Iron in PDB 1i4y: The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin

The structure of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin, PDB code: 1i4y was solved by C.S.Farmer, D.M.Kurtz Jr., Z.-J.Liu, B.C.Wang, J.Rose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.12 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.428, 130.637, 73.040, 90.00, 99.12, 90.00
R / Rfree (%)	22.4 / 24.9

The structure of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin (pdb code 1i4y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin, PDB code: 1i4y:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:12.0 occ:1.00 FE1 A:FEO601 0.0 12.0 1.0 O A:FEO601 2.0 6.8 1.0 NE2 A:HIS77 2.2 4.0 1.0 NE2 A:HIS101 2.2 12.5 1.0 OD1 A:ASP106 2.3 4.0 1.0 OE1 A:GLU58 2.3 7.1 1.0 NE2 A:HIS73 2.3 11.3 1.0 CD2 A:HIS101 3.1 11.8 1.0 CE1 A:HIS77 3.1 5.1 1.0 CD A:GLU58 3.1 8.3 1.0 CD2 A:HIS73 3.2 10.9 1.0 CD2 A:HIS77 3.2 5.1 1.0 FE2 A:FEO601 3.2 9.3 1.0 CG A:ASP106 3.2 5.6 1.0 OE2 A:GLU58 3.3 7.4 1.0 CE1 A:HIS101 3.3 11.7 1.0 CE1 A:HIS73 3.4 9.3 1.0 OD2 A:ASP106 3.5 6.4 1.0 ND1 A:HIS77 4.3 5.2 1.0 CG A:HIS101 4.3 10.9 1.0 CG A:HIS77 4.3 5.3 1.0 ND1 A:HIS101 4.4 11.8 1.0 CG A:HIS73 4.4 8.9 1.0 ND1 A:HIS73 4.5 6.5 1.0 CE1 A:PHE55 4.5 6.5 1.0 CD1 A:PHE55 4.6 7.1 1.0 CG A:GLU58 4.6 6.6 1.0 CL A:CL114 4.6 4.0 1.0 CB A:ASP106 4.6 7.7 1.0 NE2 A:HIS54 4.6 4.0 1.0 CE2 A:TYR109 4.8 6.8 1.0 CA A:ASP106 4.9 6.5 1.0

Iron binding site 2 out of 16 in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:9.3 occ:1.00 FE2 A:FEO601 0.0 9.3 1.0 O A:FEO601 1.8 6.8 1.0 OD2 A:ASP106 2.2 6.4 1.0 NE2 A:HIS54 2.2 4.0 1.0 NE2 A:HIS25 2.3 7.2 1.0 CL A:CL114 2.4 4.0 1.0 OE2 A:GLU58 2.4 7.4 1.0 CG A:ASP106 3.1 5.6 1.0 CD2 A:HIS25 3.1 7.0 1.0 CD2 A:HIS54 3.2 4.0 1.0 CE1 A:HIS54 3.2 4.0 1.0 FE1 A:FEO601 3.2 12.0 1.0 CD A:GLU58 3.3 8.3 1.0 CE1 A:HIS25 3.3 8.6 1.0 OD1 A:ASP106 3.3 4.0 1.0 OE1 A:GLU58 3.6 7.1 1.0 CD2 A:HIS101 4.2 11.8 1.0 CG A:HIS25 4.3 7.3 1.0 ND1 A:HIS54 4.3 4.0 1.0 ND1 A:HIS25 4.3 6.9 1.0 CG A:HIS54 4.4 4.9 1.0 OH A:TYR109 4.4 10.2 1.0 CB A:ASP106 4.4 7.7 1.0 NE2 A:HIS101 4.4 12.5 1.0 CG A:GLU58 4.5 6.6 1.0 CG1 A:ILE102 4.7 6.7 1.0 CE1 A:PHE55 4.7 6.5 1.0 NE2 A:HIS77 4.8 4.0 1.0 CG2 A:ILE21 4.8 7.1 1.0 CD1 A:PHE55 4.9 7.1 1.0

Iron binding site 3 out of 16 in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:10.1 occ:1.00 FE1 B:FEO602 0.0 10.1 1.0 O B:FEO602 1.9 9.1 1.0 OE1 B:GLU58 2.2 4.4 1.0 NE2 B:HIS77 2.2 4.0 1.0 NE2 B:HIS101 2.2 4.9 1.0 OD1 B:ASP106 2.3 4.0 1.0 NE2 B:HIS73 2.3 5.4 1.0 CD B:GLU58 3.1 5.7 1.0 CD2 B:HIS101 3.1 5.6 1.0 CE1 B:HIS77 3.2 4.0 1.0 FE2 B:FEO602 3.2 12.7 1.0 CD2 B:HIS77 3.2 4.0 1.0 CG B:ASP106 3.2 6.5 1.0 CE1 B:HIS101 3.2 5.4 1.0 CE1 B:HIS73 3.3 6.6 1.0 CD2 B:HIS73 3.3 6.2 1.0 OE2 B:GLU58 3.4 5.7 1.0 OD2 B:ASP106 3.5 6.6 1.0 ND1 B:HIS77 4.3 4.0 1.0 CG B:HIS77 4.3 4.0 1.0 ND1 B:HIS101 4.3 7.1 1.0 CG B:HIS101 4.3 5.3 1.0 ND1 B:HIS73 4.4 6.7 1.0 CE1 B:PHE55 4.5 4.0 1.0 CG B:HIS73 4.5 6.6 1.0 CG B:GLU58 4.5 4.1 1.0 CL B:CL114 4.6 4.0 1.0 NE2 B:HIS54 4.6 4.0 1.0 CD1 B:PHE55 4.6 4.1 1.0 CB B:ASP106 4.6 6.2 1.0 CE2 B:TYR109 4.8 6.7 1.0 CA B:ASP106 4.9 6.1 1.0 CB B:GLU58 5.0 5.0 1.0

Iron binding site 4 out of 16 in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:12.7 occ:1.00 FE2 B:FEO602 0.0 12.7 1.0 O B:FEO602 1.7 9.1 1.0 NE2 B:HIS54 2.2 4.0 1.0 OD2 B:ASP106 2.3 6.6 1.0 NE2 B:HIS25 2.3 4.1 1.0 OE2 B:GLU58 2.4 5.7 1.0 CL B:CL114 2.4 4.0 1.0 CD2 B:HIS54 3.1 4.1 1.0 CD2 B:HIS25 3.1 4.9 1.0 CG B:ASP106 3.1 6.5 1.0 FE1 B:FEO602 3.2 10.1 1.0 CE1 B:HIS54 3.3 4.0 1.0 CD B:GLU58 3.3 5.7 1.0 OD1 B:ASP106 3.4 4.0 1.0 CE1 B:HIS25 3.4 5.6 1.0 OE1 B:GLU58 3.5 4.4 1.0 CD2 B:HIS101 4.1 5.6 1.0 NE2 B:HIS101 4.3 4.9 1.0 CG B:HIS54 4.3 4.2 1.0 CG B:HIS25 4.3 4.4 1.0 OH B:TYR109 4.3 4.2 1.0 ND1 B:HIS54 4.3 4.0 1.0 ND1 B:HIS25 4.4 5.0 1.0 CB B:ASP106 4.5 6.2 1.0 CG B:GLU58 4.6 4.1 1.0 CG1 B:ILE102 4.6 4.0 1.0 CE1 B:PHE55 4.6 4.0 1.0 NE2 B:HIS77 4.7 4.0 1.0 CD1 B:PHE55 4.9 4.1 1.0 CG2 B:ILE21 5.0 4.0 1.0

