Atomistry » Zinc » PDB 6b3w-6bml » 6b9v
Atomistry »
  Zinc »
    PDB 6b3w-6bml »
      6b9v »

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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy