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Zinc in PDB 2w88: Plastocyanin Variant with N-Terminal Methionine - Open Structure

Protein crystallography data

The structure of Plastocyanin Variant with N-Terminal Methionine - Open Structure, PDB code: 2w88 was solved by P.B.Crowley, P.M.Matias, A.R.Khan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 110.43 / 2.89
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 127.700, 127.700, 94.990, 90.00, 90.00, 120.00
R / Rfree (%) 19.433 / 22.285

Other elements in 2w88:

The structure of Plastocyanin Variant with N-Terminal Methionine - Open Structure also contains other interesting chemical elements:

Copper (Cu) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Plastocyanin Variant with N-Terminal Methionine - Open Structure (pdb code 2w88). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Plastocyanin Variant with N-Terminal Methionine - Open Structure, PDB code: 2w88:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2w88

Go back to Zinc Binding Sites List in 2w88
Zinc binding site 1 out of 7 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn107

b:30.4
occ:1.00
OD1 B:ASP44 2.0 28.1 1.0
OD1 B:ASP45 2.0 29.5 1.0
NE2 A:HIS61 2.1 29.2 1.0
CG B:ASP44 2.8 27.6 1.0
OD2 B:ASP44 2.8 27.9 1.0
CG B:ASP45 3.0 28.4 1.0
CE1 A:HIS61 3.1 29.6 1.0
CD2 A:HIS61 3.1 30.0 1.0
OD2 B:ASP45 3.3 29.9 1.0
ND1 A:HIS61 4.2 29.7 1.0
N B:ASP45 4.2 27.2 1.0
CB B:ASP44 4.2 28.1 1.0
CG A:HIS61 4.2 29.8 1.0
CB B:ASP45 4.3 27.1 1.0
O A:SER71 4.4 31.9 1.0
CA B:ASP45 4.9 27.2 1.0
CA B:ASP44 4.9 28.0 1.0
CG A:MET65 4.9 33.1 1.0
N B:LYS46 5.0 27.0 1.0
SD A:MET65 5.0 34.7 1.0

Zinc binding site 2 out of 7 in 2w88

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Zinc binding site 2 out of 7 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn108

b:38.8
occ:1.00
OE2 A:GLU1 2.0 37.0 1.0
OD2 A:ASP27 2.0 32.4 1.0
ND1 A:HIS24 2.1 29.2 1.0
CG A:ASP27 2.8 28.4 1.0
CD A:GLU1 2.8 35.7 1.0
OD1 A:ASP27 2.9 29.5 1.0
CG A:HIS24 3.0 27.2 1.0
CE1 A:HIS24 3.1 27.3 1.0
CB A:HIS24 3.3 27.0 1.0
CG A:GLU1 3.3 31.5 1.0
OE1 A:GLU1 3.9 37.9 1.0
N A:HIS24 3.9 27.5 1.0
CA A:HIS24 4.2 27.1 1.0
CD2 A:HIS24 4.2 27.8 1.0
NE2 A:HIS24 4.2 27.7 1.0
CB A:ASP27 4.2 26.9 1.0
CB A:GLU1 4.7 28.4 1.0
CE1 A:PHE3 4.7 26.8 1.0
O A:HIS24 4.7 26.6 1.0
N A:GLU1 4.8 28.1 1.0
C A:HIS24 4.8 27.0 1.0
N A:MET0 4.8 28.6 1.0
CZ A:PHE3 4.9 26.5 1.0
C A:VAL23 5.0 27.9 1.0

Zinc binding site 3 out of 7 in 2w88

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Zinc binding site 3 out of 7 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn107

b:30.6
occ:1.00
OD1 A:ASP44 2.0 26.1 1.0
OD1 A:ASP45 2.0 29.1 1.0
NE2 C:HIS61 2.1 26.8 1.0
CG A:ASP45 2.7 27.6 1.0
OD2 A:ASP45 2.8 26.7 1.0
CG A:ASP44 2.8 25.4 1.0
OD2 A:ASP44 3.0 24.2 1.0
CE1 C:HIS61 3.1 26.5 1.0
CD2 C:HIS61 3.1 27.0 1.0
ND1 C:HIS61 4.2 26.3 1.0
CB A:ASP45 4.2 27.0 1.0
N A:ASP45 4.2 27.1 1.0
CG C:HIS61 4.2 26.5 1.0
CB A:ASP44 4.2 26.5 1.0
CA A:ASP45 4.8 27.4 1.0
O C:SER71 4.8 28.8 1.0
CG C:MET65 4.8 31.1 1.0
N A:LYS46 4.9 28.4 1.0
CA A:ASP44 4.9 26.9 1.0
C A:ASP44 5.0 26.8 1.0
OE2 C:GLU70 5.0 37.8 1.0

Zinc binding site 4 out of 7 in 2w88

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Zinc binding site 4 out of 7 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn108

b:40.1
occ:1.00
OD2 C:ASP27 2.0 34.9 1.0
OE2 C:GLU1 2.0 37.3 1.0
ND1 C:HIS24 2.1 30.3 1.0
CG C:ASP27 2.8 30.3 1.0
CD C:GLU1 2.9 35.7 1.0
OD1 C:ASP27 2.9 30.9 1.0
CG C:HIS24 3.0 28.5 1.0
CG C:GLU1 3.2 31.4 1.0
CE1 C:HIS24 3.2 28.8 1.0
CB C:HIS24 3.3 27.6 1.0
N C:HIS24 4.0 28.3 1.0
OE1 C:GLU1 4.1 38.9 1.0
CB C:ASP27 4.2 28.8 1.0
CD2 C:HIS24 4.2 29.2 1.0
NE2 C:HIS24 4.2 28.8 1.0
CA C:HIS24 4.2 27.8 1.0
CE1 C:PHE3 4.6 27.8 1.0
CB C:GLU1 4.7 28.5 1.0
CZ C:PHE3 4.8 28.0 1.0
N C:GLU1 4.8 27.9 1.0
O C:HIS24 4.8 27.3 1.0
N C:MET0 4.8 28.3 1.0
C C:HIS24 4.9 27.5 1.0

Zinc binding site 5 out of 7 in 2w88

Go back to Zinc Binding Sites List in 2w88
Zinc binding site 5 out of 7 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn107

b:32.0
occ:1.00
OD1 C:ASP44 2.0 29.7 1.0
OD1 C:ASP45 2.0 27.9 1.0
NE2 B:HIS61 2.1 27.1 1.0
CG C:ASP45 2.7 26.8 1.0
OD2 C:ASP45 2.7 26.8 1.0
CG C:ASP44 2.8 27.5 1.0
OD2 C:ASP44 3.0 25.9 1.0
CD2 B:HIS61 3.1 26.3 1.0
CE1 B:HIS61 3.1 25.9 1.0
CB C:ASP45 4.1 26.7 1.0
N C:ASP45 4.2 27.8 1.0
ND1 B:HIS61 4.2 26.5 1.0
CB C:ASP44 4.2 27.9 1.0
CG B:HIS61 4.2 26.8 1.0
O B:SER71 4.4 30.6 1.0
CA C:ASP45 4.7 27.0 1.0
N C:LYS46 4.8 26.8 1.0
CA C:ASP44 4.8 28.2 1.0
CG B:MET65 4.9 30.4 1.0
C C:ASP44 4.9 28.1 1.0
OE2 B:GLU70 4.9 37.8 1.0
SD B:MET65 4.9 31.8 1.0

Zinc binding site 6 out of 7 in 2w88

Go back to Zinc Binding Sites List in 2w88
Zinc binding site 6 out of 7 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn108

b:38.5
occ:1.00
OD2 B:ASP27 2.0 30.9 1.0
ND1 B:HIS24 2.2 30.0 1.0
CG B:ASP27 2.7 27.7 1.0
OD1 B:ASP27 2.8 27.6 1.0
CG B:HIS24 3.1 27.8 1.0
CE1 B:HIS24 3.1 28.3 1.0
CB B:HIS24 3.3 28.0 1.0
N B:HIS24 3.9 28.6 1.0
CD2 B:HIS24 4.2 28.3 1.0
NE2 B:HIS24 4.2 27.9 1.0
CA B:HIS24 4.2 28.3 1.0
CB B:ASP27 4.2 26.5 1.0
CE1 B:PHE3 4.6 26.8 1.0
N B:GLU1 4.7 32.1 1.0
CZ B:PHE3 4.7 27.4 1.0
CA B:MET0 4.8 33.8 1.0
C B:VAL23 4.8 28.9 1.0
C B:HIS24 5.0 28.2 1.0

Zinc binding site 7 out of 7 in 2w88

Go back to Zinc Binding Sites List in 2w88
Zinc binding site 7 out of 7 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn109

b:36.2
occ:0.50
O B:MET0 2.0 34.0 1.0
N B:MET0 2.2 34.2 1.0
C B:MET0 2.6 33.1 1.0
CA B:MET0 2.8 33.8 1.0
CB B:MET0 3.4 33.9 1.0
N B:GLU1 3.9 32.1 1.0
CA B:GLU1 4.5 31.1 1.0
CG B:MET0 4.6 35.6 1.0
CB B:GLU1 4.7 31.4 1.0

Reference:

P.B.Crowley, P.M.Matias, A.R.Khan, M.Roessle, D.I.Svergun. Metal-Mediated Self-Assembly of A Beta-Sandwich Protein. Chemistry V. 15 12672 2009.
ISSN: ISSN 0947-6539
PubMed: 19834935
DOI: 10.1002/CHEM.200901410
Page generated: Wed Dec 16 03:57:03 2020

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