Iron binding site 5 out of 16 in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe603 b:13.2 occ:1.00 FE1 C:FEO603 0.0 13.2 1.0 O C:FEO603 1.9 8.6 1.0 NE2 C:HIS77 2.2 4.5 1.0 NE2 C:HIS101 2.2 5.0 1.0 OE1 C:GLU58 2.3 4.5 1.0 NE2 C:HIS73 2.3 8.4 1.0 OD1 C:ASP106 2.3 7.8 1.0 CD2 C:HIS101 3.1 5.8 1.0 CE1 C:HIS77 3.1 4.9 1.0 CD2 C:HIS77 3.2 6.1 1.0 CD C:GLU58 3.2 4.1 1.0 CD2 C:HIS73 3.3 5.9 1.0 CE1 C:HIS73 3.3 7.8 1.0 FE2 C:FEO603 3.3 5.8 1.0 CE1 C:HIS101 3.3 6.3 1.0 CG C:ASP106 3.3 4.6 1.0 OE2 C:GLU58 3.4 4.9 1.0 OD2 C:ASP106 3.6 6.6 1.0 ND1 C:HIS77 4.3 5.1 1.0 CG C:HIS101 4.3 4.0 1.0 CG C:HIS77 4.3 4.9 1.0 ND1 C:HIS101 4.3 5.3 1.0 ND1 C:HIS73 4.4 6.6 1.0 CG C:HIS73 4.4 6.5 1.0 CE1 C:PHE55 4.5 7.3 1.0 CG C:GLU58 4.5 7.0 1.0 NE2 C:HIS54 4.6 5.7 1.0 CL C:CL114 4.6 4.0 1.0 CD1 C:PHE55 4.6 6.3 1.0 CB C:ASP106 4.7 5.7 1.0 CE2 C:TYR109 4.9 9.4 1.0 CA C:ASP106 5.0 8.2 1.0 CB C:GLU58 5.0 6.4 1.0

Iron binding site 6 out of 16 in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe603 b:5.8 occ:1.00 FE2 C:FEO603 0.0 5.8 1.0 O C:FEO603 1.9 8.6 1.0 OD2 C:ASP106 2.2 6.6 1.0 NE2 C:HIS54 2.2 5.7 1.0 NE2 C:HIS25 2.2 5.8 1.0 OE2 C:GLU58 2.4 4.9 1.0 CL C:CL114 2.5 4.0 1.0 CD2 C:HIS25 3.1 4.2 1.0 CE1 C:HIS54 3.1 7.4 1.0 CG C:ASP106 3.1 4.6 1.0 CD2 C:HIS54 3.2 6.0 1.0 CD C:GLU58 3.2 4.1 1.0 CE1 C:HIS25 3.3 5.0 1.0 FE1 C:FEO603 3.3 13.2 1.0 OD1 C:ASP106 3.3 7.8 1.0 OE1 C:GLU58 3.6 4.5 1.0 ND1 C:HIS54 4.2 6.8 1.0 CD2 C:HIS101 4.2 5.8 1.0 CG C:HIS25 4.3 4.3 1.0 ND1 C:HIS25 4.3 4.5 1.0 CG C:HIS54 4.3 6.4 1.0 OH C:TYR109 4.4 7.8 1.0 CB C:ASP106 4.4 5.7 1.0 CG C:GLU58 4.5 7.0 1.0 NE2 C:HIS101 4.5 5.0 1.0 CG1 C:ILE102 4.7 7.8 1.0 CE1 C:PHE55 4.7 7.3 1.0 NE2 C:HIS77 4.8 4.5 1.0 CG2 C:ILE21 4.8 8.7 1.0 CD1 C:PHE55 4.9 6.3 1.0

Iron binding site 7 out of 16 in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe604 b:9.0 occ:1.00 FE1 D:FEO604 0.0 9.0 1.0 O D:FEO604 1.9 14.4 1.0 OE1 D:GLU58 2.1 4.0 1.0 OD1 D:ASP106 2.2 5.8 1.0 NE2 D:HIS77 2.2 8.2 1.0 NE2 D:HIS73 2.3 6.8 1.0 NE2 D:HIS101 2.3 4.4 1.0 CD D:GLU58 3.1 5.6 1.0 CG D:ASP106 3.1 6.2 1.0 CE1 D:HIS77 3.2 6.3 1.0 CD2 D:HIS77 3.2 7.6 1.0 CD2 D:HIS101 3.2 4.3 1.0 CE1 D:HIS73 3.2 6.3 1.0 FE2 D:FEO604 3.3 6.4 1.0 CD2 D:HIS73 3.3 6.2 1.0 OE2 D:GLU58 3.3 7.2 1.0 CE1 D:HIS101 3.3 6.0 1.0 OD2 D:ASP106 3.4 5.1 1.0 ND1 D:HIS77 4.3 7.2 1.0 CG D:HIS77 4.4 7.4 1.0 ND1 D:HIS73 4.4 7.0 1.0 CG D:HIS101 4.4 6.1 1.0 CG D:GLU58 4.4 4.0 1.0 ND1 D:HIS101 4.4 4.0 1.0 CG D:HIS73 4.4 8.0 1.0 CB D:ASP106 4.5 5.4 1.0 CL D:CL114 4.6 4.0 1.0 CE1 D:PHE55 4.6 10.9 1.0 NE2 D:HIS54 4.6 4.0 1.0 CD1 D:PHE55 4.7 10.0 1.0 CE2 D:TYR109 4.8 4.5 1.0 CA D:ASP106 4.8 6.7 1.0 CB D:GLU58 5.0 5.8 1.0

Iron binding site 8 out of 16 in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe604 b:6.4 occ:1.00 FE2 D:FEO604 0.0 6.4 1.0 O D:FEO604 1.8 14.4 1.0 OD2 D:ASP106 2.1 5.1 1.0 NE2 D:HIS54 2.1 4.0 1.0 NE2 D:HIS25 2.2 5.0 1.0 OE2 D:GLU58 2.4 7.2 1.0 CL D:CL114 2.4 4.0 1.0 CD2 D:HIS25 3.1 6.4 1.0 CE1 D:HIS54 3.1 4.0 1.0 CG D:ASP106 3.1 6.2 1.0 CD2 D:HIS54 3.1 4.0 1.0 CD D:GLU58 3.3 5.6 1.0 FE1 D:FEO604 3.3 9.0 1.0 CE1 D:HIS25 3.3 5.5 1.0 OD1 D:ASP106 3.5 5.8 1.0 OE1 D:GLU58 3.6 4.0 1.0 ND1 D:HIS54 4.2 4.8 1.0 CD2 D:HIS101 4.2 4.3 1.0 CG D:HIS25 4.3 5.1 1.0 CG D:HIS54 4.3 4.0 1.0 OH D:TYR109 4.3 6.1 1.0 ND1 D:HIS25 4.3 4.0 1.0 CB D:ASP106 4.4 5.4 1.0 NE2 D:HIS101 4.4 4.4 1.0 CG1 D:ILE102 4.5 5.8 1.0 CG D:GLU58 4.5 4.0 1.0 CE1 D:PHE55 4.7 10.9 1.0 NE2 D:HIS77 4.8 8.2 1.0 CD1 D:PHE55 4.9 10.0 1.0 CG2 D:ILE21 4.9 7.0 1.0

