Zinc in PDB 8uar: Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B

The structure of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B, PDB code: 8uar was solved by L.A.Wilson, G.Schenk, L.W.Guddat, C.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.18 / 2.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.295, 158.177, 272.938, 90, 91.05, 90
R / Rfree (%)	19.3 / 24.6

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B (pdb code 8uar). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B, PDB code: 8uar:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:30.9 occ:1.00 SG A:CYS95 2.2 18.2 1.0 SG A:CYS92 2.2 31.6 1.0 SG A:CYS106 2.2 28.5 1.0 SG A:CYS98 2.2 31.1 1.0 CB A:CYS106 3.3 24.9 1.0 CB A:CYS92 3.4 27.0 1.0 N A:CYS92 3.4 28.4 1.0 CB A:CYS98 3.5 30.2 1.0 CB A:CYS95 3.6 19.0 1.0 CA A:CYS106 3.8 23.3 1.0 N A:CYS95 3.8 19.7 1.0 N A:GLY93 3.8 22.4 1.0 CA A:CYS92 3.8 25.0 1.0 C A:CYS92 4.2 23.8 1.0 N A:ALA94 4.2 22.2 1.0 CA A:CYS95 4.2 19.5 1.0 N A:THR107 4.3 26.0 1.0 N A:CYS98 4.3 27.8 1.0 C A:GLY91 4.4 31.6 1.0 C A:CYS106 4.4 24.7 1.0 CA A:CYS98 4.4 27.9 1.0 CB A:ARG108 4.6 32.6 1.0 N A:ARG108 4.6 27.4 1.0 CA A:GLY91 4.6 29.6 1.0 CA A:GLY93 4.8 21.6 1.0 C A:ALA94 4.9 21.3 1.0 C A:CYS95 4.9 21.3 1.0 O A:CYS95 4.9 23.8 1.0 C A:GLY93 4.9 22.9 1.0 CG A:ARG108 5.0 40.1 1.0 N A:CYS106 5.0 21.8 1.0

Zinc binding site 2 out of 24 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:61.4 occ:1.00 OD2 A:ASP153 1.8 36.2 1.0 NE2 A:HIS62 2.2 43.6 1.0 SG A:CYS38 2.4 57.3 1.0 OE2 A:GLU63 2.6 50.6 1.0 CB A:CYS38 2.6 42.5 1.0 CE1 A:HIS62 2.8 45.9 1.0 CG A:ASP153 3.0 33.1 1.0 CD2 A:HIS62 3.2 40.5 1.0 CD A:GLU63 3.5 46.2 1.0 CG A:GLU63 3.7 37.3 1.0 CB A:ASP153 3.7 27.9 1.0 C16 A:W46503 3.8 41.4 1.0 NH1 A:ARG340 3.9 43.5 1.0 ND1 A:HIS62 3.9 43.6 1.0 OD1 A:ASP153 4.1 31.9 1.0 OG A:SER40 4.1 44.6 1.0 CA A:CYS38 4.1 39.5 1.0 CG A:HIS62 4.1 39.1 1.0 CB A:SER40 4.5 41.1 1.0 C17 A:W46503 4.6 37.5 1.0 OE1 A:GLU63 4.7 48.6 1.0 N06 A:W46503 4.8 45.4 1.0 CZ A:ARG340 4.9 42.1 1.0 C07 A:W46503 4.9 43.4 1.0 C A:CYS38 4.9 42.4 1.0 N A:CYS38 4.9 35.6 1.0

Zinc binding site 3 out of 24 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:28.9 occ:1.00 SG B:CYS106 2.1 21.8 1.0 SG B:CYS98 2.1 26.1 1.0 SG B:CYS95 2.2 19.4 1.0 SG B:CYS92 2.3 27.9 1.0 CB B:CYS106 3.2 20.6 1.0 CB B:CYS98 3.3 26.3 1.0 N B:CYS92 3.3 26.4 1.0 CB B:CYS92 3.4 26.6 1.0 CB B:CYS95 3.4 21.9 1.0 CA B:CYS106 3.7 21.5 1.0 N B:CYS95 3.7 28.9 1.0 CA B:CYS92 3.8 26.3 1.0 N B:GLY93 3.8 24.6 1.0 CA B:CYS95 4.1 25.3 1.0 C B:CYS92 4.1 25.8 1.0 N B:CYS98 4.2 24.8 1.0 N B:ALA94 4.3 27.3 1.0 N B:THR107 4.3 20.8 1.0 CA B:CYS98 4.3 24.5 1.0 C B:CYS106 4.4 20.7 1.0 C B:GLY91 4.4 25.6 1.0 N B:ARG108 4.5 30.4 1.0 CA B:GLY91 4.7 23.3 1.0 C B:CYS95 4.8 26.0 1.0 CA B:GLY93 4.8 24.0 1.0 O B:CYS95 4.9 29.6 1.0 CB B:ARG108 4.9 38.5 1.0 C B:ALA94 4.9 31.9 1.0 C B:GLY93 4.9 25.6 1.0 N B:CYS106 4.9 22.4 1.0

