Nickel in PDB 5cxm: Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803

The structure of Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803, PDB code: 5cxm was solved by S.Veit, K.Takeda, K.Miki, M.Roegner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.53 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	21.747, 55.011, 80.709, 80.44, 89.87, 84.11
R / Rfree (%)	18.5 / 21.6

The structure of Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803 also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Nickel atom in the Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803 (pdb code 5cxm). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803, PDB code: 5cxm:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:18.7 occ:1.00 O B:HOH314 1.6 12.7 1.0 O B:HOH312 1.6 17.3 1.0 NE2 B:HIS98 1.9 13.8 1.0 NE2 A:HIS79 2.0 16.0 1.0 O A:HOH360 2.2 39.6 1.0 O B:HOH361 2.3 24.5 1.0 CE1 B:HIS98 2.8 15.0 1.0 CE1 A:HIS79 3.0 16.4 1.0 CD2 B:HIS98 3.1 11.1 1.0 CD2 A:HIS79 3.1 16.2 1.0 ND2 A:ASN80 3.9 32.6 1.0 ND1 B:HIS98 4.0 14.1 1.0 ND1 A:HIS79 4.1 13.0 1.0 CG B:HIS98 4.1 12.1 1.0 CG A:HIS79 4.2 13.3 1.0 OD1 A:ASN80 4.3 34.5 1.0 CG A:ASN80 4.4 30.1 1.0 ND2 B:ASN80 4.7 34.0 1.0 O B:CYS97 5.0 14.5 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:18.9 occ:1.00 O B:HOH301 1.5 9.9 1.0 O A:HOH316 1.7 25.2 1.0 NE2 A:HIS98 2.0 14.5 1.0 NE2 B:HIS79 2.0 14.6 1.0 O B:HOH354 2.1 33.7 1.0 O A:HOH357 2.3 20.0 1.0 CE1 A:HIS98 2.9 14.4 1.0 CE1 B:HIS79 3.0 17.0 1.0 CD2 A:HIS98 3.1 14.3 1.0 CD2 B:HIS79 3.1 15.3 1.0 ND1 A:HIS98 4.0 13.1 1.0 ND2 B:ASN80 4.1 34.0 1.0 ND1 B:HIS79 4.1 12.7 1.0 CG A:HIS98 4.1 13.8 1.0 CG B:HIS79 4.2 11.0 1.0 OD1 B:ASN80 4.4 29.9 1.0 CG B:ASN80 4.5 28.3 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni202 b:20.4 occ:1.00 O D:HOH303 1.6 18.6 1.0 O C:HOH312 1.6 14.6 1.0 NE2 D:HIS98 1.9 15.1 1.0 NE2 C:HIS79 2.1 18.5 1.0 O D:HOH354 2.2 25.5 1.0 O C:HOH368 2.2 31.4 1.0 CE1 D:HIS98 2.8 17.1 1.0 CE1 C:HIS79 3.0 20.3 1.0 CD2 D:HIS98 3.0 14.5 1.0 CD2 C:HIS79 3.1 17.9 1.0 ND2 C:ASN80 3.9 30.6 1.0 ND1 D:HIS98 4.0 14.8 1.0 CG D:HIS98 4.1 13.9 1.0 ND1 C:HIS79 4.1 13.0 1.0 CG C:HIS79 4.2 15.9 1.0 OD1 C:ASN80 4.2 29.8 1.0 CG C:ASN80 4.4 27.1 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Cyanobacterial Plasma Membrane Rieske Protein PETC3 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni203 b:21.0 occ:1.00 O C:HOH305 1.5 14.1 1.0 O C:HOH329 1.7 27.4 1.0 NE2 C:HIS98 2.0 15.4 1.0 NE2 D:HIS79 2.1 19.6 1.0 O D:HOH353 2.1 37.0 1.0 O C:HOH370 2.3 25.3 1.0 CE1 C:HIS98 2.8 17.3 1.0 CE1 D:HIS79 3.1 18.2 1.0 CD2 D:HIS79 3.1 17.9 1.0 CD2 C:HIS98 3.1 16.1 1.0 ND1 C:HIS98 4.0 14.8 1.0 OD1 D:ASN80 4.1 35.7 1.0 CG C:HIS98 4.2 15.3 1.0 ND1 D:HIS79 4.2 15.2 1.0 CG D:HIS79 4.2 16.7 1.0 ND2 C:ASN80 4.9 30.6 1.0 O C:CYS97 5.0 15.7 1.0

S.Veit, K.Takeda, Y.Tsunoyama, F.Baymann, R.Nevo, Z.Reich, M.Rogner, K.Miki, S.Rexroth. Structural and Functional Characterisation of the Cyanobacterial PETC3 Rieske Protein Family. Biochim. Biophys. Acta V.1857 1879 2016.
ISSN: ISSN 0006-3002
PubMed: 27663073
DOI: 10.1016/J.BBABIO.2016.09.007