Iron binding site 9 out of 16 in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe605 b:13.9 occ:1.00 FE1 E:FEO605 0.0 13.9 1.0 O E:FEO605 1.8 10.0 1.0 NE2 E:HIS73 2.2 4.1 1.0 NE2 E:HIS77 2.2 12.1 1.0 OE1 E:GLU58 2.2 8.7 1.0 OD1 E:ASP106 2.3 4.1 1.0 NE2 E:HIS101 2.3 7.6 1.0 CE1 E:HIS77 3.0 13.8 1.0 CD E:GLU58 3.1 8.6 1.0 CE1 E:HIS73 3.1 8.0 1.0 CD2 E:HIS101 3.2 9.1 1.0 CD2 E:HIS73 3.2 5.8 1.0 FE2 E:FEO605 3.2 15.4 1.0 CD2 E:HIS77 3.3 12.0 1.0 CG E:ASP106 3.3 6.8 1.0 OE2 E:GLU58 3.3 5.8 1.0 CE1 E:HIS101 3.4 8.4 1.0 OD2 E:ASP106 3.6 7.6 1.0 ND1 E:HIS77 4.2 11.5 1.0 ND1 E:HIS73 4.2 5.0 1.0 CG E:HIS73 4.3 6.9 1.0 CG E:HIS77 4.4 11.8 1.0 CG E:HIS101 4.4 10.6 1.0 ND1 E:HIS101 4.4 8.5 1.0 CG E:GLU58 4.5 5.8 1.0 CE1 E:PHE55 4.6 9.2 1.0 CL E:CL114 4.6 4.0 1.0 CB E:ASP106 4.6 6.0 1.0 CD1 E:PHE55 4.7 8.2 1.0 NE2 E:HIS54 4.7 5.8 1.0 CE2 E:TYR109 4.8 4.0 1.0 CA E:ASP106 4.9 5.8 1.0 CE E:MET62 4.9 7.8 1.0 CB E:GLU58 5.0 8.1 1.0

Iron binding site 10 out of 16 in the The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Crystal Structure of Phascolopsis Gouldii Wild Type Methemerythrin within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe605 b:15.4 occ:1.00 FE2 E:FEO605 0.0 15.4 1.0 O E:FEO605 1.7 10.0 1.0 NE2 E:HIS54 2.2 5.8 1.0 OD2 E:ASP106 2.2 7.6 1.0 NE2 E:HIS25 2.3 5.7 1.0 OE2 E:GLU58 2.4 5.8 1.0 CL E:CL114 2.4 4.0 1.0 CG E:ASP106 3.1 6.8 1.0 CE1 E:HIS54 3.1 5.9 1.0 CD2 E:HIS25 3.1 5.7 1.0 CD2 E:HIS54 3.2 6.9 1.0 FE1 E:FEO605 3.2 13.9 1.0 CD E:GLU58 3.3 8.6 1.0 OD1 E:ASP106 3.3 4.1 1.0 CE1 E:HIS25 3.3 6.7 1.0 OE1 E:GLU58 3.6 8.7 1.0 CD2 E:HIS101 4.2 9.1 1.0 ND1 E:HIS54 4.3 5.7 1.0 CG E:HIS54 4.3 7.1 1.0 CG E:HIS25 4.3 4.7 1.0 ND1 E:HIS25 4.4 5.6 1.0 NE2 E:HIS101 4.4 7.6 1.0 CB E:ASP106 4.4 6.0 1.0 OH E:TYR109 4.4 4.8 1.0 CG E:GLU58 4.5 5.8 1.0 NE2 E:HIS77 4.7 12.1 1.0 CE1 E:PHE55 4.7 9.2 1.0 CG1 E:ILE102 4.7 5.2 1.0 CG2 E:ILE21 4.9 8.6 1.0 CD1 E:PHE55 4.9 8.2 1.0 CB E:GLU58 5.0 8.1 1.0

C.S.Farmer, D.M.Kurtz Jr., Z.J.Liu, B.C.Wang, J.Rose, J.Ai, J.Sanders-Loehr. The Crystal Structures of Phascolopsis Gouldii Wild Type and L98Y Methemerythrins: Structural and Functional Alterations of the O2 Binding Pocket. J.Biol.Inorg.Chem. V. 6 418 2001.
ISSN: ISSN 0949-8257
PubMed: 11372200
DOI: 10.1007/S007750100218