Zinc in PDB 7dgo: The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin

The structure of The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin, PDB code: 7dgo was solved by S.Nagao, A.Idomoto, N.Shibata, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.98 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.738, 63.141, 79.466, 90, 90, 90
R / Rfree (%)	21.3 / 26.5

The structure of The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin (pdb code 7dgo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin, PDB code: 7dgo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:26.9 occ:1.00 OD2 A:ASP141 2.0 26.2 1.0 ND1 B:HIS79 2.0 26.2 1.0 NE2 A:HIS82 2.0 29.8 1.0 O B:HOH339 2.1 19.6 1.0 CE1 A:HIS82 2.9 31.9 1.0 CE1 B:HIS79 3.0 27.0 1.0 CG B:HIS79 3.1 26.9 1.0 CG A:ASP141 3.1 26.1 1.0 CD2 A:HIS82 3.1 29.4 1.0 CB B:HIS79 3.4 25.9 1.0 CB A:ASP141 3.5 27.8 1.0 ND1 A:HIS82 4.0 31.6 1.0 NE2 B:HIS79 4.1 25.9 1.0 OD1 A:ASP141 4.1 26.5 1.0 CD2 B:HIS79 4.2 29.1 1.0 CG A:HIS82 4.2 30.9 1.0 CA B:HIS79 4.4 26.1 1.0 CD2 A:LEU86 4.4 40.1 1.0 O B:HOH328 4.5 37.8 1.0 O A:LEU137 4.8 24.9 1.0 CD1 A:LEU86 4.8 37.6 1.0 CA A:PHE138 4.9 22.8 1.0 CG2 B:ILE75 4.9 29.6 1.0 O A:HOH342 5.0 37.4 1.0

Zinc binding site 2 out of 5 in the The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:31.1 occ:1.00 ND1 A:HIS36 2.0 23.4 1.0 OE1 A:GLU38 2.0 30.4 1.0 O A:HOH338 2.1 25.9 1.0 O A:HOH346 2.2 24.1 1.0 CD A:GLU38 2.8 33.3 1.0 OE2 A:GLU38 3.0 26.9 1.0 CE1 A:HIS36 3.0 24.1 1.0 CG A:HIS36 3.0 23.4 1.0 CB A:HIS36 3.4 22.7 1.0 O A:HOH317 3.7 21.4 1.0 CE2 B:PHE106 3.7 25.9 1.0 CA A:HIS36 3.8 23.0 1.0 O A:HOH345 3.9 47.3 1.0 CZ B:PHE106 3.9 26.5 1.0 NE2 A:HIS36 4.1 21.8 1.0 CD2 A:HIS36 4.1 22.8 1.0 CG A:GLU38 4.2 38.6 1.0 CD2 B:PHE106 4.3 25.8 1.0 O A:GLY35 4.4 21.1 1.0 CE1 B:PHE106 4.7 25.9 1.0 C A:HIS36 4.8 24.4 1.0 N A:HIS36 4.9 22.2 1.0

Zinc binding site 3 out of 5 in the The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:30.4 occ:0.50 CD2 A:HIS24 1.6 39.5 0.5 OD2 A:ASP20 1.9 59.9 0.5 ND1 A:HIS24 2.0 29.6 0.5 O A:HOH341 2.1 29.3 0.5 OD2 A:ASP20 2.1 43.0 0.5 NE2 B:HIS119 2.1 34.5 0.5 NE2 A:HIS24 2.6 40.3 0.5 CG A:HIS24 2.6 38.0 0.5 CE1 B:HIS119 2.7 47.5 0.5 CG A:ASP20 2.8 57.0 0.5 CG A:ASP20 2.8 51.9 0.5 CE1 A:HIS24 3.0 30.4 0.5 CE1 B:HIS119 3.0 34.2 0.5 CG A:HIS24 3.0 30.9 0.5 OD1 A:ASP20 3.1 52.7 0.5 CD2 B:HIS119 3.1 34.9 0.5 OD1 A:ASP20 3.2 51.8 0.5 NE2 B:HIS119 3.3 49.9 0.5 CB A:HIS24 3.3 35.6 0.5 CB A:HIS24 3.4 30.6 0.5 ZN A:ZN206 3.4 49.5 0.5 ND1 B:HIS119 3.6 49.6 0.5 CE1 A:HIS24 3.7 40.8 0.5 ND1 A:HIS24 3.7 39.1 0.5 CB A:ASP20 4.1 50.6 0.5 NE2 A:HIS24 4.1 30.6 0.5 CB A:ASP20 4.1 54.5 0.5 CD2 A:HIS24 4.1 30.3 0.5 ND1 B:HIS119 4.2 36.1 0.5 CG B:HIS119 4.3 37.4 0.5 CB B:LYS118 4.4 39.0 1.0 CD2 B:HIS119 4.4 47.4 0.5 CG B:HIS119 4.5 46.6 0.5 CA A:VAL17 4.6 45.1 1.0 CG2 A:VAL17 4.6 43.6 1.0 CA A:HIS24 4.7 36.1 0.5 CA A:HIS24 4.7 33.1 0.5 N A:HIS24 4.7 38.8 0.5 N A:HIS24 4.7 36.8 0.5 CG B:LYS118 4.8 41.9 1.0 CD1 B:LEU115 4.9 46.6 1.0

Zinc binding site 4 out of 5 in the The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:49.5 occ:0.50 NE2 A:HIS24 2.0 40.3 0.5 O A:HOH347 2.1 55.4 1.0 OD1 A:ASP20 2.1 52.7 0.5 NE2 B:HIS119 2.1 49.9 0.5 CE1 A:HIS24 2.1 30.4 0.5 OD1 A:ASP20 2.8 51.8 0.5 CE1 B:HIS119 2.8 34.2 0.5 CE1 A:HIS24 2.9 40.8 0.5 ND1 A:HIS24 3.0 29.6 0.5 CD2 A:HIS24 3.0 39.5 0.5 CE1 B:HIS119 3.0 47.5 0.5 CD2 B:HIS119 3.1 47.4 0.5 CG A:ASP20 3.2 57.0 0.5 NE2 A:HIS24 3.2 30.6 0.5 NE2 B:HIS119 3.3 34.5 0.5 ZN A:ZN205 3.4 30.4 0.5 CG A:ASP20 3.5 51.9 0.5 OD2 A:ASP20 3.7 59.9 0.5 ND1 B:HIS119 3.7 36.1 0.5 OD2 A:ASP20 4.0 43.0 0.5 ND1 A:HIS24 4.0 39.1 0.5 CG A:HIS24 4.1 38.0 0.5 ND1 B:HIS119 4.1 49.6 0.5 CG A:HIS24 4.2 30.9 0.5 CG B:HIS119 4.2 46.6 0.5 CD2 A:HIS24 4.3 30.3 0.5 CD2 B:HIS119 4.3 34.9 0.5 CB A:ASP20 4.3 50.6 0.5 CB A:ASP20 4.4 54.5 0.5 CB B:LYS118 4.5 39.0 1.0 CG B:HIS119 4.6 37.4 0.5 O A:ALA22 4.7 61.3 1.0 O B:LYS118 4.7 43.8 1.0 CA A:ASP20 4.9 52.6 0.5 CA A:ASP20 4.9 54.6 0.5

Zinc binding site 5 out of 5 in the The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Zn-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:27.5 occ:1.00 ND1 A:HIS79 2.0 26.6 1.0 NE2 B:HIS82 2.0 27.0 1.0 OD1 B:ASP141 2.0 27.8 1.0 O A:HOH349 2.1 19.9 1.0 CE1 B:HIS82 2.8 27.6 1.0 CE1 A:HIS79 2.9 29.8 1.0 CG A:HIS79 3.0 27.7 1.0 CG B:ASP141 3.1 25.9 1.0 CD2 B:HIS82 3.1 28.7 1.0 CB A:HIS79 3.4 29.3 1.0 CB B:ASP141 3.5 25.5 1.0 ND1 B:HIS82 4.0 29.7 1.0 NE2 A:HIS79 4.1 30.6 1.0 CD2 A:HIS79 4.1 29.7 1.0 CG B:HIS82 4.2 30.0 1.0 OD2 B:ASP141 4.2 27.9 1.0 CD2 B:LEU86 4.3 41.1 1.0 CA A:HIS79 4.4 27.5 1.0 O A:HOH313 4.6 44.3 1.0 O B:LEU137 4.7 28.2 1.0 CD1 B:LEU86 4.8 43.7 1.0 CA B:PHE138 4.8 24.4 1.0 CG2 A:ILE75 4.9 31.7 1.0

S.Nagao, A.Idomoto, N.Shibata, Y.Higuchi, S.Hirota. Rational Design of Metal-Binding Sites in Domain-Swapped Myoglobin Dimers. J.Inorg.Biochem. 2021.
ISSN: ISSN 0162-0134
DOI: 10.1016/J.JINORGBIO.2021.111374