Zinc in PDB 9j9o: Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN)

The structure of Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN), PDB code: 9j9o was solved by W.J.Jeong, W.J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.28 / 2.99
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	137.8, 137.8, 49.545, 90, 90, 120
R / Rfree (%)	19.2 / 23.9

The binding sites of Zinc atom in the Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN) (pdb code 9j9o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN), PDB code: 9j9o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:108.4 occ:0.79 OE1 A:GLU83 2.3 84.7 1.0 NE2 A:HIS60 2.4 71.0 1.0 ND1 A:HIS62 2.5 106.3 1.0 CD A:GLU83 3.1 82.8 1.0 CG A:HIS62 3.2 98.7 1.0 CE1 A:HIS60 3.2 78.8 1.0 CE1 A:HIS62 3.3 101.8 1.0 OE2 A:GLU83 3.3 88.0 1.0 CD2 A:HIS60 3.4 70.6 1.0 CB A:HIS62 3.6 92.5 1.0 CD2 A:HIS62 4.1 100.0 1.0 NE2 A:HIS62 4.1 110.7 1.0 ND1 A:HIS60 4.3 86.4 1.0 CG A:HIS60 4.4 74.6 1.0 CG A:GLU83 4.5 78.6 1.0 CB A:GLU83 4.8 77.1 1.0 NZ A:LYS46 4.9 92.7 1.0

Zinc binding site 2 out of 4 in the Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:100.2 occ:1.00 NE2 A:HIS132 2.1 69.6 1.0 NE2 A:HIS102 2.1 81.6 1.0 OE2 A:GLU83 2.6 88.0 1.0 CE1 A:HIS132 2.7 68.6 1.0 CE1 A:HIS102 2.8 81.6 1.0 CD2 A:HIS102 3.2 90.3 1.0 CD2 A:HIS132 3.3 72.5 1.0 CD A:GLU83 3.8 82.8 1.0 ND1 A:HIS132 3.9 70.0 1.0 ND1 A:HIS102 4.0 84.2 1.0 CG A:HIS102 4.2 70.6 1.0 CG A:HIS132 4.3 74.4 1.0 CG A:GLU83 4.5 78.6 1.0 NE A:ARG82 4.8 106.1 1.0 OE1 A:GLU83 4.8 84.7 1.0

Zinc binding site 3 out of 4 in the Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:102.2 occ:0.78 OE1 B:GLU83 2.3 85.8 1.0 NE2 B:HIS60 2.4 70.2 1.0 ND1 B:HIS62 2.4 105.9 1.0 CD B:GLU83 3.1 82.4 1.0 CE1 B:HIS62 3.2 94.1 1.0 CG B:HIS62 3.2 93.4 1.0 CE1 B:HIS60 3.3 72.2 1.0 OE2 B:GLU83 3.3 83.8 1.0 CD2 B:HIS60 3.4 68.2 1.0 CB B:HIS62 3.6 84.7 1.0 NE2 B:HIS62 4.1 101.2 1.0 CD2 B:HIS62 4.1 97.0 1.0 ND1 B:HIS60 4.3 87.7 1.0 CG B:HIS60 4.4 75.0 1.0 CG B:GLU83 4.5 77.4 1.0 CB B:GLU83 4.8 71.6 1.0 NZ B:LYS46 4.9 78.7 1.0

Zinc binding site 4 out of 4 in the Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Artificial Dinuclear Zn-Bound Metalloprotein 1 (D1:2ZN) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:85.8 occ:1.00 NE2 B:HIS132 2.0 76.1 1.0 NE2 B:HIS102 2.2 79.7 1.0 OE2 B:GLU83 2.5 83.8 1.0 CE1 B:HIS132 2.7 69.6 1.0 CE1 B:HIS102 2.8 80.8 1.0 CD2 B:HIS132 3.2 71.6 1.0 CD2 B:HIS102 3.3 84.5 1.0 CD B:GLU83 3.7 82.4 1.0 ND1 B:HIS132 3.9 70.6 1.0 ND1 B:HIS102 3.9 83.5 1.0 NH2 B:ARG82 4.1 105.9 1.0 CG B:HIS132 4.2 67.9 1.0 CG B:HIS102 4.2 71.3 1.0 CG B:GLU83 4.3 77.4 1.0 OE1 B:GLU83 4.7 85.8 1.0 CZ B:ARG82 4.8 100.7 1.0

W.J.Jeong, W.J.Song. Metal-Installer: A Protein Designer Tool to Create Metal-Binding Sites To Be Published.