00
SI05 H:W3O503 0.0 72.8 1.0
O08 H:W3O503 1.7 64.9 1.0
C07 H:W3O503 1.9 58.2 1.0
C06 H:W3O503 1.9 57.6 1.0
C02 H:W3O503 1.9 65.1 1.0
C09 H:W3O503 2.8 53.0 1.0
C03 H:W3O503 2.8 63.9 1.0
C01 H:W3O503 2.8 60.3 1.0
C04 H:W3O503 2.9 69.6 1.0
C10 H:W3O503 3.8 51.4 1.0
HB2 H:SER40 3.9 71.3 1.0
HB3 H:SER40 3.9 71.3 1.0
HE1 H:TYR294 4.4 48.7 1.0
CB H:SER40 4.4 59.4 1.0
C20 H:W3O503 4.6 52.4 1.0
N12 H:W3O503 4.6 55.7 1.0
C11 H:W3O503 4.8 50.6 1.0
HG H:SER40 4.8 79.6 1.0
HD13 H:LEU119 4.8 49.9 1.0

Silicon binding site 7 out of 10 in 8uas

Go back to Silicon Binding Sites List in 8uas
Silicon binding site 7 out of 10 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 7 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Si405

b:60.3
occ:1.00
SI05 I:W3O405 0.0 60.3 1.0
O08 I:W3O405 1.7 54.3 1.0
C07 I:W3O405 1.9 47.7 1.0
C06 I:W3O405 1.9 46.4 1.0
C02 I:W3O405 1.9 66.2 1.0
C09 I:W3O405 2.8 48.0 1.0
C03 I:W3O405 2.8 60.4 1.0
C01 I:W3O405 2.8 66.8 1.0
C04 I:W3O405 2.9 64.4 1.0
HG I:SER40 3.7 65.5 1.0
C10 I:W3O405 3.8 48.2 1.0
HB3 I:SER40 4.0 65.7 1.0
OG I:SER40 4.1 54.5 1.0
C20 I:W3O405 4.3 42.8 1.0
N12 I:W3O405 4.3 48.7 1.0
HE1 I:TYR294 4.4 45.3 1.0
C11 I:W3O405 4.6 46.3 1.0
CB I:SER40 4.6 54.7 1.0
C16 I:W3O405 4.7 47.3 1.0
C13 I:W3O405 4.8 48.0 1.0
HD13 I:LEU119 4.8 60.9 1.0

Silicon binding site 8 out of 10 in 8uas

Go back to Silicon Binding Sites List in 8uas
Silicon binding site 8 out of 10 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 8 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Si503

b:70.4
occ:1.00
SI05 J:W3O503 0.0 70.4 1.0
O08 J:W3O503 1.7 60.1 1.0
C07 J:W3O503 1.9 59.4 1.0
C06 J:W3O503 1.9 60.0 1.0
C02 J:W3O503 1.9 62.5 1.0
C09 J:W3O503 2.8 52.7 1.0
C01 J:W3O503 2.8 64.0 1.0
C03 J:W3O503 2.9 60.4 1.0
C04 J:W3O503 2.9 55.1 1.0
HB3 J:SER40 3.6 61.6 1.0
HG J:SER40 3.8 63.9 1.0
C10 J:W3O503 4.1 48.5 1.0
OG J:SER40 4.2 53.1 1.0
C20 J:W3O503 4.3 43.1 1.0
N12 J:W3O503 4.4 52.6 1.0
CB J:SER40 4.4 51.2 1.0
HE1 J:TYR294 4.5 41.1 1.0
HD13 J:ILE271 4.6 61.0 1.0
C16 J:W3O503 4.7 44.1 1.0
C11 J:W3O503 4.7 47.5 1.0
C13 J:W3O503 4.8 49.9 1.0
HA J:SER40 5.0 53.4 1.0

