Atomistry » Zinc » PDB 2vqx-2w13 » 2vxx
Atomistry »
  Zinc »
    PDB 2vqx-2w13 »
      2vxx »

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

Protein crystallography data

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

Other elements in 2vxx:

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

Iron (Fe) 2 atoms

Zinc Binding Sites:

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 2vxx

Go back to Zinc Binding Sites List in 2vxx
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 2vxx

Go back to Zinc Binding Sites List in 2vxx
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 2vxx

Go back to Zinc Binding Sites List in 2vxx
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 2vxx

Go back to Zinc Binding Sites List in 2vxx
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 2vxx

Go back to Zinc Binding Sites List in 2vxx
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 2vxx

Go back to Zinc Binding Sites List in 2vxx
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 2vxx

Go back to Zinc Binding Sites List in 2vxx
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 2vxx

Go back to Zinc Binding Sites List in 2vxx
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

Reference:

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
Page generated: Wed Dec 16 03:56:34 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy