Iron in PDB 8wvr: Complex Structure of the Azoxy Synthase Vlmb and Its Substrate

The structure of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate, PDB code: 8wvr was solved by X.Zang, J.H.Zhou, D.Yiling, S.Jingkun, Z.Zhijie, S.Zhuanglin, Z.Guiyun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.88 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.82, 95.18, 183.25, 90, 90, 90
R / Rfree (%)	19.5 / 24.1

The binding sites of Iron atom in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate (pdb code 8wvr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate, PDB code: 8wvr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:24.3 occ:1.00 O A:HOH596 1.8 24.8 1.0 OE2 A:GLU84 2.0 22.3 1.0 OE1 A:GLU114 2.2 23.0 1.0 ND1 A:HIS117 2.2 23.1 1.0 N1 A:IMD401 2.3 28.1 1.0 CE1 A:HIS117 2.9 23.1 1.0 CD A:GLU84 3.0 24.2 1.0 C5 A:IMD401 3.1 29.8 1.0 CD A:GLU114 3.2 21.7 1.0 C2 A:IMD401 3.3 30.5 1.0 CG A:HIS117 3.3 25.5 1.0 FE A:FE403 3.4 25.7 1.0 OE1 A:GLU84 3.5 31.2 1.0 OE2 A:GLU114 3.6 24.2 1.0 CB A:HIS117 3.9 23.2 1.0 NE2 A:HIS117 4.1 25.2 1.0 CG A:GLU84 4.3 24.9 1.0 C4 A:IMD401 4.3 28.3 1.0 CD2 A:HIS117 4.4 22.7 1.0 N3 A:IMD401 4.4 26.8 1.0 OE2 A:GLU180 4.4 27.9 1.0 CG A:GLU114 4.5 19.4 1.0 OE1 A:GLU212 4.6 24.5 1.0 CA A:GLU114 4.6 21.2 1.0 CE1 A:HIS215 4.7 23.4 1.0 ND1 A:HIS215 4.8 19.4 1.0 CB A:GLU114 4.8 20.6 1.0

Iron binding site 2 out of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:25.7 occ:1.00 OE2 A:GLU180 1.9 27.9 1.0 O A:HOH596 2.0 24.8 1.0 ND1 A:HIS215 2.1 19.4 1.0 OE1 A:GLU212 2.1 24.5 1.0 OE2 A:GLU114 2.2 24.2 1.0 CD A:GLU180 2.9 25.9 1.0 CE1 A:HIS215 2.9 23.4 1.0 CD A:GLU114 3.1 21.7 1.0 CD A:GLU212 3.1 27.3 1.0 CG A:HIS215 3.2 23.2 1.0 OE1 A:GLU180 3.3 28.6 1.0 OE1 A:GLU114 3.4 23.0 1.0 FE A:FE402 3.4 24.3 1.0 OE2 A:GLU212 3.5 34.4 1.0 CB A:HIS215 3.7 23.8 1.0 NE2 A:GLN110 3.8 19.1 1.0 NE2 A:HIS215 4.1 20.4 1.0 CG A:GLU180 4.2 25.7 1.0 CD2 A:HIS215 4.3 18.9 1.0 CG A:GLU212 4.4 24.4 1.0 CG A:GLU114 4.5 19.4 1.0 CA A:GLU212 4.6 23.2 1.0 CE1 A:HIS117 4.6 23.1 1.0 C5 A:IMD401 4.6 29.8 1.0 CB A:GLU212 4.6 24.2 1.0 N1 A:IMD401 4.7 28.1 1.0 CD A:GLN110 4.7 26.2 1.0 ND1 A:HIS117 4.8 23.1 1.0 CG A:GLN110 5.0 19.0 1.0

Iron binding site 3 out of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:24.6 occ:1.00 O B:HOH556 1.9 26.0 1.0 OE2 B:GLU84 2.0 22.6 1.0 OE1 B:GLU114 2.1 21.5 1.0 N1 B:IMD401 2.2 28.6 1.0 ND1 B:HIS117 2.3 22.9 1.0 CD B:GLU84 3.0 24.5 1.0 C5 B:IMD401 3.1 28.7 1.0 CE1 B:HIS117 3.1 23.4 1.0 CD B:GLU114 3.2 22.0 1.0 C2 B:IMD401 3.2 27.0 1.0 OE1 B:GLU84 3.3 30.9 1.0 FE B:FE403 3.4 24.4 1.0 CG B:HIS117 3.4 23.3 1.0 OE2 B:GLU114 3.5 23.4 1.0 CB B:HIS117 3.9 22.6 1.0 C4 B:IMD401 4.2 28.1 1.0 N3 B:IMD401 4.3 31.5 1.0 NE2 B:HIS117 4.3 22.5 1.0 CG B:GLU84 4.3 25.4 1.0 OE2 B:GLU180 4.4 28.4 1.0 OE1 B:GLU212 4.4 25.2 1.0 CD2 B:HIS117 4.5 23.4 1.0 CG B:GLU114 4.5 22.0 1.0 CA B:GLU114 4.6 21.1 1.0 CE1 B:HIS215 4.8 23.0 1.0 ND1 B:HIS215 4.8 22.5 1.0 CB B:GLU114 4.8 19.8 1.0 CD B:GLU212 4.9 27.1 1.0

Iron binding site 4 out of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:24.4 occ:1.00 OE2 B:GLU180 1.9 28.4 1.0 O B:HOH556 1.9 26.0 1.0 OE1 B:GLU212 2.0 25.2 1.0 OE2 B:GLU114 2.2 23.4 1.0 ND1 B:HIS215 2.2 22.5 1.0 CD B:GLU180 2.9 27.0 1.0 CD B:GLU212 3.0 27.1 1.0 CE1 B:HIS215 3.0 23.0 1.0 CD B:GLU114 3.1 22.0 1.0 OE1 B:GLU180 3.2 26.1 1.0 CG B:HIS215 3.3 22.9 1.0 OE2 B:GLU212 3.4 31.9 1.0 OE1 B:GLU114 3.4 21.5 1.0 FE B:FE402 3.4 24.6 1.0 CB B:HIS215 3.7 22.0 1.0 NE2 B:GLN110 3.8 20.9 1.0 CG B:GLU180 4.2 23.6 1.0 NE2 B:HIS215 4.2 23.6 1.0 CD2 B:HIS215 4.3 20.2 1.0 CG B:GLU212 4.4 23.0 1.0 CG B:GLU114 4.5 22.0 1.0 CA B:GLU212 4.6 22.7 1.0 C5 B:IMD401 4.6 28.7 1.0 N1 B:IMD401 4.6 28.6 1.0 CB B:GLU212 4.7 23.9 1.0 CD B:GLN110 4.7 23.5 1.0 CE1 B:HIS117 4.7 23.4 1.0 ND1 B:HIS117 4.8 22.9 1.0 CG B:GLN110 4.9 21.8 1.0

Iron binding site 5 out of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe403 b:22.6 occ:1.00 O C:HOH590 2.0 24.4 1.0 OE2 C:GLU84 2.0 25.1 1.0 OE1 C:GLU114 2.1 21.8 1.0 ND1 C:HIS117 2.3 20.3 1.0 N1 C:IMD401 2.3 27.7 1.0 N08 C:XBN402 2.7 25.9 0.6 N07 C:XBN402 2.8 26.9 0.6 C5 C:IMD401 2.9 28.0 1.0 CD C:GLU84 3.0 28.4 1.0 CE1 C:HIS117 3.1 21.2 1.0 CD C:GLU114 3.2 21.9 1.0 OE1 C:GLU84 3.3 33.2 1.0 FE C:FE404 3.4 23.1 1.0 CG C:HIS117 3.4 21.6 1.0 C2 C:IMD401 3.5 26.9 1.0 C06 C:XBN402 3.5 27.5 0.6 OE2 C:GLU114 3.6 21.2 1.0 C09 C:XBN402 3.6 30.3 0.6 CB C:HIS117 3.9 20.5 1.0 C4 C:IMD401 4.2 26.7 1.0 NE2 C:HIS117 4.3 21.1 1.0 CG C:GLU84 4.4 24.6 1.0 OE2 C:GLU180 4.5 24.1 1.0 N3 C:IMD401 4.5 26.4 1.0 CD2 C:HIS117 4.5 19.4 1.0 C12 C:XBN402 4.5 34.3 0.6 O13 C:XBN402 4.5 39.0 0.6 CG C:GLU114 4.5 20.1 1.0 OE1 C:GLU212 4.6 21.4 1.0 CA C:GLU114 4.6 20.9 1.0 CB C:GLU114 4.8 22.8 1.0 CE1 C:HIS215 4.8 23.5 1.0 ND1 C:HIS215 4.9 21.8 1.0 C10 C:XBN402 4.9 29.9 0.6 CD C:GLU212 5.0 23.7 1.0

Iron binding site 6 out of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe404 b:23.1 occ:1.00 O C:HOH590 1.9 24.4 1.0 OE2 C:GLU180 1.9 24.1 1.0 OE1 C:GLU212 2.1 21.4 1.0 OE2 C:GLU114 2.2 21.2 1.0 ND1 C:HIS215 2.2 21.8 1.0 N07 C:XBN402 2.9 26.9 0.6 CD C:GLU180 2.9 26.7 1.0 CE1 C:HIS215 3.0 23.5 1.0 CD C:GLU114 3.1 21.9 1.0 CD C:GLU212 3.1 23.7 1.0 OE1 C:GLU114 3.3 21.8 1.0 CG C:HIS215 3.3 22.1 1.0 FE C:FE403 3.4 22.6 1.0 OE1 C:GLU180 3.4 27.4 1.0 OE2 C:GLU212 3.5 33.1 1.0 C06 C:XBN402 3.7 27.5 0.6 CB C:HIS215 3.7 20.1 1.0 NE2 C:GLN110 3.8 24.1 1.0 N08 C:XBN402 4.0 25.9 0.6 CG C:GLU180 4.2 27.6 1.0 NE2 C:HIS215 4.2 20.2 1.0 CD2 C:HIS215 4.4 22.9 1.0 CG C:GLU212 4.4 23.3 1.0 C09 C:XBN402 4.5 30.3 0.6 CG C:GLU114 4.5 20.1 1.0 C5 C:IMD401 4.5 28.0 1.0 CA C:GLU212 4.6 20.7 1.0 CB C:GLU212 4.6 23.2 1.0 CD C:GLN110 4.7 23.3 1.0 C05 C:XBN402 4.7 30.5 0.6 CE1 C:HIS117 4.7 21.2 1.0 ND1 C:HIS117 4.8 20.3 1.0 N1 C:IMD401 4.8 27.7 1.0 C10 C:XBN402 4.8 29.9 0.6 CG C:GLN110 4.9 22.3 1.0

Iron binding site 7 out of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe402 b:42.7 occ:1.00 O D:HOH536 2.0 29.3 1.0 OE2 D:GLU84 2.0 42.4 1.0 OE1 D:GLU114 2.2 35.2 1.0 ND1 D:HIS117 2.3 36.3 1.0 N1 D:IMD401 2.8 44.1 1.0 C2 D:IMD401 2.9 43.5 1.0 CE1 D:HIS117 3.0 37.7 1.0 CD D:GLU84 3.1 39.9 1.0 CD D:GLU114 3.2 35.9 1.0 OE1 D:GLU84 3.4 42.4 1.0 FE D:FE403 3.5 39.1 1.0 CG D:HIS117 3.5 35.3 1.0 OE2 D:GLU114 3.6 36.3 1.0 CB D:HIS117 4.0 32.7 1.0 C5 D:IMD401 4.1 48.1 1.0 N3 D:IMD401 4.2 46.5 1.0 NE2 D:HIS117 4.2 35.9 1.0 CG D:GLU84 4.4 41.8 1.0 CD2 D:HIS117 4.5 34.4 1.0 OE2 D:GLU180 4.5 39.6 1.0 OE1 D:GLU212 4.5 42.2 1.0 CG D:GLU114 4.6 34.7 1.0 CA D:GLU114 4.6 31.5 1.0 C4 D:IMD401 4.8 49.1 1.0 CB D:GLU114 4.8 31.2 1.0 ND1 D:HIS215 4.9 36.5 1.0 CE1 D:HIS215 4.9 34.1 1.0

Iron binding site 8 out of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe403 b:39.1 occ:1.00 O D:HOH536 1.9 29.3 1.0 OE2 D:GLU180 2.0 39.6 1.0 OE1 D:GLU212 2.2 42.2 1.0 OE2 D:GLU114 2.3 36.3 1.0 ND1 D:HIS215 2.3 36.5 1.0 CD D:GLU180 3.0 42.9 1.0 CE1 D:HIS215 3.1 34.1 1.0 CD D:GLU114 3.2 35.9 1.0 CD D:GLU212 3.2 43.6 1.0 CG D:HIS215 3.3 35.3 1.0 OE1 D:GLU180 3.3 42.9 1.0 OE1 D:GLU114 3.5 35.2 1.0 FE D:FE402 3.5 42.7 1.0 OE2 D:GLU212 3.6 50.7 1.0 CB D:HIS215 3.7 36.4 1.0 NE2 D:GLN110 3.8 35.6 1.0 CG D:GLU180 4.2 39.0 1.0 NE2 D:HIS215 4.3 35.1 1.0 CD2 D:HIS215 4.4 35.0 1.0 CG D:GLU212 4.5 42.0 1.0 CG D:GLU114 4.6 34.7 1.0 CA D:GLU212 4.6 35.3 1.0 CD D:GLN110 4.6 36.6 1.0 C2 D:IMD401 4.7 43.5 1.0 CB D:GLU212 4.8 38.3 1.0 CE1 D:HIS117 4.8 37.7 1.0 CG D:GLN110 4.8 32.5 1.0 ND1 D:HIS117 5.0 36.3 1.0 CE1 D:PHE175 5.0 37.4 1.0

X.Zang, J.H.Zhou, D.Yiling, S.Jingkun, Z.Zhijie, S.Zhuanglin, Z.Guiyun. A Conserved Enzymatic Route For Azoxy Bond Formation in Natural Product Biosynthesis To Be Published.