Zinc in PDB 2vxx: X-Ray Structure of Dpsa From Thermosynechococcus Elongatus

The structure of X-Ray Structure of Dpsa From Thermosynechococcus Elongatus, PDB code: 2vxx was solved by S.Franceschini, A.Ilari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	123.09 / 2.40
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	174.504, 174.504, 174.504, 90.00, 90.00, 90.00
R / Rfree (%)	16.486 / 21.567

The structure of X-Ray Structure of Dpsa From Thermosynechococcus Elongatus also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the X-Ray Structure of Dpsa From Thermosynechococcus Elongatus (pdb code 2vxx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the X-Ray Structure of Dpsa From Thermosynechococcus Elongatus, PDB code: 2vxx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the X-Ray Structure of Dpsa From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Dpsa From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:25.6 occ:1.00 O B:HOH2055 1.9 40.6 1.0 NE2 B:HIS78 2.0 24.0 1.0 NE2 A:HIS51 2.1 21.2 1.0 OE1 B:GLU82 2.3 23.5 1.0 CE1 B:HIS78 2.6 24.8 1.0 O B:HOH2057 2.9 34.4 1.0 CE1 A:HIS51 3.0 20.5 1.0 CD2 A:HIS51 3.1 20.0 1.0 CD2 B:HIS78 3.2 22.7 1.0 CD B:GLU82 3.2 25.3 1.0 OE2 B:GLU82 3.6 26.3 1.0 ND1 B:HIS78 3.8 24.2 1.0 NE2 A:HIS63 3.9 26.5 1.0 OE1 A:GLN67 3.9 26.8 1.0 CG B:HIS78 4.1 21.7 1.0 ZN A:ZN202 4.1 45.4 1.0 CE1 A:HIS63 4.1 25.9 1.0 ND1 A:HIS51 4.2 20.6 1.0 CG A:HIS51 4.2 20.2 1.0 CG B:GLU82 4.6 23.2 1.0 CD2 A:HIS63 4.8 25.3 1.0 O A:HOH2053 4.9 44.1 1.0 CD A:GLN67 4.9 25.3 1.0 CB B:GLU82 5.0 21.0 1.0

Zinc binding site 2 out of 8 in the X-Ray Structure of Dpsa From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Dpsa From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:45.4 occ:1.00 NE2 A:HIS63 2.1 26.5 1.0 OE2 B:GLU82 2.3 26.3 1.0 O B:HOH2057 3.0 34.4 1.0 CD2 A:HIS63 3.0 25.3 1.0 CE1 A:HIS63 3.1 25.9 1.0 CD B:GLU82 3.5 25.3 1.0 OE1 B:GLU82 4.0 23.5 1.0 CG A:HIS63 4.1 24.8 1.0 ZN A:ZN201 4.1 25.6 1.0 ND1 A:HIS63 4.1 26.3 1.0 O B:HOH2055 4.1 40.6 1.0 CG B:GLU82 4.7 23.2 1.0 CZ A:PHE59 4.8 25.2 1.0 NE2 A:HIS51 4.9 21.2 1.0 CE1 A:HIS51 5.0 20.5 1.0

Zinc binding site 3 out of 8 in the X-Ray Structure of Dpsa From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of Dpsa From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:41.6 occ:1.00 NE2 B:HIS63 2.0 26.1 1.0 OE2 A:GLU82 2.2 27.1 1.0 O B:HOH2050 2.5 37.3 1.0 CD2 B:HIS63 2.9 25.1 1.0 CE1 B:HIS63 3.1 25.1 1.0 CD A:GLU82 3.3 25.6 1.0 O B:HOH2041 3.3 32.9 1.0 OE1 A:GLU82 3.8 24.8 1.0 ZN B:ZN202 3.8 26.3 1.0 CG B:HIS63 4.1 24.7 1.0 ND1 B:HIS63 4.1 25.3 1.0 CG A:GLU82 4.6 23.4 1.0 NE2 B:HIS51 4.7 18.9 1.0 CE1 B:HIS51 4.7 18.8 1.0 CZ B:PHE59 4.9 24.8 1.0

Zinc binding site 4 out of 8 in the X-Ray Structure of Dpsa From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of Dpsa From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:26.3 occ:1.00 NE2 A:HIS78 2.0 26.1 1.0 O B:HOH2041 2.1 32.9 1.0 OE1 A:GLU82 2.1 24.8 1.0 NE2 B:HIS51 2.2 18.9 1.0 CE1 A:HIS78 2.8 27.2 1.0 CE1 B:HIS51 3.1 18.8 1.0 CD A:GLU82 3.1 25.6 1.0 CD2 A:HIS78 3.1 25.1 1.0 CD2 B:HIS51 3.2 18.4 1.0 OE2 A:GLU82 3.4 27.1 1.0 ZN B:ZN201 3.8 41.6 1.0 NE2 B:HIS63 4.0 26.1 1.0 ND1 A:HIS78 4.0 26.8 1.0 CG A:HIS78 4.2 24.0 1.0 ND1 B:HIS51 4.2 18.6 1.0 CE1 B:HIS63 4.2 25.1 1.0 OE1 B:GLN67 4.3 29.7 1.0 CG B:HIS51 4.3 18.6 1.0 CG A:GLU82 4.5 23.4 1.0 CD B:GLN67 4.8 28.2 1.0 CB A:GLU82 4.8 21.4 1.0 NE2 B:GLN67 4.8 29.2 1.0 CD2 B:HIS63 4.9 25.1 1.0

