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Zinc in PDB 6b9v: Crystal Structure of A New Diphosphatase From the Phnp Family

Protein crystallography data

The structure of Crystal Structure of A New Diphosphatase From the Phnp Family, PDB code: 6b9v was solved by Q.Li, S.D.Bruner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.28 / 1.88
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.780, 41.364, 96.034, 90.00, 95.20, 90.00
R / Rfree (%) 15.9 / 19.6

Other elements in 6b9v:

The structure of Crystal Structure of A New Diphosphatase From the Phnp Family also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A New Diphosphatase From the Phnp Family (pdb code 6b9v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A New Diphosphatase From the Phnp Family, PDB code: 6b9v:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6b9v

Go back to Zinc Binding Sites List in 6b9v
Zinc binding site 1 out of 2 in the Crystal Structure of A New Diphosphatase From the Phnp Family


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A New Diphosphatase From the Phnp Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:20.1
occ:1.00
ND1 A:HIS234 2.0 29.1 1.0
SG A:CYS28 2.3 19.1 1.0
SG A:CYS23 2.3 21.0 1.0
SG A:CYS25 2.3 19.5 1.0
CE1 A:HIS234 3.0 22.7 1.0
CG A:HIS234 3.1 21.1 1.0
CB A:CYS28 3.2 18.6 1.0
CB A:CYS23 3.3 21.8 1.0
CB A:CYS25 3.4 22.0 1.0
CB A:HIS234 3.5 16.1 1.0
N A:CYS25 4.1 22.4 1.0
N A:CYS28 4.1 17.6 1.0
NE2 A:HIS234 4.1 29.3 1.0
CD2 A:HIS234 4.2 19.0 1.0
CA A:CYS28 4.3 15.6 1.0
CA A:CYS25 4.3 19.6 1.0
CA A:CYS23 4.6 20.4 1.0
C A:CYS23 4.6 22.3 1.0
CB A:THR20 4.8 29.4 1.0
O A:CYS23 4.8 26.2 1.0
C A:CYS25 4.8 20.1 1.0
O A:HOH610 4.9 46.3 1.0
O A:CYS25 4.9 21.4 1.0
N A:THR20 5.0 17.6 1.0
CA A:HIS234 5.0 15.2 1.0
OG1 A:THR20 5.0 28.5 1.0

Zinc binding site 2 out of 2 in 6b9v

Go back to Zinc Binding Sites List in 6b9v
Zinc binding site 2 out of 2 in the Crystal Structure of A New Diphosphatase From the Phnp Family


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A New Diphosphatase From the Phnp Family within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:21.6
occ:1.00
SG B:CYS28 2.3 19.4 1.0
ND1 B:HIS234 2.3 31.1 1.0
SG B:CYS23 2.3 20.1 1.0
SG B:CYS25 2.4 21.7 1.0
CB B:CYS28 3.2 15.5 1.0
CB B:CYS23 3.2 21.3 1.0
CG B:HIS234 3.2 28.4 1.0
CE1 B:HIS234 3.3 33.6 1.0
CB B:CYS25 3.3 27.8 1.0
CB B:HIS234 3.5 16.3 1.0
N B:CYS25 4.0 24.9 1.0
N B:CYS28 4.1 20.5 1.0
CA B:CYS25 4.2 30.7 1.0
CA B:CYS28 4.2 19.3 1.0
NE2 B:HIS234 4.4 28.8 1.0
CD2 B:HIS234 4.4 25.0 1.0
CA B:CYS23 4.5 19.3 1.0
C B:CYS23 4.6 20.9 1.0
C B:CYS25 4.7 26.3 1.0
O B:CYS25 4.7 21.0 1.0
O B:CYS23 4.8 24.6 1.0
CA B:HIS234 4.9 20.8 1.0
N B:ASP24 5.0 21.7 1.0

Reference:

G.A.W.Beaudoin, Q.Li, S.D.Bruner, A.D.Hanson. An Unusual Diphosphatase From the Phnp Family Cleaves Reactive Fad Photoproducts. Biochem.J. V. 475 261 2018.
ISSN: ESSN 1470-8728
PubMed: 29229761
DOI: 10.1042/BCJ20170817
Page generated: Wed Dec 16 11:31:41 2020

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