Zinc in PDB 7uni: De Novo Designed Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam

The structure of De Novo Designed Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam, PDB code: 7uni was solved by M.A.Kennedy, B.L.Stoddard, N.M.Ennist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.26 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.855, 54.961, 89.365, 87.83, 84.06, 69.45
R / Rfree (%)	19.9 / 25.2

The binding sites of Zinc atom in the De Novo Designed Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam (pdb code 7uni). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the De Novo Designed Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam, PDB code: 7uni:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the De Novo Designed Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam


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 Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:47.9 occ:1.00 ZN1 A:OE9301 0.0 47.9 1.0 N4 A:OE9301 2.0 49.1 1.0 N2 A:OE9301 2.1 49.0 1.0 N3 A:OE9301 2.1 55.5 1.0 N1 A:OE9301 2.2 51.0 1.0 NE2 A:HIS178 2.5 50.1 1.0 C30 A:OE9301 3.0 46.2 1.0 CE1 A:HIS178 3.0 51.5 1.0 C23 A:OE9301 3.1 50.8 1.0 C13 A:OE9301 3.1 47.9 1.0 C20 A:OE9301 3.1 50.7 1.0 C27 A:OE9301 3.1 51.6 1.0 C16 A:OE9301 3.1 50.7 1.0 C8 A:OE9301 3.2 45.9 1.0 C5 A:OE9301 3.2 47.5 1.0 C2 A:OE9301 3.4 44.7 1.0 C3 A:OE9301 3.4 53.2 1.0 C4 A:OE9301 3.5 45.6 1.0 C10 B:OE9301 3.5 46.2 1.0 C1 A:OE9301 3.5 46.1 1.0 CD2 A:HIS178 3.7 45.5 1.0 C11 B:OE9301 4.2 49.2 1.0 C29 A:OE9301 4.2 47.1 1.0 ND1 A:HIS178 4.2 52.9 1.0 C14 A:OE9301 4.3 47.1 1.0 C28 A:OE9301 4.3 50.8 1.0 C22 A:OE9301 4.3 55.4 1.0 C21 A:OE9301 4.3 54.4 1.0 C15 A:OE9301 4.3 48.7 1.0 CE A:MET182 4.4 47.8 1.0 C7 A:OE9301 4.5 52.4 1.0 C6 A:OE9301 4.5 51.0 1.0 CG A:HIS178 4.6 49.0 1.0 C6 B:OE9301 4.8 52.5 1.0 C5 B:OE9301 4.9 50.1 1.0 C35 A:OE9301 4.9 51.0 1.0 C1 B:OE9301 4.9 45.4 1.0 C33 B:OE9301 4.9 49.0 1.0

Zinc binding site 2 out of 4 in the De Novo Designed Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam


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 Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:100.0 occ:1.00 ZN1 C:OE9301 0.0 100.0 1.0 N4 C:OE9301 2.0 88.1 1.0 N2 C:OE9301 2.1 91.0 1.0 N3 C:OE9301 2.1 91.0 1.0 N1 C:OE9301 2.3 91.0 1.0 CE1 C:HIS178 2.6 86.2 1.0 NE2 C:HIS178 2.7 85.9 1.0 C30 C:OE9301 3.0 86.6 1.0 C13 C:OE9301 3.1 91.3 1.0 C23 C:OE9301 3.1 90.2 1.0 C27 C:OE9301 3.1 86.8 1.0 C20 C:OE9301 3.1 89.4 1.0 C16 C:OE9301 3.2 88.9 1.0 C8 C:OE9301 3.2 92.5 1.0 C5 C:OE9301 3.3 88.9 1.0 C2 C:OE9301 3.5 91.4 1.0 C3 C:OE9301 3.5 88.1 1.0 C4 C:OE9301 3.5 89.3 1.0 C1 C:OE9301 3.5 87.0 1.0 C10 D:OE9301 3.5 86.6 1.0 C11 D:OE9301 3.7 88.9 1.0 ND1 C:HIS178 3.8 79.3 1.0 CD2 C:HIS178 4.0 82.6 1.0 C29 C:OE9301 4.2 88.3 1.0 C14 C:OE9301 4.3 94.2 1.0 C28 C:OE9301 4.3 85.3 1.0 C22 C:OE9301 4.3 92.0 1.0 C15 C:OE9301 4.3 91.8 1.0 C21 C:OE9301 4.4 90.2 1.0 SD C:MET182 4.5 86.0 1.0 CG C:HIS178 4.6 75.6 1.0 C7 C:OE9301 4.6 91.6 1.0 C6 C:OE9301 4.6 91.8 1.0 C12 D:OE9301 4.7 87.7 1.0 C6 D:OE9301 4.8 85.6 1.0 O1 D:OE9301 4.8 89.8 1.0 C5 D:OE9301 4.9 85.0 1.0 C33 C:OE9301 5.0 87.4 1.0

Zinc binding site 3 out of 4 in the De Novo Designed Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam


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 Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:42.6 occ:1.00 ZN1 B:OE9301 0.0 42.6 1.0 N4 B:OE9301 2.0 46.1 1.0 N2 B:OE9301 2.0 42.8 1.0 N3 B:OE9301 2.1 47.0 1.0 N1 B:OE9301 2.3 49.3 1.0 NE2 B:HIS178 2.3 46.6 1.0 CE1 B:HIS178 2.8 49.0 1.0 C30 B:OE9301 3.0 43.1 1.0 C13 B:OE9301 3.1 44.0 1.0 C16 B:OE9301 3.1 41.8 1.0 C23 B:OE9301 3.1 46.4 1.0 C20 B:OE9301 3.1 43.4 1.0 C27 B:OE9301 3.1 45.7 1.0 C8 B:OE9301 3.2 46.1 1.0 C5 B:OE9301 3.3 50.1 1.0 C3 B:OE9301 3.4 41.6 1.0 C2 B:OE9301 3.5 45.3 1.0 C4 B:OE9301 3.5 47.9 1.0 C10 A:OE9301 3.5 47.1 1.0 CD2 B:HIS178 3.5 45.4 1.0 C1 B:OE9301 3.6 45.4 1.0 ND1 B:HIS178 4.1 46.6 1.0 C29 B:OE9301 4.2 49.1 1.0 C11 A:OE9301 4.2 47.1 1.0 C14 B:OE9301 4.2 44.8 1.0 C15 B:OE9301 4.3 45.2 1.0 C28 B:OE9301 4.3 43.5 1.0 C22 B:OE9301 4.3 45.1 1.0 C21 B:OE9301 4.3 46.2 1.0 CG B:HIS178 4.5 42.7 1.0 C7 B:OE9301 4.6 48.7 1.0 C6 B:OE9301 4.6 52.5 1.0 C6 A:OE9301 4.8 51.0 1.0 C5 A:OE9301 4.9 47.5 1.0

Zinc binding site 4 out of 4 in the De Novo Designed Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam


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 Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:84.1 occ:1.00 ZN1 D:OE9301 0.0 84.1 1.0 N4 D:OE9301 2.0 82.5 1.0 N2 D:OE9301 2.1 78.9 1.0 N3 D:OE9301 2.1 75.9 1.0 N1 D:OE9301 2.3 83.0 1.0 NE2 D:HIS178 2.5 77.9 1.0 C30 D:OE9301 3.0 84.4 1.0 C13 D:OE9301 3.1 77.5 1.0 C23 D:OE9301 3.1 78.2 1.0 C20 D:OE9301 3.1 78.3 1.0 C27 D:OE9301 3.1 82.3 1.0 C16 D:OE9301 3.2 79.0 1.0 C8 D:OE9301 3.2 81.0 1.0 C10 C:OE9301 3.2 85.4 1.0 C5 D:OE9301 3.2 85.0 1.0 CD2 D:HIS178 3.4 71.5 1.0 C2 D:OE9301 3.4 79.0 1.0 CE1 D:HIS178 3.5 73.8 1.0 C4 D:OE9301 3.5 80.2 1.0 C3 D:OE9301 3.5 76.5 1.0 C1 D:OE9301 3.5 85.9 1.0 C29 D:OE9301 4.2 84.7 1.0 C14 D:OE9301 4.3 77.7 1.0 C28 D:OE9301 4.3 84.5 1.0 C22 D:OE9301 4.3 78.4 1.0 C21 D:OE9301 4.3 77.2 1.0 C15 D:OE9301 4.4 79.5 1.0 C6 C:OE9301 4.4 91.8 1.0 C7 D:OE9301 4.5 82.9 1.0 CG D:HIS178 4.6 64.5 1.0 C6 D:OE9301 4.6 85.6 1.0 ND1 D:HIS178 4.6 70.9 1.0 C5 C:OE9301 4.6 88.9 1.0 C1 C:OE9301 4.8 87.0 1.0 C33 C:OE9301 4.9 87.4 1.0 C7 C:OE9301 5.0 91.6 1.0

M.A.Kennedy, B.L.Stoddard, N.M.Ennist. De Novo Designed Chlorophyll Dimer Protein with Zn Pheophorbide A Methyl Ester, SP2-Znppam To Be Published.