Zinc binding site 4 out of 24 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:39.9 occ:1.00 OD2 B:ASP153 1.9 34.8 1.0 OE2 B:GLU63 2.0 33.5 1.0 SG B:CYS38 2.1 26.3 1.0 NE2 B:HIS62 2.1 21.0 1.0 CD B:GLU63 2.9 31.0 1.0 CG B:ASP153 3.0 32.6 1.0 CD2 B:HIS62 3.0 22.9 1.0 CE1 B:HIS62 3.1 23.7 1.0 CG B:GLU63 3.2 25.7 1.0 CB B:CYS38 3.3 26.7 1.0 CB B:ASP153 3.4 28.5 1.0 OE1 B:GLU63 4.0 34.6 1.0 OD1 B:ASP153 4.1 33.3 1.0 CG B:HIS62 4.2 24.1 1.0 ND1 B:HIS62 4.2 25.0 1.0 NH2 B:ARG340 4.3 56.1 1.0 CA B:CYS38 4.4 27.5 1.0 N B:CYS38 4.4 26.1 1.0 NH1 B:ARG340 4.6 44.3 1.0 C16 B:W46504 4.7 38.3 1.0 CB B:GLU63 4.7 24.5 1.0 CB B:SER40 4.8 22.8 1.0 C B:LEU37 4.9 27.1 1.0 OG B:SER40 4.9 24.5 1.0 CA B:ASP153 4.9 24.8 1.0 CZ B:ARG340 5.0 49.5 1.0

Zinc binding site 5 out of 24 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:41.3 occ:1.00 SG C:CYS95 2.1 27.8 1.0 SG C:CYS106 2.1 24.5 1.0 SG C:CYS92 2.2 36.8 1.0 SG C:CYS98 2.3 27.4 1.0 CB C:CYS106 3.3 25.5 1.0 N C:CYS92 3.4 29.0 1.0 CB C:CYS92 3.4 29.2 1.0 CB C:CYS95 3.5 24.5 1.0 CB C:CYS98 3.5 28.4 1.0 N C:GLY93 3.7 26.8 1.0 N C:CYS95 3.7 26.7 1.0 CA C:CYS92 3.8 28.2 1.0 CA C:CYS106 3.8 25.1 1.0 CA C:CYS95 4.1 26.1 1.0 C C:CYS92 4.1 28.2 1.0 N C:ALA94 4.2 25.0 1.0 N C:CYS98 4.2 27.6 1.0 C C:GLY91 4.4 27.2 1.0 N C:THR107 4.4 30.0 1.0 CA C:CYS98 4.4 26.8 1.0 C C:CYS106 4.4 27.6 1.0 O C:CYS95 4.6 29.7 1.0 C C:CYS95 4.6 27.9 1.0 CA C:GLY91 4.6 26.8 1.0 CA C:GLY93 4.6 23.8 1.0 N C:ARG108 4.7 30.6 1.0 CB C:ARG108 4.7 32.5 1.0 C C:GLY93 4.7 24.2 1.0 C C:ALA94 4.8 27.9 1.0

Zinc binding site 6 out of 24 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:57.0 occ:1.00 OD2 C:ASP153 1.9 41.8 1.0 SG C:CYS38 2.1 60.3 1.0 OE2 C:GLU63 2.2 50.5 1.0 NE2 C:HIS62 2.4 40.0 1.0 CB C:CYS38 2.6 52.2 1.0 CE1 C:HIS62 2.9 45.8 1.0 CG C:ASP153 3.0 40.9 1.0 CD C:GLU63 3.2 45.3 1.0 CD2 C:HIS62 3.4 38.6 1.0 CB C:ASP153 3.4 34.1 1.0 CG C:GLU63 3.5 39.9 1.0 CA C:CYS38 3.9 49.0 1.0 ND1 C:HIS62 4.0 43.6 1.0 OD1 C:ASP153 4.1 41.0 1.0 N C:CYS38 4.2 43.8 1.0 CG C:HIS62 4.2 40.4 1.0 C16 C:W46503 4.3 45.4 1.0 OE1 C:GLU63 4.4 46.0 1.0 OG C:SER40 4.4 49.2 1.0 C C:CYS38 4.7 47.3 1.0 NE C:ARG340 4.8 58.7 1.0 C C:LEU37 4.9 39.4 1.0 CA C:ASP153 4.9 29.8 1.0 CB C:SER40 5.0 40.5 1.0

