Zinc in PDB 1pl6: Human Sdh/Nadh/Inhibitor Complex

All present enzymatic activity of Human Sdh/Nadh/Inhibitor Complex:
1.1.1.14;

The structure of Human Sdh/Nadh/Inhibitor Complex, PDB code: 1pl6 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)	57.84 / 2.00
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	134.814, 134.814, 225.184, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 21.1

The binding sites of Zinc atom in the Human Sdh/Nadh/Inhibitor Complex (pdb code 1pl6). 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/Nadh/Inhibitor Complex, PDB code: 1pl6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human Sdh/Nadh/Inhibitor 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/Nadh/Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:20.2 occ:1.00 N3 A:572405 2.1 19.5 1.0 O A:HOH1064 2.1 17.8 1.0 NE2 A:HIS69 2.1 17.1 1.0 O30 A:572405 2.4 18.7 1.0 SG A:CYS44 2.5 16.6 1.0 C7 A:572405 3.0 20.4 1.0 CE1 A:HIS69 3.0 15.4 1.0 C6 A:572405 3.1 23.0 1.0 CD2 A:HIS69 3.2 12.6 1.0 C14 A:572405 3.2 18.5 1.0 CB A:CYS44 3.3 17.0 1.0 OG A:SER46 3.6 12.5 0.5 OE2 A:GLU70 3.9 17.2 1.0 OE1 A:GLU155 4.0 13.4 1.0 ND1 A:HIS69 4.2 14.2 1.0 N4 A:572405 4.3 22.6 1.0 OE2 A:GLU155 4.3 14.7 1.0 CG A:HIS69 4.3 11.7 1.0 C5 A:572405 4.4 22.6 1.0 CD A:GLU155 4.5 14.8 1.0 CG A:GLU70 4.6 15.1 1.0 CD A:GLU70 4.7 16.4 1.0 CA A:CYS44 4.7 16.5 1.0 O A:HOH1363 4.7 27.5 1.0 CB A:SER46 4.8 14.8 0.5 CB A:SER46 4.8 18.4 0.5 C2 A:572405 4.9 23.1 1.0

Zinc binding site 2 out of 4 in the Human Sdh/Nadh/Inhibitor 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/Nadh/Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:21.5 occ:1.00 N3 B:572407 2.1 25.8 1.0 O B:HOH1543 2.1 12.5 1.0 NE2 B:HIS69 2.2 14.5 1.0 O30 B:572407 2.4 21.8 1.0 SG B:CYS44 2.5 15.8 1.0 C7 B:572407 3.0 24.8 1.0 CE1 B:HIS69 3.1 14.1 1.0 C6 B:572407 3.1 27.1 1.0 C14 B:572407 3.2 22.4 1.0 CB B:CYS44 3.2 18.2 1.0 CD2 B:HIS69 3.2 13.7 1.0 OG B:SER46 3.8 10.5 0.5 OE2 B:GLU70 3.8 18.4 1.0 OE1 B:GLU155 3.9 15.7 1.0 ND1 B:HIS69 4.2 13.6 1.0 N4 B:572407 4.3 26.0 1.0 OE2 B:GLU155 4.3 14.6 1.0 CG B:HIS69 4.3 12.2 1.0 C5 B:572407 4.4 26.2 1.0 CD B:GLU155 4.5 14.7 1.0 CG B:GLU70 4.5 14.7 1.0 O B:HOH1034 4.6 37.0 1.0 CD B:GLU70 4.6 14.7 1.0 CA B:CYS44 4.7 17.5 1.0 CB B:SER46 4.8 18.5 0.5 CB B:SER46 4.8 14.2 0.5 C2 B:572407 4.9 26.1 1.0 C5N B:NAD406 5.0 18.4 1.0

Zinc binding site 3 out of 4 in the Human Sdh/Nadh/Inhibitor 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/Nadh/Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:22.3 occ:1.00 N3 C:572409 2.1 26.0 1.0 O C:HOH1055 2.1 13.9 1.0 NE2 C:HIS69 2.2 15.2 1.0 O30 C:572409 2.4 21.5 1.0 SG C:CYS44 2.5 16.6 1.0 CE1 C:HIS69 3.0 14.9 1.0 C7 C:572409 3.0 25.0 1.0 C6 C:572409 3.1 27.2 1.0 CB C:CYS44 3.2 17.7 1.0 CD2 C:HIS69 3.2 14.4 1.0 C14 C:572409 3.3 23.1 1.0 OG C:SER46 3.7 10.6 0.5 OE2 C:GLU70 3.9 19.0 1.0 OE1 C:GLU155 4.0 15.2 1.0 ND1 C:HIS69 4.2 15.0 1.0 OE2 C:GLU155 4.3 14.3 1.0 N4 C:572409 4.3 26.1 1.0 CG C:HIS69 4.3 13.5 1.0 C5 C:572409 4.4 26.9 1.0 CD C:GLU155 4.5 14.6 1.0 CG C:GLU70 4.5 16.3 1.0 O C:HOH1681 4.6 33.9 1.0 CD C:GLU70 4.7 16.9 1.0 CA C:CYS44 4.7 17.9 1.0 CB C:SER46 4.8 19.0 0.5 CB C:SER46 4.8 14.8 0.5 C2 C:572409 4.9 26.0 1.0 C5N C:NAD408 5.0 18.2 1.0

Zinc binding site 4 out of 4 in the Human Sdh/Nadh/Inhibitor 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/Nadh/Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:20.2 occ:1.00 N3 D:572411 2.1 20.2 1.0 O D:HOH1042 2.1 16.0 1.0 NE2 D:HIS69 2.1 17.7 1.0 O30 D:572411 2.4 19.2 1.0 SG D:CYS44 2.5 18.0 1.0 C7 D:572411 3.0 20.3 1.0 C6 D:572411 3.0 23.2 1.0 CE1 D:HIS69 3.0 16.9 1.0 C14 D:572411 3.2 18.2 1.0 CD2 D:HIS69 3.2 13.9 1.0 CB D:CYS44 3.3 17.3 1.0 OG D:SER46 3.6 11.3 0.5 OE2 D:GLU70 3.9 17.6 1.0 OE1 D:GLU155 4.0 14.0 1.0 ND1 D:HIS69 4.2 15.0 1.0 N4 D:572411 4.2 22.6 1.0 CG D:HIS69 4.3 13.2 1.0 OE2 D:GLU155 4.3 13.1 1.0 C5 D:572411 4.4 22.9 1.0 CD D:GLU155 4.5 14.5 1.0 CG D:GLU70 4.6 15.1 1.0 O D:HOH1484 4.6 29.3 1.0 CD D:GLU70 4.7 16.0 1.0 CA D:CYS44 4.7 16.9 1.0 CB D:SER46 4.8 18.7 0.5 CB D:SER46 4.8 14.4 0.5 C2 D:572411 4.8 23.5 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