Zinc in PDB 4ymk: Crystal Structure of Stearoyl-Coenzyme A Desaturase 1

All present enzymatic activity of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1:
1.14.19.1;

The structure of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1, PDB code: 4ymk was solved by Y.Bai, J.G.Mccoy, K.R.Rajashankar, M.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.41 / 2.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.061, 113.766, 141.698, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23.5

The binding sites of Zinc atom in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 (pdb code 4ymk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1, PDB code: 4ymk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:34.9 occ:1.00 NE2 A:HIS297 2.0 31.5 1.0 NE2 A:HIS153 2.0 29.8 1.0 NE2 A:HIS121 2.2 22.1 1.0 NE2 A:HIS157 2.2 26.5 1.0 NE2 A:HIS116 2.4 23.4 1.0 CE1 A:HIS153 2.8 21.9 1.0 CE1 A:HIS297 2.9 31.8 1.0 CE1 A:HIS121 3.0 28.6 1.0 CD2 A:HIS297 3.0 24.3 1.0 CE1 A:HIS157 3.1 27.6 1.0 CD2 A:HIS153 3.1 28.5 1.0 CD2 A:HIS116 3.2 23.4 1.0 CD2 A:HIS157 3.2 26.3 1.0 CD2 A:HIS121 3.3 23.1 1.0 CE1 A:HIS116 3.5 21.9 1.0 ND1 A:HIS153 4.0 24.9 1.0 ND1 A:HIS297 4.1 23.1 1.0 CG A:HIS297 4.1 23.3 1.0 CG A:HIS153 4.2 21.9 1.0 ND1 A:HIS121 4.2 29.3 1.0 ND1 A:HIS157 4.2 24.5 1.0 CG A:HIS157 4.3 29.9 1.0 CG A:HIS121 4.3 22.4 1.0 CG A:HIS116 4.4 24.5 1.0 ND1 A:HIS116 4.5 24.8 1.0 C10 A:ST9403 4.7 45.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:31.8 occ:1.00 NE2 A:HIS294 2.0 36.3 1.0 NE2 A:HIS156 2.2 24.2 1.0 NE2 A:HIS265 2.2 34.3 1.0 O A:HOH542 2.2 50.1 1.0 NE2 A:HIS298 2.3 32.1 1.0 CE1 A:HIS294 2.9 33.1 1.0 CE1 A:HIS156 3.0 24.1 1.0 CD2 A:HIS294 3.0 27.5 1.0 CE1 A:HIS265 3.1 28.5 1.0 CD2 A:HIS298 3.2 30.6 1.0 CE1 A:HIS298 3.3 34.1 1.0 CD2 A:HIS265 3.3 36.9 1.0 CD2 A:HIS156 3.3 23.2 1.0 ND1 A:HIS294 4.0 25.9 1.0 CG A:HIS294 4.1 29.2 1.0 ND1 A:HIS156 4.2 30.8 1.0 ND1 A:HIS265 4.2 31.8 1.0 CG A:HIS298 4.3 29.2 1.0 CG A:HIS156 4.4 28.1 1.0 ND1 A:HIS298 4.4 32.0 1.0 CG A:HIS265 4.4 34.3 1.0 O A:VAL260 4.4 37.9 1.0 ND2 A:ASN261 4.5 26.9 1.0 OG A:SER278 4.9 63.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:38.4 occ:1.00 NE2 D:HIS297 2.0 36.3 1.0 NE2 D:HIS153 2.1 40.3 1.0 NE2 D:HIS121 2.2 37.5 1.0 NE2 D:HIS157 2.2 47.3 1.0 NE2 D:HIS116 2.3 30.9 1.0 CE1 D:HIS121 2.7 34.0 1.0 CE1 D:HIS297 2.9 31.7 1.0 CE1 D:HIS153 3.0 35.7 1.0 CD2 D:HIS157 3.1 42.2 1.0 CD2 D:HIS153 3.1 33.3 1.0 CD2 D:HIS297 3.1 34.3 1.0 CD2 D:HIS116 3.1 27.6 1.0 CE1 D:HIS157 3.1 40.6 1.0 CE1 D:HIS116 3.3 26.1 1.0 CD2 D:HIS121 3.4 43.9 1.0 ND1 D:HIS121 4.0 30.6 1.0 ND1 D:HIS297 4.1 33.4 1.0 ND1 D:HIS153 4.1 32.4 1.0 ND1 D:HIS157 4.2 39.9 1.0 CG D:HIS297 4.2 27.4 1.0 CG D:HIS157 4.2 37.7 1.0 CG D:HIS153 4.2 32.1 1.0 CG D:HIS121 4.3 28.4 1.0 CG D:HIS116 4.3 30.3 1.0 ND1 D:HIS116 4.4 36.5 1.0 C10 D:ST9403 4.7 41.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:38.6 occ:1.00 NE2 D:HIS294 2.0 38.3 1.0 NE2 D:HIS156 2.1 34.9 1.0 NE2 D:HIS298 2.2 38.1 1.0 NE2 D:HIS265 2.2 36.8 1.0 O D:HOH530 2.2 56.2 1.0 CD2 D:HIS294 2.8 33.1 1.0 CE1 D:HIS156 2.9 34.6 1.0 CE1 D:HIS265 3.0 40.6 1.0 CE1 D:HIS294 3.1 30.0 1.0 CE1 D:HIS298 3.1 37.5 1.0 CD2 D:HIS298 3.2 30.7 1.0 CD2 D:HIS156 3.3 34.0 1.0 CD2 D:HIS265 3.4 37.4 1.0 CG D:HIS294 4.0 31.8 1.0 ND1 D:HIS156 4.1 35.1 1.0 ND1 D:HIS294 4.1 29.9 1.0 ND1 D:HIS265 4.2 38.9 1.0 ND1 D:HIS298 4.2 37.3 1.0 CG D:HIS298 4.3 38.4 1.0 CG D:HIS156 4.3 33.1 1.0 CG D:HIS265 4.4 37.0 1.0 O D:VAL260 4.4 39.5 1.0 OG D:SER278 4.5 68.3 1.0 ND2 D:ASN261 4.5 44.2 1.0 O D:HOH504 4.9 31.4 1.0

Y.Bai, J.G.Mccoy, E.J.Levin, P.Sobrado, K.R.Rajashankar, B.G.Fox, M.Zhou. X-Ray Structure of A Mammalian Stearoyl-Coa Desaturase. Nature V. 524 252 2015.
ISSN: ESSN 1476-4687
PubMed: 26098370
DOI: 10.1038/NATURE14549