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Zinc in PDB 2q5b: High Resolution Structure of Plastocyanin From Phormidium Laminosum

Protein crystallography data

The structure of High Resolution Structure of Plastocyanin From Phormidium Laminosum, PDB code: 2q5b was solved by R.Fromme, Y.S.Bukhman-Deruyter, I.Grotjohann, H.Mi, P.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.99 / 1.45
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.329, 84.329, 90.536, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21

Other elements in 2q5b:

The structure of High Resolution Structure of Plastocyanin From Phormidium Laminosum also contains other interesting chemical elements:

Potassium (K) 5 atoms
Copper (Cu) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the High Resolution Structure of Plastocyanin From Phormidium Laminosum (pdb code 2q5b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the High Resolution Structure of Plastocyanin From Phormidium Laminosum, PDB code: 2q5b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2q5b

Go back to Zinc Binding Sites List in 2q5b
Zinc binding site 1 out of 4 in the High Resolution Structure of Plastocyanin From Phormidium Laminosum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Structure of Plastocyanin From Phormidium Laminosum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn107

b:12.4
occ:1.00
O A:HOH613 2.0 14.8 1.0
OD1 A:ASP44 2.0 9.8 1.0
NE2 B:HIS61 2.1 10.0 1.0
OD1 A:ASP45 2.2 10.3 1.0
O B:HOH507 2.2 12.3 1.0
CG A:ASP44 2.8 11.7 1.0
OD2 A:ASP44 2.9 13.2 1.0
CD2 B:HIS61 3.0 10.5 1.0
CE1 B:HIS61 3.0 10.0 1.0
CG A:ASP45 3.1 12.2 1.0
OD2 A:ASP45 3.5 11.7 1.0
O B:HOH579 4.0 18.3 1.0
O A:HOH622 4.1 17.6 1.0
O B:HOH525 4.1 19.8 1.0
N A:ASP45 4.1 11.2 1.0
ND1 B:HIS61 4.2 9.6 1.0
CG B:HIS61 4.2 10.6 1.0
CB A:ASP44 4.2 10.3 1.0
CB A:ASP45 4.5 12.7 1.0
OE2 B:GLU70 4.5 19.7 1.0
CA A:ASP44 4.8 10.2 1.0
N A:LYS46 4.8 13.2 1.0
CA A:ASP45 4.8 12.9 1.0
CG B:MET65 4.8 13.6 1.0
C A:ASP44 4.9 11.2 1.0
O A:HOH644 5.0 20.2 1.0

Zinc binding site 2 out of 4 in 2q5b

Go back to Zinc Binding Sites List in 2q5b
Zinc binding site 2 out of 4 in the High Resolution Structure of Plastocyanin From Phormidium Laminosum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Structure of Plastocyanin From Phormidium Laminosum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn107

b:15.2
occ:1.00
NE2 C:HIS61 2.0 13.4 1.0
OD1 B:ASP45 2.0 23.0 1.0
O C:HOH595 2.0 33.0 1.0
OD2 B:ASP45 2.7 25.9 1.0
CG B:ASP45 2.7 23.1 1.0
CE1 C:HIS61 3.0 13.2 1.0
CD2 C:HIS61 3.1 14.8 1.0
OE2 C:GLU70 4.1 22.6 1.0
ND1 C:HIS61 4.1 13.5 1.0
CG B:LYS46 4.2 25.8 1.0
CB B:ASP45 4.2 21.1 1.0
CG C:HIS61 4.2 13.8 1.0
C B:ASP45 4.7 21.6 1.0
N B:LYS46 4.7 22.1 1.0
CG C:MET65 4.8 16.1 1.0
CA B:ASP45 4.8 21.4 1.0
SD C:MET65 4.8 20.5 1.0
O C:HOH528 4.9 20.8 1.0
O C:SER71 5.0 15.5 1.0
N B:ASP45 5.0 20.6 1.0

Zinc binding site 3 out of 4 in 2q5b

Go back to Zinc Binding Sites List in 2q5b
Zinc binding site 3 out of 4 in the High Resolution Structure of Plastocyanin From Phormidium Laminosum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High Resolution Structure of Plastocyanin From Phormidium Laminosum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn107

b:9.7
occ:1.00
OD1 C:ASP44 2.0 10.5 1.0
NE2 A:HIS61 2.0 8.8 1.0
O C:HOH505 2.0 11.6 1.0
OD1 C:ASP45 2.1 10.2 1.0
O C:HOH511 2.2 11.0 1.0
CG C:ASP44 2.8 10.2 1.0
OD2 C:ASP44 2.9 10.8 1.0
CD2 A:HIS61 3.0 9.9 1.0
CE1 A:HIS61 3.0 9.2 1.0
CG C:ASP45 3.1 10.6 1.0
OD2 C:ASP45 3.5 10.9 1.0
O C:HOH523 4.0 17.5 1.0
N C:ASP45 4.1 9.7 1.0
O A:HOH611 4.1 13.9 1.0
ND1 A:HIS61 4.1 9.2 1.0
CG A:HIS61 4.2 9.3 1.0
CB C:ASP44 4.2 9.7 1.0
CH3 A:ACT601 4.2 19.4 1.0
CB C:ASP45 4.4 10.5 1.0
O A:SER71 4.5 10.8 1.0
CG C:LYS46 4.6 14.5 1.0
N C:LYS46 4.7 11.8 1.0
CA C:ASP44 4.8 9.4 1.0
CA C:ASP45 4.8 10.8 1.0
C C:ASP44 4.9 9.8 1.0

Zinc binding site 4 out of 4 in 2q5b

Go back to Zinc Binding Sites List in 2q5b
Zinc binding site 4 out of 4 in the High Resolution Structure of Plastocyanin From Phormidium Laminosum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High Resolution Structure of Plastocyanin From Phormidium Laminosum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn108

b:24.7
occ:1.00
O C:HOH582 2.0 17.5 1.0
OE2 C:GLU104 2.0 20.7 1.0
CE1 C:HIS24 2.4 23.5 1.0
ND1 C:HIS24 2.5 24.4 1.0
CD C:GLU104 2.9 23.3 1.0
OE1 C:GLU104 3.2 24.5 1.0
NE2 C:HIS24 3.4 16.7 1.0
CG C:HIS24 3.6 22.4 1.0
CD2 C:HIS24 4.1 22.5 1.0
O C:HOH559 4.1 24.8 1.0
O C:THR22 4.1 16.9 1.0
CG C:GLU104 4.3 22.1 1.0
N C:HIS24 4.5 17.4 1.0
CB C:HIS24 4.6 19.3 1.0
C C:VAL23 4.6 17.2 1.0
CG2 C:THR22 4.8 16.3 1.0
C C:THR22 4.8 16.7 1.0
CA C:HIS24 4.9 18.7 1.0
CA C:VAL23 5.0 16.7 1.0

Reference:

Y.S.Bukhman-Deruyter, R.Fromme, I.Grotjohann, B.Schlarb-Ridley, H.Mi, P.Fromme. Plastocyanin at High Resolution From Phormidium Laminosum and the Double Mutant D44A, D45A To Be Published.
Page generated: Wed Dec 16 03:49:53 2020

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