Zinc in PDB 7jh6: De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein

The structure of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein, PDB code: 7jh6 was solved by N.Schmidt, L.Liu, W.F.Degrado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.24 / 3.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.478, 27.825, 188.494, 90.00, 117.16, 90.00
R / Rfree (%)	26.1 / 28.3

The structure of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein also contains other interesting chemical elements:

Fluorine

(F)

48 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein (pdb code 7jh6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein, PDB code: 7jh6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:0.7 occ:1.00 OE1 A:GLU165 2.0 0.8 1.0 ND1 A:HIS168 2.1 0.5 1.0 OE1 A:GLU13 2.2 0.6 1.0 OE2 A:GLU100 2.4 0.6 1.0 OE2 A:GLU13 2.4 0.5 1.0 CD A:GLU13 2.6 0.1 1.0 CD A:GLU100 2.8 0.6 1.0 CE1 A:HIS168 2.9 0.2 1.0 CD A:GLU165 3.1 0.8 1.0 CG A:HIS168 3.2 0.8 1.0 OE1 A:GLU100 3.2 0.9 1.0 CG A:GLU100 3.6 1.0 1.0 OE2 A:GLU165 3.6 0.3 1.0 CB A:HIS168 3.7 0.8 1.0 ZN A:ZN202 3.8 0.3 1.0 NE2 A:HIS168 4.0 0.7 1.0 CG A:GLU13 4.2 0.9 1.0 CD2 A:HIS168 4.2 0.4 1.0 CA A:GLU165 4.2 0.7 1.0 CG A:GLU165 4.3 0.2 1.0 CG2 A:ILE96 4.4 0.3 1.0 CE1 A:HIS103 4.5 0.1 1.0 ND1 A:HIS103 4.6 0.2 1.0 CB A:GLU165 4.6 0.6 1.0 O A:ASP164 4.9 0.3 1.0 CB A:GLU13 4.9 0.2 1.0 O A:GLU165 4.9 0.1 1.0 CB A:GLU100 4.9 0.5 1.0 N A:GLU165 5.0 0.1 1.0 OH A:TYR81 5.0 0.7 1.0

Zinc binding site 2 out of 12 in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:0.3 occ:1.00 OE1 A:GLU100 2.0 0.9 1.0 OE2 A:GLU74 2.1 0.4 1.0 ND1 A:HIS103 2.1 0.2 1.0 OE2 A:GLU165 2.1 0.3 1.0 CD A:GLU74 2.7 0.1 1.0 CD A:GLU165 2.8 0.8 1.0 OE1 A:GLU74 2.8 0.3 1.0 CE1 A:HIS103 3.0 0.1 1.0 CG A:HIS103 3.1 1.0 1.0 CD A:GLU100 3.1 0.6 1.0 OE1 A:GLU165 3.3 0.8 1.0 CB A:HIS103 3.4 0.3 1.0 ZN A:ZN201 3.8 0.7 1.0 OE2 A:GLU100 3.8 0.6 1.0 CG A:GLU165 3.8 0.2 1.0 CG2 A:ILE161 3.9 0.6 1.0 CG A:GLU74 4.1 0.6 1.0 NE2 A:HIS103 4.1 0.9 1.0 CD2 A:HIS103 4.2 0.2 1.0 CG A:GLU100 4.2 1.0 1.0 CA A:GLU100 4.3 0.3 1.0 CB A:GLU100 4.6 0.5 1.0 OH A:TYR20 4.7 0.7 1.0 CB A:GLU74 4.8 0.7 1.0 O A:GLU100 5.0 0.8 1.0 CE1 A:HIS168 5.0 0.2 1.0 CA A:HIS103 5.0 0.2 1.0

Zinc binding site 3 out of 12 in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:0.2 occ:1.00 ZN A:7BU203 0.0 0.2 1.0 ND4 A:7BU203 2.1 0.3 1.0 NE2 A:HIS63 2.1 0.4 1.0 NB2 A:7BU203 2.1 0.2 1.0 NA1 A:7BU203 2.1 0.1 1.0 NC3 A:7BU203 2.1 0.7 1.0 CD2 A:HIS63 3.0 0.0 1.0 C4D A:7BU203 3.0 0.8 1.0 C4B A:7BU203 3.1 1.0 1.0 C1D A:7BU203 3.1 0.1 1.0 C1A A:7BU203 3.1 0.5 1.0 CE1 A:HIS63 3.1 0.3 1.0 C1B A:7BU203 3.1 0.4 1.0 C1C A:7BU203 3.1 0.8 1.0 C4C A:7BU203 3.1 0.1 1.0 C4A A:7BU203 3.1 0.1 1.0 CHA A:7BU203 3.4 0.9 1.0 CHC A:7BU203 3.5 0.5 1.0 CHD A:7BU203 3.5 0.6 1.0 CHB A:7BU203 3.5 1.0 1.0 CG A:HIS63 4.1 0.1 1.0 ND1 A:HIS63 4.2 0.9 1.0 C3D A:7BU203 4.2 0.2 1.0 C2D A:7BU203 4.2 0.9 1.0 C3B A:7BU203 4.3 0.0 1.0 C2B A:7BU203 4.3 0.7 1.0 C2A A:7BU203 4.3 0.9 1.0 C2C A:7BU203 4.3 0.6 1.0 C3C A:7BU203 4.3 0.1 1.0 C3A A:7BU203 4.3 0.2 1.0 CG2 A:ILE150 4.7 0.1 1.0 C1FA A:7BU203 4.8 0.5 1.0 C1FC A:7BU203 4.9 0.3 1.0

Zinc binding site 4 out of 12 in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:0.5 occ:1.00 OE1 B:GLU165 1.9 0.5 1.0 ND1 B:HIS168 2.0 0.6 1.0 OE1 B:GLU13 2.2 0.9 1.0 OE2 B:GLU13 2.5 0.3 1.0 OE2 B:GLU100 2.6 0.5 1.0 CD B:GLU13 2.6 0.1 1.0 CE1 B:HIS168 2.7 0.8 1.0 CD B:GLU100 2.9 0.1 1.0 CG B:HIS168 3.0 0.9 1.0 CD B:GLU165 3.1 0.5 1.0 OE1 B:GLU100 3.4 0.3 1.0 CB B:HIS168 3.5 0.1 1.0 OE2 B:GLU165 3.7 0.5 1.0 CG B:GLU100 3.7 0.3 1.0 ZN B:ZN202 3.8 0.7 1.0 NE2 B:HIS168 3.9 0.8 1.0 CD2 B:HIS168 4.0 0.0 1.0 CA B:GLU165 4.1 0.1 1.0 CG B:GLU13 4.1 0.1 1.0 CG B:GLU165 4.2 0.4 1.0 CG2 B:ILE96 4.4 1.0 1.0 CE1 B:HIS103 4.5 0.6 1.0 CB B:GLU165 4.5 0.0 1.0 ND1 B:HIS103 4.6 0.6 1.0 O B:ASP164 4.7 0.4 1.0 O B:GLU165 4.8 0.4 1.0 N B:GLU165 4.8 0.8 1.0 CB B:GLU13 4.9 0.7 1.0 OH B:TYR81 5.0 0.7 1.0 C B:GLU165 5.0 0.4 1.0

Zinc binding site 5 out of 12 in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:0.7 occ:1.00 OE2 B:GLU165 1.9 0.5 1.0 ND1 B:HIS103 2.0 0.6 1.0 OE2 B:GLU74 2.2 0.5 1.0 OE1 B:GLU100 2.3 0.3 1.0 CD B:GLU165 2.5 0.5 1.0 CE1 B:HIS103 2.8 0.6 1.0 CD B:GLU74 2.9 0.2 1.0 OE1 B:GLU74 3.0 0.2 1.0 OE1 B:GLU165 3.1 0.5 1.0 CG B:HIS103 3.1 0.3 1.0 CD B:GLU100 3.4 0.1 1.0 CG B:GLU165 3.5 0.4 1.0 CB B:HIS103 3.5 0.5 1.0 CG2 B:ILE161 3.7 0.6 1.0 ZN B:ZN201 3.8 0.5 1.0 OE2 B:GLU100 4.0 0.5 1.0 NE2 B:HIS103 4.0 0.9 1.0 CD2 B:HIS103 4.1 0.8 1.0 CG B:GLU74 4.3 0.2 1.0 CG B:GLU100 4.4 0.3 1.0 CA B:GLU100 4.5 0.4 1.0 OH B:TYR20 4.7 0.1 1.0 CB B:GLU100 4.9 0.3 1.0 CB B:GLU165 4.9 0.0 1.0 CE1 B:HIS168 4.9 0.8 1.0 OE1 B:GLU13 5.0 0.9 1.0 CB B:ILE161 5.0 0.0 1.0 ND1 B:HIS168 5.0 0.6 1.0

Zinc binding site 6 out of 12 in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:0.0 occ:1.00 ZN B:7BU203 0.0 0.0 1.0 NE2 B:HIS63 2.1 0.4 1.0 ND4 B:7BU203 2.1 0.6 1.0 NB2 B:7BU203 2.1 0.7 1.0 NA1 B:7BU203 2.1 0.7 1.0 NC3 B:7BU203 2.2 0.2 1.0 CE1 B:HIS63 3.0 0.6 1.0 CD2 B:HIS63 3.0 0.2 1.0 C4D B:7BU203 3.1 0.7 1.0 C4B B:7BU203 3.1 0.2 1.0 C1A B:7BU203 3.1 0.8 1.0 C1B B:7BU203 3.1 0.5 1.0 C4A B:7BU203 3.1 0.8 1.0 C1D B:7BU203 3.1 0.4 1.0 C1C B:7BU203 3.1 0.8 1.0 C4C B:7BU203 3.1 0.1 1.0 CHA B:7BU203 3.5 0.4 1.0 CHC B:7BU203 3.5 0.5 1.0 CHB B:7BU203 3.5 1.0 1.0 CHD B:7BU203 3.6 0.7 1.0 ND1 B:HIS63 4.1 0.9 1.0 CG B:HIS63 4.1 0.6 1.0 C3D B:7BU203 4.2 0.7 1.0 C2D B:7BU203 4.3 0.2 1.0 C3B B:7BU203 4.3 0.9 1.0 C2B B:7BU203 4.3 0.5 1.0 C3A B:7BU203 4.3 0.9 1.0 C2A B:7BU203 4.3 0.6 1.0 C2C B:7BU203 4.3 0.7 1.0 C3C B:7BU203 4.3 0.8 1.0 CG2 B:ILE150 4.7 1.0 1.0 C1FA B:7BU203 4.9 0.2 1.0 C1FC B:7BU203 4.9 0.7 1.0 C1FB B:7BU203 5.0 0.3 1.0

Zinc binding site 7 out of 12 in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:0.5 occ:1.00 OE1 C:GLU13 1.9 1.0 1.0 OE1 C:GLU165 2.0 0.6 1.0 OE2 C:GLU13 2.2 0.2 1.0 ND1 C:HIS168 2.2 0.3 1.0 CD C:GLU13 2.3 0.9 1.0 OE2 C:GLU100 2.4 0.1 1.0 CD C:GLU100 2.9 0.6 1.0 CE1 C:HIS168 3.1 0.5 1.0 CD C:GLU165 3.2 0.1 1.0 CG C:HIS168 3.2 0.6 1.0 OE1 C:GLU100 3.4 0.7 1.0 CB C:HIS168 3.6 0.4 1.0 OE2 C:GLU165 3.7 0.2 1.0 CG C:GLU100 3.7 0.9 1.0 CG C:GLU13 3.8 0.0 1.0 ZN C:ZN202 4.1 1.0 1.0 NE2 C:HIS168 4.1 0.7 1.0 CD2 C:HIS168 4.2 0.1 1.0 CA C:GLU165 4.3 0.1 1.0 CG2 C:ILE96 4.3 0.7 1.0 CG C:GLU165 4.4 0.6 1.0 CB C:GLU13 4.6 0.9 1.0 CB C:GLU165 4.7 0.9 1.0 OH C:TYR81 4.8 0.5 1.0 CE1 C:HIS103 4.8 0.1 1.0 O C:GLU165 4.8 0.8 1.0 ND1 C:HIS103 4.9 0.1 1.0 CE2 C:TYR81 5.0 0.7 1.0 O C:ASP164 5.0 0.1 1.0

Zinc binding site 8 out of 12 in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:1.0 occ:1.00 OE2 C:GLU74 2.0 0.2 1.0 OE1 C:GLU100 2.0 0.7 1.0 ND1 C:HIS103 2.1 0.1 1.0 OE2 C:GLU165 2.2 0.2 1.0 CD C:GLU74 2.6 0.8 1.0 OE1 C:GLU74 2.8 0.8 1.0 CD C:GLU165 2.9 0.1 1.0 CG C:HIS103 3.0 0.9 1.0 CE1 C:HIS103 3.1 0.1 1.0 CD C:GLU100 3.2 0.6 1.0 CB C:HIS103 3.3 0.5 1.0 OE1 C:GLU165 3.4 0.6 1.0 OE2 C:GLU100 3.8 0.1 1.0 CG C:GLU165 4.0 0.6 1.0 CG C:GLU74 4.0 0.2 1.0 CG2 C:ILE161 4.0 0.2 1.0 ZN C:ZN201 4.1 0.5 1.0 NE2 C:HIS103 4.2 0.7 1.0 CD2 C:HIS103 4.2 0.9 1.0 CA C:GLU100 4.2 0.0 1.0 CG C:GLU100 4.2 0.9 1.0 CB C:GLU100 4.5 0.4 1.0 CB C:GLU74 4.6 0.1 1.0 OH C:TYR20 4.7 0.3 1.0 O C:GLU100 4.8 0.8 1.0 CA C:HIS103 4.9 0.6 1.0 N C:GLU100 5.0 0.7 1.0

Zinc binding site 9 out of 12 in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:1.0 occ:1.00 ZN C:7BU203 0.0 1.0 1.0 ND4 C:7BU203 2.1 0.6 1.0 NB2 C:7BU203 2.1 0.8 1.0 NA1 C:7BU203 2.1 0.5 1.0 NE2 C:HIS63 2.1 0.7 1.0 NC3 C:7BU203 2.2 0.2 1.0 CE1 C:HIS63 3.0 0.3 1.0 C4D C:7BU203 3.0 0.7 1.0 C1D C:7BU203 3.1 0.1 1.0 C1A C:7BU203 3.1 0.4 1.0 C1B C:7BU203 3.1 1.0 1.0 C4A C:7BU203 3.1 0.7 1.0 C4B C:7BU203 3.1 0.7 1.0 C4C C:7BU203 3.1 0.3 1.0 C1C C:7BU203 3.2 0.8 1.0 CD2 C:HIS63 3.2 0.1 1.0 CHA C:7BU203 3.4 0.3 1.0 CHB C:7BU203 3.5 0.6 1.0 CHD C:7BU203 3.5 0.1 1.0 CHC C:7BU203 3.6 0.2 1.0 ND1 C:HIS63 4.1 0.8 1.0 C3D C:7BU203 4.2 0.2 1.0 C2D C:7BU203 4.2 0.2 1.0 CG C:HIS63 4.2 1.0 1.0 C3A C:7BU203 4.3 0.2 1.0 C2B C:7BU203 4.3 0.3 1.0 C2A C:7BU203 4.3 0.8 1.0 C3B C:7BU203 4.3 0.9 1.0 C3C C:7BU203 4.3 0.8 1.0 C2C C:7BU203 4.3 0.0 1.0 CB C:THR154 4.7 0.5 1.0 CG2 C:ILE150 4.8 0.3 1.0 C1FA C:7BU203 4.8 0.4 1.0 C1FB C:7BU203 5.0 0.0 1.0 C1FC C:7BU203 5.0 0.4 1.0

Zinc binding site 10 out of 12 in the De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:0.1 occ:1.00 OE1 D:GLU165 2.0 0.9 1.0 OE1 D:GLU13 2.1 0.5 1.0 OE2 D:GLU13 2.3 0.3 1.0 ND1 D:HIS168 2.3 0.0 1.0 OE2 D:GLU100 2.3 0.1 1.0 CD D:GLU13 2.5 0.4 1.0 CD D:GLU100 2.8 0.8 1.0 CE1 D:HIS168 3.0 0.7 1.0 CD D:GLU165 3.1 0.4 1.0 OE1 D:GLU100 3.3 0.9 1.0 CG D:HIS168 3.3 0.1 1.0 CG D:GLU100 3.6 0.6 1.0 OE2 D:GLU165 3.7 0.7 1.0 CB D:HIS168 3.7 0.3 1.0 ZN D:ZN202 3.8 0.1 1.0 CG D:GLU13 4.0 0.3 1.0 NE2 D:HIS168 4.1 0.4 1.0 CD2 D:HIS168 4.3 0.3 1.0 CG2 D:ILE96 4.3 0.2 1.0 CA D:GLU165 4.3 0.1 1.0 CG D:GLU165 4.4 0.1 1.0 CE1 D:HIS103 4.7 0.3 1.0 CB D:GLU165 4.7 0.5 1.0 ND1 D:HIS103 4.8 0.9 1.0 CB D:GLU13 4.8 0.2 1.0 OH D:TYR81 4.8 0.0 1.0 CE2 D:TYR81 4.9 0.4 1.0 O D:GLU165 5.0 0.4 1.0

N.Schmidt, L.Liu, W.F.Degrado. De Novo Designed Two-Domain Di-Zn(II) and Porphyrin-Binding Protein To Be Published.