Iron in PDB 6wf2: Crystal Structure of Mouse SCD1 with A Diiron Center

All present enzymatic activity of Crystal Structure of Mouse SCD1 with A Diiron Center:
1.14.19.1;

The structure of Crystal Structure of Mouse SCD1 with A Diiron Center, PDB code: 6wf2 was solved by J.Shen, M.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.63 / 3.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.647, 113.981, 140.971, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.7

The binding sites of Iron atom in the Crystal Structure of Mouse SCD1 with A Diiron Center (pdb code 6wf2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Mouse SCD1 with A Diiron Center, PDB code: 6wf2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Mouse SCD1 with A Diiron Center


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Mouse SCD1 with A Diiron Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:48.9 occ:1.00 NE2 A:HIS297 1.9 50.6 1.0 NE2 A:HIS153 2.0 57.0 1.0 NE2 A:HIS121 2.1 55.9 1.0 NE2 A:HIS116 2.1 53.0 1.0 NE2 A:HIS157 2.1 57.6 1.0 CE1 A:HIS121 2.8 53.2 1.0 CE1 A:HIS297 2.8 50.4 1.0 CE1 A:HIS153 2.9 60.4 1.0 CD2 A:HIS116 3.0 56.3 1.0 CE1 A:HIS157 3.0 58.3 1.0 CD2 A:HIS297 3.0 51.6 1.0 CD2 A:HIS153 3.1 59.6 1.0 CD2 A:HIS157 3.2 59.5 1.0 CD2 A:HIS121 3.2 58.6 1.0 CE1 A:HIS116 3.2 51.7 1.0 ND1 A:HIS297 4.0 48.1 1.0 ND1 A:HIS121 4.0 56.0 1.0 ND1 A:HIS153 4.0 63.9 1.0 ND1 A:HIS157 4.1 61.3 1.0 CG A:HIS297 4.1 50.3 1.0 CG A:HIS153 4.2 63.1 1.0 CG A:HIS116 4.2 54.6 1.0 CG A:HIS157 4.2 62.2 1.0 CG A:HIS121 4.2 59.3 1.0 ND1 A:HIS116 4.3 53.8 1.0 C09 A:3VV403 4.5 54.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Mouse SCD1 with A Diiron Center


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Mouse SCD1 with A Diiron Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:49.0 occ:1.00 NE2 A:HIS294 1.7 50.5 1.0 NE2 A:HIS156 2.1 57.8 1.0 NE2 A:HIS265 2.1 62.1 1.0 NE2 A:HIS298 2.3 52.1 1.0 CE1 A:HIS294 2.6 57.7 1.0 CD2 A:HIS294 2.8 52.7 1.0 CE1 A:HIS156 2.8 57.8 1.0 CD2 A:HIS298 3.0 54.5 1.0 CE1 A:HIS265 3.1 67.0 1.0 CD2 A:HIS265 3.1 63.9 1.0 CD2 A:HIS156 3.3 57.1 1.0 CE1 A:HIS298 3.4 55.3 1.0 ND1 A:HIS294 3.7 58.1 1.0 CG A:HIS294 3.8 56.6 1.0 ND1 A:HIS156 4.0 56.6 1.0 ND1 A:HIS265 4.2 72.3 1.0 CG A:HIS298 4.2 50.5 1.0 CG A:HIS265 4.2 66.7 1.0 CG A:HIS156 4.3 53.7 1.0 O A:VAL260 4.3 63.5 1.0 ND1 A:HIS298 4.4 54.4 1.0 OG A:SER278 4.6 67.6 1.0 C10 A:3VV403 4.6 57.3 1.0 OD1 A:ASN261 4.6 59.1 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Mouse SCD1 with A Diiron Center


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Mouse SCD1 with A Diiron Center within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:48.8 occ:1.00 NE2 B:HIS297 1.9 60.7 1.0 NE2 B:HIS153 1.9 64.6 1.0 NE2 B:HIS116 2.1 56.0 1.0 NE2 B:HIS157 2.1 61.6 1.0 NE2 B:HIS121 2.3 60.1 1.0 CE1 B:HIS121 2.8 57.5 1.0 CD2 B:HIS297 2.9 61.8 1.0 CD2 B:HIS153 2.9 61.1 1.0 CE1 B:HIS297 2.9 61.7 1.0 CE1 B:HIS153 3.0 68.0 1.0 CE1 B:HIS116 3.1 58.5 1.0 CD2 B:HIS116 3.1 56.6 1.0 CD2 B:HIS157 3.1 65.8 1.0 CE1 B:HIS157 3.1 67.1 1.0 CD2 B:HIS121 3.5 60.3 1.0 ND1 B:HIS121 4.0 57.9 1.0 ND1 B:HIS297 4.0 61.6 1.0 CG B:HIS297 4.0 62.2 1.0 CG B:HIS153 4.0 65.8 1.0 ND1 B:HIS153 4.1 69.2 1.0 ND1 B:HIS116 4.2 57.8 1.0 CG B:HIS116 4.2 53.1 1.0 ND1 B:HIS157 4.2 70.0 1.0 CG B:HIS157 4.3 71.5 1.0 CG B:HIS121 4.4 57.7 1.0 C09 B:3VV403 4.5 60.6 1.0 CE1 B:HIS294 4.8 74.2 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Mouse SCD1 with A Diiron Center


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Mouse SCD1 with A Diiron Center within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:55.6 occ:1.00 NE2 B:HIS294 2.0 71.4 1.0 NE2 B:HIS156 2.0 62.2 1.0 NE2 B:HIS265 2.1 74.6 1.0 NE2 B:HIS298 2.2 60.4 1.0 CE1 B:HIS265 2.6 74.8 1.0 CD2 B:HIS294 2.7 62.0 1.0 CE1 B:HIS156 2.9 67.7 1.0 CE1 B:HIS298 3.1 67.8 1.0 CE1 B:HIS294 3.1 74.2 1.0 CD2 B:HIS156 3.2 64.2 1.0 CD2 B:HIS265 3.2 69.9 1.0 CD2 B:HIS298 3.2 63.6 1.0 ND1 B:HIS265 3.6 75.9 1.0 CG B:HIS294 3.9 61.7 1.0 CG B:HIS265 3.9 72.9 1.0 ND2 B:ASN261 4.1 78.0 1.0 ND1 B:HIS294 4.1 68.6 1.0 ND1 B:HIS156 4.1 63.8 1.0 ND1 B:HIS298 4.2 67.5 1.0 CG B:HIS156 4.2 63.6 1.0 CG B:HIS298 4.3 64.5 1.0 O B:VAL260 4.3 68.5 1.0 C10 B:3VV403 4.8 60.6 1.0

J.Shen, G.Wu, A.L.Tsai, M.Zhou. Structure and Mechanism of A Unique Diiron Center in Mammalian Stearoyl-Coa Desaturase. J.Mol.Biol. 2020.
ISSN: ESSN 1089-8638
PubMed: 32470559
DOI: 10.1016/J.JMB.2020.05.017