Zinc in PDB 1pl8: Human Sdh/Nad+ Complex

All present enzymatic activity of Human Sdh/Nad+ Complex:
1.1.1.14;

The structure of Human Sdh/Nad+ Complex, PDB code: 1pl8 was solved by T.A.Pauly, J.L.Ekstrom, D.A.Beebe, B.Chrunyk, D.Cunningham, M.Griffor, A.Kamath, S.E.Lee, R.Madura, D.Mcguire, T.Subashi, D.Wasilko, P.Watts, B.L.Mylari, P.J.Oates, P.D.Adams, V.L.Rath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.82 / 1.90
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	133.776, 133.776, 224.708, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 22.2

The binding sites of Zinc atom in the Human Sdh/Nad+ Complex (pdb code 1pl8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Sdh/Nad+ Complex, PDB code: 1pl8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human Sdh/Nad+ Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Sdh/Nad+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:30.2 occ:1.00 NE2 A:HIS69 2.1 19.9 1.0 OE2 A:GLU70 2.1 22.2 1.0 O A:HOH1862 2.2 21.9 1.0 SG A:CYS44 2.5 25.0 1.0 CE1 A:HIS69 2.9 18.6 1.0 CD A:GLU70 3.1 17.9 1.0 CD2 A:HIS69 3.2 16.4 1.0 CB A:CYS44 3.2 24.3 1.0 O A:HOH2154 3.3 42.9 1.0 CG A:GLU70 3.4 15.8 1.0 OE1 A:GLU155 3.5 20.5 1.0 OG A:SER46 4.0 31.2 0.5 O A:HOH1062 4.0 25.2 1.0 ND1 A:HIS69 4.1 18.4 1.0 O A:HOH1264 4.1 27.1 1.0 CD A:GLU155 4.2 18.5 1.0 CG A:HIS69 4.2 16.9 1.0 OE1 A:GLU70 4.3 18.2 1.0 OE2 A:GLU155 4.3 17.3 1.0 O A:HOH1353 4.3 39.0 1.0 CA A:CYS44 4.5 22.8 1.0 N A:CYS44 4.6 21.7 1.0 O A:HOH1027 4.6 13.8 1.0 O A:HOH1924 4.7 38.8 1.0 CB A:GLU70 4.9 15.8 1.0 OD2 A:ASP47 4.9 23.8 1.0 OG A:SER46 5.0 25.6 0.5

Zinc binding site 2 out of 4 in the Human Sdh/Nad+ Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Sdh/Nad+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:30.4 occ:1.00 OE2 B:GLU70 2.2 22.7 1.0 NE2 B:HIS69 2.2 17.6 1.0 SG B:CYS44 2.4 25.2 1.0 CE1 B:HIS69 2.9 16.9 1.0 CD B:GLU70 3.1 17.5 1.0 CB B:CYS44 3.2 25.2 1.0 CD2 B:HIS69 3.3 16.3 1.0 CG B:GLU70 3.4 16.3 1.0 OE1 B:GLU155 3.5 17.7 1.0 O B:HOH1249 4.0 29.7 1.0 OG B:SER46 4.1 27.4 0.5 ND1 B:HIS69 4.1 16.9 1.0 O B:HOH1033 4.1 28.8 1.0 CD B:GLU155 4.2 16.9 1.0 OE1 B:GLU70 4.3 20.0 1.0 CG B:HIS69 4.3 16.0 1.0 OE2 B:GLU155 4.3 15.6 1.0 CA B:CYS44 4.4 23.9 1.0 N B:CYS44 4.5 23.0 1.0 O B:HOH1020 4.6 18.6 1.0 O B:HOH1596 4.7 39.7 1.0 OD2 B:ASP47 4.9 22.7 1.0 NZ B:LYS344 4.9 20.7 1.0 CB B:GLU70 4.9 16.2 1.0 O B:HOH1523 4.9 40.1 1.0 OG B:SER46 4.9 26.1 0.5

Zinc binding site 3 out of 4 in the Human Sdh/Nad+ Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Sdh/Nad+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:32.2 occ:1.00 OE2 C:GLU70 2.1 24.6 1.0 NE2 C:HIS69 2.2 19.8 1.0 SG C:CYS44 2.4 25.6 1.0 CE1 C:HIS69 2.8 18.8 1.0 CD C:GLU70 3.1 17.6 1.0 CB C:CYS44 3.2 24.8 1.0 CD2 C:HIS69 3.3 18.3 1.0 CG C:GLU70 3.4 17.2 1.0 OE1 C:GLU155 3.5 17.2 1.0 O C:HOH1305 3.9 31.2 1.0 ND1 C:HIS69 4.0 18.1 1.0 O C:HOH1053 4.0 22.7 1.0 OG C:SER46 4.1 28.0 0.5 CD C:GLU155 4.2 17.0 1.0 OE1 C:GLU70 4.2 19.2 1.0 CG C:HIS69 4.3 17.7 1.0 OE2 C:GLU155 4.4 15.6 1.0 CA C:CYS44 4.4 23.3 1.0 N C:CYS44 4.5 22.9 1.0 O C:HOH1011 4.7 18.5 1.0 O C:HOH1653 4.7 37.9 1.0 OG C:SER46 4.8 27.3 0.5 O C:HOH1911 4.8 44.3 1.0 OD2 C:ASP47 4.9 23.1 1.0 NZ C:LYS344 4.9 19.3 1.0 CB C:GLU70 4.9 16.5 1.0 CB C:SER46 5.0 26.9 0.5

Zinc binding site 4 out of 4 in the Human Sdh/Nad+ Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Sdh/Nad+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:29.8 occ:1.00 NE2 D:HIS69 2.2 19.2 1.0 OE2 D:GLU70 2.2 21.7 1.0 O D:HOH1863 2.2 22.7 1.0 SG D:CYS44 2.5 25.1 1.0 CE1 D:HIS69 3.0 18.2 1.0 CD D:GLU70 3.1 19.5 1.0 CD2 D:HIS69 3.2 15.2 1.0 CB D:CYS44 3.2 24.1 1.0 CG D:GLU70 3.4 16.3 1.0 O D:HOH1987 3.5 36.4 1.0 OE1 D:GLU155 3.5 17.8 1.0 O D:HOH1280 4.0 29.6 1.0 O D:HOH1994 4.0 28.2 1.0 OG D:SER46 4.1 30.1 0.5 ND1 D:HIS69 4.1 16.8 1.0 CD D:GLU155 4.2 18.2 1.0 CG D:HIS69 4.2 15.9 1.0 OE1 D:GLU70 4.2 17.7 1.0 OE2 D:GLU155 4.3 18.0 1.0 CA D:CYS44 4.5 22.6 1.0 O D:HOH1019 4.6 15.8 1.0 N D:CYS44 4.6 21.4 1.0 O D:HOH1898 4.7 34.1 1.0 CB D:GLU70 4.9 15.9 1.0 O D:HOH1524 5.0 37.0 1.0 OD2 D:ASP47 5.0 21.9 1.0

T.A.Pauly, J.L.Ekstrom, D.A.Beebe, B.Chrunyk, D.Cunningham, M.Griffor, A.Kamath, S.E.Lee, R.Madura, D.Mcguire, T.Subashi, D.Wasilko, P.Watts, B.L.Mylari, P.J.Oates, P.D.Adams, V.L.Rath. X-Ray Crystallographic and Kinetic Studies of Human Sorbitol Dehydrogenase. Structure V. 11 1071 2003.
ISSN: ISSN 0969-2126
PubMed: 12962626
DOI: 10.1016/S0969-2126(03)00167-9