Zinc binding site 5 out of 8 in the X-Ray Structure of Dpsa From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Structure of Dpsa From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:32.4 occ:1.00 NE2 C:HIS63 2.0 25.4 1.0 O D:HOH2055 2.1 31.3 1.0 OE2 D:GLU82 2.1 25.5 1.0 O C:HOH2106 2.3 24.9 1.0 CD2 C:HIS63 2.9 24.8 1.0 CE1 C:HIS63 3.1 25.1 1.0 CD D:GLU82 3.2 24.1 1.0 O1 C:PEG1177 3.6 70.1 1.0 OE1 D:GLU82 3.7 23.0 1.0 ZN C:ZN202 3.7 24.9 1.0 O D:HOH2056 4.0 28.5 1.0 CG C:HIS63 4.1 24.6 1.0 ND1 C:HIS63 4.1 25.4 1.0 O C:HOH2046 4.1 24.7 1.0 CG D:GLU82 4.5 22.1 1.0 NE2 C:HIS51 4.6 20.5 1.0 CE1 C:HIS51 4.8 19.7 1.0 CZ C:PHE59 4.9 24.7 1.0 C1 C:PEG1177 4.9 70.2 1.0

Zinc binding site 6 out of 8 in the X-Ray Structure of Dpsa From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Structure of Dpsa From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:24.9 occ:1.00 NE2 D:HIS78 2.0 24.2 1.0 OE1 D:GLU82 2.1 23.0 1.0 NE2 C:HIS51 2.2 20.5 1.0 O D:HOH2055 2.3 31.3 1.0 O C:HOH2046 2.3 24.7 1.0 CE1 D:HIS78 2.9 25.3 1.0 CE1 C:HIS51 3.1 19.7 1.0 CD D:GLU82 3.1 24.1 1.0 CD2 D:HIS78 3.1 22.9 1.0 CD2 C:HIS51 3.2 19.2 1.0 OE2 D:GLU82 3.5 25.5 1.0 ZN C:ZN201 3.7 32.4 1.0 NE2 C:HIS63 3.8 25.4 1.0 OE1 C:GLN67 3.9 26.8 1.0 ND1 D:HIS78 4.0 24.3 1.0 CE1 C:HIS63 4.1 25.1 1.0 CG D:HIS78 4.2 21.3 1.0 ND1 C:HIS51 4.2 19.7 1.0 CG C:HIS51 4.3 19.7 1.0 CG D:GLU82 4.4 22.1 1.0 CB D:GLU82 4.8 20.4 1.0 CD2 C:HIS63 4.8 24.8 1.0 O1 C:PEG1177 4.8 70.1 1.0

Zinc binding site 7 out of 8 in the X-Ray Structure of Dpsa From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Structure of Dpsa From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:32.8 occ:1.00 OE2 C:GLU82 2.1 24.5 1.0 NE2 D:HIS63 2.2 25.2 1.0 O A:HOH2100 2.3 24.3 1.0 NE2 A:HIS164 2.3 22.7 1.0 O D:HOH2037 2.9 21.8 1.0 CE1 D:HIS63 3.1 24.4 1.0 CE1 A:HIS164 3.1 22.9 1.0 CD C:GLU82 3.2 23.3 1.0 CD2 D:HIS63 3.2 24.2 1.0 CD2 A:HIS164 3.4 23.5 1.0 OE1 C:GLU82 3.5 23.1 1.0 ZN D:ZN202 3.6 22.8 1.0 ND1 D:HIS63 4.2 25.2 1.0 ND1 A:HIS164 4.3 23.1 1.0 CG D:HIS63 4.3 24.4 1.0 CG A:HIS164 4.4 23.0 1.0 CG C:GLU82 4.4 22.4 1.0 NE2 D:HIS51 4.6 19.2 1.0 CE1 D:HIS51 4.6 19.0 1.0 OE2 A:GLU160 4.6 32.1 1.0

Zinc binding site 8 out of 8 in the X-Ray Structure of Dpsa From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Structure of Dpsa From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:22.8 occ:1.00 O D:HOH2037 2.0 21.8 1.0 OE1 C:GLU82 2.1 23.1 1.0 NE2 C:HIS78 2.1 25.9 1.0 NE2 D:HIS51 2.1 19.2 1.0 CE1 C:HIS78 3.0 26.5 1.0 CE1 D:HIS51 3.1 19.0 1.0 CD C:GLU82 3.1 23.3 1.0 CD2 D:HIS51 3.2 19.3 1.0 CD2 C:HIS78 3.2 24.5 1.0 OE2 C:GLU82 3.5 24.5 1.0 ZN D:ZN201 3.6 32.8 1.0 OE1 D:GLN67 4.1 28.6 1.0 NE2 D:HIS63 4.1 25.2 1.0 ND1 C:HIS78 4.2 26.5 1.0 ND1 D:HIS51 4.2 19.9 1.0 CG D:HIS51 4.3 19.2 1.0 CG C:HIS78 4.3 23.2 1.0 CE1 D:HIS63 4.3 24.4 1.0 CG C:GLU82 4.4 22.4 1.0 CB C:GLU82 4.7 21.0 1.0 CD D:GLN67 4.8 26.9 1.0

F.Alaleona, S.Franceschini, P.Ceci, A.Ilari, E.Chiancone. Thermosynechococcus Elongatus Dpsa Binds Zn(II) at A Unique Three Histidine-Containing Ferroxidase Center and Utilizes O2 As Iron Oxidant with Very High Efficiency, Unlike the Typical Dps Proteins. Febs J. V. 277 903 2010.
ISSN: ISSN 1742-464X
PubMed: 20088882
DOI: 10.1111/J.1742-4658.2009.07532.X