Silicon binding site 9 out of 10 in 8uas

Go back to Silicon Binding Sites List in 8uas
Silicon binding site 9 out of 10 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 9 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Si503

b:76.6
occ:1.00
SI05 K:W3O503 0.0 76.6 1.0
O08 K:W3O503 1.7 71.8 1.0
C07 K:W3O503 1.9 66.8 1.0
C06 K:W3O503 1.9 63.4 1.0
C02 K:W3O503 1.9 67.1 1.0
C09 K:W3O503 2.8 63.0 1.0
C03 K:W3O503 2.8 67.5 1.0
C01 K:W3O503 2.8 70.4 1.0
C04 K:W3O503 2.9 60.3 1.0
HB3 K:SER40 3.5 66.8 1.0
HD13 K:ILE271 3.9 84.1 1.0
C10 K:W3O503 3.9 55.1 1.0
HG K:SER40 3.9 72.7 1.0
HD11 K:ILE271 4.2 84.1 1.0
CB K:SER40 4.3 55.6 1.0
OG K:SER40 4.3 60.5 1.0
HE1 K:TYR294 4.4 51.0 1.0
CD1 K:ILE271 4.5 70.0 1.0
HD13 K:LEU119 4.6 55.8 1.0
C20 K:W3O503 4.8 54.4 1.0
N12 K:W3O503 4.8 55.7 1.0
HB2 K:SER40 4.9 66.8 1.0
C11 K:W3O503 4.9 50.5 1.0
HG23 K:VAL44 4.9 74.2 1.0
HA K:SER40 5.0 64.5 1.0

Silicon binding site 10 out of 10 in 8uas

Go back to Silicon Binding Sites List in 8uas
Silicon binding site 10 out of 10 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 10 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Si401

b:78.1
occ:1.00
SI05 L:W3O401 0.0 78.1 1.0
O08 L:W3O401 1.7 68.3 1.0
C07 L:W3O401 1.9 66.6 1.0
C06 L:W3O401 1.9 67.7 1.0
C02 L:W3O401 1.9 72.5 1.0
H071 L:W3O401 2.4 80.0 1.0
H072 L:W3O401 2.4 80.0 1.0
H073 L:W3O401 2.4 80.0 1.0
H062 L:W3O401 2.4 81.3 1.0
H063 L:W3O401 2.4 81.3 1.0
H061 L:W3O401 2.4 81.3 1.0
C09 L:W3O401 2.8 58.2 1.0
H033 L:W3O401 2.8 82.0 1.0
H092 L:W3O401 2.8 70.0 1.0
C03 L:W3O401 2.8 68.2 1.0
H041 L:W3O401 2.8 84.7 1.0
C04 L:W3O401 2.9 70.5 1.0
C01 L:W3O401 2.9 71.3 1.0
H012 L:W3O401 2.9 85.7 1.0
H011 L:W3O401 3.1 85.7 1.0
H043 L:W3O401 3.1 84.7 1.0
H031 L:W3O401 3.1 82.0 1.0
H091 L:W3O401 3.2 70.0 1.0
HB3 L:SER40 3.3 71.6 1.0
HG L:SER40 3.4 77.5 1.0
H032 L:W3O401 3.6 82.0 1.0
H042 L:W3O401 3.7 84.7 1.0
H013 L:W3O401 3.7 85.7 1.0
OG L:SER40 3.9 64.5 1.0
C10 L:W3O401 4.0 54.5 1.0
N12 L:W3O401 4.0 58.8 1.0
C20 L:W3O401 4.0 56.9 1.0
CB L:SER40 4.1 59.6 1.0
H102 L:W3O401 4.2 65.5 1.0
HE1 L:TYR294 4.3 50.3 1.0
H201 L:W3O401 4.3 68.4 1.0
C13 L:W3O401 4.3 56.7 1.0
C16 L:W3O401 4.4 58.3 1.0
C11 L:W3O401 4.4 55.7 1.0
H112 L:W3O401 4.5 66.9 1.0
C14 L:W3O401 4.6 57.0 1.0
HB2 L:SER40 4.6 71.6 1.0
C15 L:W3O401 4.6 56.7 1.0
H131 L:W3O401 4.7 68.1 1.0
H101 L:W3O401 4.8 65.5 1.0
HA L:SER40 4.9 67.1 1.0

Reference:

R.A.Rocha, L.A.Wilson, B.D.Schwartz, A.C.Warden, L.W.Guddat, R.E.Speight, L.Malins, G.Schenk, C.Scott. Structural Characterization of Enzymatic Interactions with Functional Nicotinamide Cofactor Biomimetics Catalysts V. 14 2024.
ISSN: ESSN 2073-4344
DOI: 10.3390/CATAL14070399
Page generated: Thu Oct 10 13:41:40 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy