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Zinc in PDB 5vjs: De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations

Protein crystallography data

The structure of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations, PDB code: 5vjs was solved by N.M.Ennist, P.L.Dutton, S.E.Stayrook, C.C.Moser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.43 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 43.749, 43.749, 245.737, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 27.8

Other elements in 5vjs:

The structure of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations (pdb code 5vjs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations, PDB code: 5vjs:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5vjs

Go back to Zinc Binding Sites List in 5vjs
Zinc binding site 1 out of 3 in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:33.9
occ:0.70
ZN A:9D7202 0.0 33.9 0.7
CD2 A:HIS124 1.9 29.6 1.0
NB A:9D7202 2.1 41.4 0.7
NC A:9D7202 2.1 37.6 0.7
NE2 A:HIS124 2.1 32.0 1.0
ND A:9D7202 2.1 35.6 0.7
NA A:9D7202 2.1 38.2 0.7
C4C A:9D7202 3.1 35.4 0.7
C1B A:9D7202 3.1 42.6 0.7
C4A A:9D7202 3.1 39.6 0.7
C1C A:9D7202 3.1 35.0 0.7
C4B A:9D7202 3.1 39.3 0.7
C1D A:9D7202 3.1 38.9 0.7
C4D A:9D7202 3.2 37.3 0.7
C1A A:9D7202 3.2 34.1 0.7
CG A:HIS124 3.2 33.6 1.0
CE1 A:HIS124 3.4 33.5 1.0
CD2 A:LEU171 3.4 62.6 1.0
CHB A:9D7202 3.5 41.0 0.7
CHD A:9D7202 3.5 36.6 0.7
CHC A:9D7202 3.5 39.3 0.7
CHA A:9D7202 3.6 37.0 0.7
CG2 A:ILE23 3.8 37.8 1.0
ND1 A:HIS124 3.9 37.6 1.0
CB A:HIS124 4.3 40.0 1.0
CD2 A:LEU74 4.3 42.8 1.0
C3C A:9D7202 4.3 40.4 0.7
C2C A:9D7202 4.3 36.6 0.7
C2B A:9D7202 4.3 39.3 0.7
C3B A:9D7202 4.4 40.1 0.7
C3A A:9D7202 4.4 41.0 0.7
C2A A:9D7202 4.4 39.7 0.7
C3D A:9D7202 4.4 37.7 0.7
C2D A:9D7202 4.4 38.0 0.7
CG A:LEU171 4.7 59.3 1.0
CD1 A:LEU171 4.8 59.7 1.0
O A:HIS124 4.8 45.5 1.0
CBE A:9D7202 5.0 40.7 0.7

Zinc binding site 2 out of 3 in 5vjs

Go back to Zinc Binding Sites List in 5vjs
Zinc binding site 2 out of 3 in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:30.5
occ:1.00
NE2 A:HIS138 2.0 21.0 1.0
OD2 A:ASP63 2.0 34.2 1.0
OD1 A:ASP134 2.0 34.4 1.0
CL A:CL207 2.4 34.9 1.0
CG A:ASP134 2.8 35.9 1.0
CG A:ASP63 2.9 30.2 1.0
CD2 A:HIS138 2.9 24.3 1.0
OD2 A:ASP134 2.9 36.6 1.0
CE1 A:HIS138 3.0 25.9 1.0
CB A:ASP63 3.1 26.7 1.0
CG A:HIS138 4.0 24.8 1.0
OD1 A:ASP63 4.0 35.1 1.0
O A:ASP134 4.1 25.1 1.0
ND1 A:HIS138 4.1 23.5 1.0
CE A:LYS59 4.1 37.5 1.0
CB A:ASP134 4.1 29.7 1.0
CA A:ASP134 4.5 24.2 1.0
C A:ASP134 4.6 22.4 1.0
NZ A:LYS59 4.7 40.1 1.0
CA A:ASP63 4.7 24.6 1.0
O A:LYS59 4.8 22.5 1.0
CD A:LYS59 4.9 38.5 1.0
CB A:LYS137 4.9 32.2 1.0

Zinc binding site 3 out of 3 in 5vjs

Go back to Zinc Binding Sites List in 5vjs
Zinc binding site 3 out of 3 in the De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, A Synthetic Zn Porphyrin, and Zn(II) Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:53.6
occ:1.00
OE1 A:GLU34 2.0 50.8 1.0
OE1 A:GLU64 2.0 37.6 1.0
OE1 A:GLU135 2.1 45.1 1.0
ND1 A:HIS67 2.1 32.1 1.0
CD A:GLU34 2.7 51.6 1.0
OE2 A:GLU34 2.9 59.2 1.0
CD A:GLU64 3.0 34.5 1.0
CE1 A:HIS67 3.0 31.9 1.0
CD A:GLU135 3.0 40.9 1.0
CG A:HIS67 3.2 29.6 1.0
OE2 A:GLU64 3.3 43.9 1.0
OE2 A:GLU135 3.3 49.3 1.0
CB A:HIS67 3.6 27.0 1.0
OH A:TYR168 3.9 53.9 1.0
O A:HOH305 4.1 39.8 1.0
CG A:GLU34 4.1 45.7 1.0
NE2 A:HIS67 4.1 28.6 1.0
CD2 A:HIS67 4.2 29.2 1.0
CG A:GLU64 4.3 31.0 1.0
CG A:GLU135 4.4 37.8 1.0
CG2 A:ILE131 4.5 29.9 1.0
CA A:GLU64 4.5 24.4 1.0
CE2 A:TYR168 4.6 44.9 1.0
CZ A:TYR168 4.6 52.0 1.0
CB A:GLU64 4.6 26.8 1.0
O A:GLU64 4.8 22.6 1.0
CB A:GLU135 4.8 28.4 1.0
OE2 A:GLU161 4.9 61.3 1.0

Reference:

N.M.Ennist, Z.Zhao, S.E.Stayrook, P.L.Dutton, C.C.Moser. Design, Structure, and Action of An Artificial Photosynthetic Reaction Center Protein To Be Published.
Page generated: Wed Dec 16 11:10:48 2020

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