Zinc in PDB 8gf4: Crystal Structure of Domain Related to Iron (Dri) in Complex with Heme

The structure of Crystal Structure of Domain Related to Iron (Dri) in Complex with Heme, PDB code: 8gf4 was solved by D.Kumaran, E.C.Blaby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.25 / 3.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	42.976, 42.976, 379.484, 90, 90, 120
R / Rfree (%)	20.1 / 27.9

The structure of Crystal Structure of Domain Related to Iron (Dri) in Complex with Heme also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Domain Related to Iron (Dri) in Complex with Heme (pdb code 8gf4). 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 Domain Related to Iron (Dri) in Complex with Heme, PDB code: 8gf4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Domain Related to Iron (Dri) in Complex with Heme


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 Domain Related to Iron (Dri) in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:64.7 occ:1.00 NE2 A:HIS21 2.0 56.6 1.0 OE2 B:GLU76 2.0 88.6 1.0 ND1 B:HIS79 2.1 44.2 1.0 NE2 A:HIS16 2.2 59.3 1.0 OE1 B:GLU76 2.5 59.5 1.0 CD B:GLU76 2.6 72.2 1.0 CE1 A:HIS21 2.7 53.3 1.0 CD2 A:HIS16 2.9 54.4 1.0 CE1 B:HIS79 2.9 44.7 1.0 CD2 A:HIS21 3.2 56.1 1.0 CG B:HIS79 3.2 40.2 1.0 CE1 A:HIS16 3.2 56.2 1.0 CB B:HIS79 3.6 42.7 1.0 ND1 A:HIS21 3.9 52.5 1.0 CG A:HIS16 4.0 51.1 1.0 CG B:GLU76 4.1 64.9 1.0 NE2 B:HIS79 4.1 45.0 1.0 ND1 A:HIS16 4.1 54.6 1.0 NE2 B:GLN80 4.1 68.8 1.0 CG A:HIS21 4.2 53.4 1.0 CB A:ASP20 4.2 58.9 1.0 CD2 B:HIS79 4.3 41.9 1.0 O B:GLU76 4.7 54.3 1.0 CA B:GLU76 4.9 61.4 1.0 CG A:ASP20 5.0 64.0 1.0 O A:ASP20 5.0 51.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Domain Related to Iron (Dri) in Complex with Heme


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 Domain Related to Iron (Dri) in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:62.2 occ:1.00 NE2 B:HIS21 2.0 40.7 1.0 ND1 A:HIS79 2.1 50.8 1.0 NE2 B:HIS16 2.2 60.1 1.0 OE1 A:GLU76 2.3 43.9 1.0 OE2 A:GLU76 2.7 55.0 1.0 CD A:GLU76 2.8 54.6 1.0 CE1 A:HIS79 2.8 51.5 1.0 CD2 B:HIS21 2.8 36.5 1.0 CE1 B:HIS16 3.1 55.0 1.0 CE1 B:HIS21 3.2 42.5 1.0 CD2 B:HIS16 3.2 58.0 1.0 CG A:HIS79 3.3 42.8 1.0 CB A:HIS79 3.8 42.5 1.0 CG B:HIS21 4.0 36.2 1.0 NE2 A:HIS79 4.0 50.3 1.0 CB B:ASP20 4.1 51.3 1.0 ND1 B:HIS16 4.2 54.7 1.0 ND1 B:HIS21 4.2 36.6 1.0 CG B:HIS16 4.2 53.9 1.0 CD2 A:HIS79 4.3 43.0 1.0 CG A:GLU76 4.3 55.7 1.0 O B:ASP20 4.5 51.3 1.0 C B:ASP20 4.9 55.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Domain Related to Iron (Dri) in Complex with Heme


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 Domain Related to Iron (Dri) in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:109.8 occ:1.00 ND1 D:HIS79 2.0 63.4 1.0 NE2 C:HIS16 2.0 92.1 1.0 NE2 C:HIS21 2.2 65.5 1.0 OE1 D:GLU76 2.3 89.6 1.0 CE1 D:HIS79 2.6 66.3 1.0 OE2 D:GLU76 2.8 84.0 1.0 CD D:GLU76 2.9 90.5 1.0 CD2 C:HIS16 2.9 81.5 1.0 CE1 C:HIS16 3.0 94.2 1.0 CD2 C:HIS21 3.1 61.2 1.0 CE1 C:HIS21 3.2 63.8 1.0 CG D:HIS79 3.2 63.4 1.0 NE2 D:HIS79 3.9 66.5 1.0 CB D:HIS79 3.9 60.6 1.0 CG C:HIS16 4.0 84.2 1.0 ND1 C:HIS16 4.0 99.9 1.0 CD2 D:HIS79 4.2 65.4 1.0 CG C:HIS21 4.2 58.8 1.0 ND1 C:HIS21 4.2 62.2 1.0 OE1 D:GLN80 4.3 59.2 1.0 CG D:GLU76 4.4 85.1 1.0 CB C:ASP20 4.4 70.5 1.0 OD2 C:ASP20 4.8 69.2 1.0 C4C C:HEM202 4.9 47.1 1.0 CG C:ASP20 5.0 67.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Domain Related to Iron (Dri) in Complex with Heme


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 Domain Related to Iron (Dri) in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:73.3 occ:1.00 NE2 D:HIS16 2.1 128.3 1.0 ND1 C:HIS79 2.2 68.4 1.0 NE2 D:HIS21 2.2 48.8 1.0 OE1 C:GLU76 2.3 105.2 1.0 CD2 D:HIS16 2.6 119.9 1.0 OE2 C:GLU76 2.6 106.0 1.0 CD C:GLU76 2.8 102.6 1.0 CE1 C:HIS79 3.1 67.3 1.0 CG C:HIS79 3.2 66.1 1.0 CD2 D:HIS21 3.2 52.9 1.0 CE1 D:HIS21 3.2 49.4 1.0 CE1 D:HIS16 3.4 123.2 1.0 CB C:HIS79 3.5 66.1 1.0 CG D:HIS16 3.9 108.9 1.0 OD2 D:ASP20 4.0 74.5 1.0 NE2 C:HIS79 4.2 71.7 1.0 ND1 D:HIS16 4.2 125.0 1.0 CB D:ASP20 4.2 75.4 1.0 CD2 C:HIS79 4.2 67.7 1.0 ND1 D:HIS21 4.3 49.0 1.0 CG D:HIS21 4.3 53.5 1.0 CG C:GLU76 4.3 92.5 1.0 OE1 C:GLN80 4.3 86.8 1.0 CG D:ASP20 4.5 78.7 1.0 O C:GLU76 4.7 94.9 1.0

D.Kumaran, E.C.Blaby. Crystal Structure of Domain Related to Iron (Dri) in Complex with Heme. To Be Published.