Zinc binding site 7 out of 24 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:31.1 occ:1.00 SG D:CYS98 2.2 26.1 1.0 SG D:CYS106 2.2 25.5 1.0 SG D:CYS92 2.2 22.3 1.0 SG D:CYS95 2.4 30.9 1.0 CB D:CYS106 3.3 23.3 1.0 CB D:CYS92 3.4 22.2 1.0 N D:CYS92 3.4 26.5 1.0 CB D:CYS98 3.5 26.2 1.0 CB D:CYS95 3.6 25.1 1.0 CA D:CYS106 3.7 21.2 1.0 CA D:CYS92 3.8 22.5 1.0 N D:GLY93 3.8 21.1 1.0 N D:CYS95 3.8 23.5 1.0 C D:CYS92 4.2 21.9 1.0 CA D:CYS95 4.2 23.7 1.0 N D:THR107 4.3 22.1 1.0 N D:CYS98 4.3 24.0 1.0 C D:CYS106 4.3 21.4 1.0 N D:ALA94 4.4 17.9 1.0 C D:GLY91 4.4 29.1 1.0 CB D:ARG108 4.5 30.9 1.0 CA D:CYS98 4.5 24.8 1.0 N D:ARG108 4.5 31.8 1.0 CA D:GLY91 4.7 27.2 1.0 CA D:GLY93 4.8 18.6 1.0 C D:CYS95 4.8 23.8 1.0 O D:CYS95 4.9 23.6 1.0 C D:GLY93 4.9 18.1 1.0 C D:ALA94 5.0 22.3 1.0

Zinc binding site 8 out of 24 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:45.0 occ:1.00 OD2 D:ASP153 2.0 36.4 1.0 NE2 D:HIS62 2.1 30.4 1.0 OE2 D:GLU63 2.3 42.6 1.0 SG D:CYS38 2.3 56.9 1.0 CB D:CYS38 2.5 42.7 1.0 CE1 D:HIS62 2.9 31.4 1.0 CG D:ASP153 3.1 32.9 1.0 CD2 D:HIS62 3.2 31.4 1.0 CD D:GLU63 3.3 38.6 1.0 CG D:GLU63 3.5 31.9 1.0 CB D:ASP153 3.7 29.1 1.0 CA D:CYS38 3.9 43.8 1.0 ND1 D:HIS62 4.0 31.8 1.0 CG D:HIS62 4.2 31.5 1.0 OD1 D:ASP153 4.2 32.3 1.0 OE1 D:GLU63 4.4 40.0 1.0 O D:LEU37 4.4 43.0 1.0 OG D:SER40 4.5 39.8 1.0 N D:CYS38 4.5 41.6 1.0 C D:LEU37 4.7 39.3 1.0 NE D:ARG340 4.8 52.0 1.0 CB D:SER40 4.9 37.0 1.0 C16 D:W46503 4.9 37.8 1.0 C D:CYS38 4.9 44.6 1.0

Zinc binding site 9 out of 24 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:40.4 occ:1.00 SG E:CYS106 2.0 33.6 1.0 SG E:CYS98 2.3 33.0 1.0 SG E:CYS92 2.3 39.0 1.0 SG E:CYS95 2.3 38.9 1.0 CB E:CYS106 3.1 36.1 1.0 CB E:CYS92 3.3 37.2 1.0 N E:CYS92 3.4 36.4 1.0 CB E:CYS98 3.4 32.3 1.0 CB E:CYS95 3.5 35.4 1.0 CA E:CYS106 3.7 37.4 1.0 N E:GLY93 3.7 38.6 1.0 CA E:CYS92 3.8 36.4 1.0 N E:CYS95 3.9 39.4 1.0 N E:THR107 4.2 44.0 1.0 C E:CYS92 4.3 38.9 1.0 CA E:CYS95 4.3 38.4 1.0 C E:CYS106 4.3 40.0 1.0 N E:CYS98 4.3 31.9 1.0 C E:GLY91 4.4 36.8 1.0 CA E:CYS98 4.4 31.7 1.0 N E:ALA94 4.5 38.7 1.0 N E:ARG108 4.5 50.1 1.0 CA E:GLY91 4.7 37.8 1.0 CA E:GLY93 4.8 34.5 1.0 N E:CYS106 4.9 37.0 1.0 CB E:ARG108 4.9 53.6 1.0 N E:ALA109 5.0 48.0 1.0

Zinc binding site 10 out of 24 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:49.7 occ:1.00 OD2 E:ASP153 1.8 47.1 1.0 NE2 E:HIS62 2.1 40.8 1.0 SG E:CYS38 2.2 43.6 1.0 OE2 E:GLU63 2.5 61.3 1.0 CG E:ASP153 2.9 42.6 1.0 CD2 E:HIS62 3.0 41.1 1.0 CE1 E:HIS62 3.1 41.6 1.0 CB E:CYS38 3.2 40.5 1.0 CB E:ASP153 3.3 36.6 1.0 CD E:GLU63 3.4 49.6 1.0 CG E:GLU63 3.5 43.1 1.0 OD1 E:ASP153 4.0 43.1 1.0 CG E:HIS62 4.1 41.0 1.0 ND1 E:HIS62 4.1 44.1 1.0 CA E:CYS38 4.3 38.7 1.0 N E:CYS38 4.4 36.5 1.0 OE1 E:GLU63 4.5 50.0 1.0 C16 E:W46503 4.6 41.3 1.0 CB E:SER40 4.7 39.6 1.0 OG E:SER40 4.8 36.2 1.0 CA E:ASP153 4.8 33.6 1.0 C E:LEU37 4.8 39.5 1.0 C07 E:W46503 4.9 43.8 1.0 OD2 E:ASP41 4.9 45.6 1.0 O E:LEU37 5.0 46.6 1.0 CB E:GLU63 5.0 43.5 1.0

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