Atomistry » Zinc » PDB 5k16-5kar » 5k8c
Atomistry »
  Zinc »
    PDB 5k16-5kar »
      5k8c »

Zinc in PDB 5k8c: X-Ray Structure of Kdnb, 3-Deoxy-Alpha-D-Manno-Octulosonate 8-Oxidase, From Shewanella Oneidensis

Enzymatic activity of X-Ray Structure of Kdnb, 3-Deoxy-Alpha-D-Manno-Octulosonate 8-Oxidase, From Shewanella Oneidensis

All present enzymatic activity of X-Ray Structure of Kdnb, 3-Deoxy-Alpha-D-Manno-Octulosonate 8-Oxidase, From Shewanella Oneidensis:
1.1.3.48;

Protein crystallography data

The structure of X-Ray Structure of Kdnb, 3-Deoxy-Alpha-D-Manno-Octulosonate 8-Oxidase, From Shewanella Oneidensis, PDB code: 5k8c was solved by H.M.Holden, J.B.Thoden, T.R.Zachman-Brockmeyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.18 / 1.85
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 107.594, 107.594, 149.861, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 21.8

Other elements in 5k8c:

The structure of X-Ray Structure of Kdnb, 3-Deoxy-Alpha-D-Manno-Octulosonate 8-Oxidase, From Shewanella Oneidensis also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Kdnb, 3-Deoxy-Alpha-D-Manno-Octulosonate 8-Oxidase, From Shewanella Oneidensis (pdb code 5k8c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the X-Ray Structure of Kdnb, 3-Deoxy-Alpha-D-Manno-Octulosonate 8-Oxidase, From Shewanella Oneidensis, PDB code: 5k8c:

Zinc binding site 1 out of 1 in 5k8c

Go back to Zinc Binding Sites List in 5k8c
Zinc binding site 1 out of 1 in the X-Ray Structure of Kdnb, 3-Deoxy-Alpha-D-Manno-Octulosonate 8-Oxidase, From Shewanella Oneidensis


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 Kdnb, 3-Deoxy-Alpha-D-Manno-Octulosonate 8-Oxidase, From Shewanella Oneidensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:37.4
occ:1.00
 NE2 A:HIS272 2.2 24.3 1.0
OD1 A:ASP194 2.2 24.0 1.0
NE2 A:HIS258 2.4 22.2 1.0
O A:HOH807 2.4 36.2 1.0
O A:HOH773 2.8 39.6 1.0
OD2 A:ASP194 2.8 24.3 1.0
CG A:ASP194 2.9 22.6 1.0
CE1 A:HIS272 3.1 26.9 1.0
CD2 A:HIS272 3.2 23.6 1.0
CD2 A:HIS258 3.2 25.2 1.0
CE1 A:HIS258 3.4 25.2 1.0
ND2 A:ASN276 3.6 34.2 1.0
C5N A:NAD401 3.9 19.4 1.0
ND1 A:HIS272 4.2 25.6 1.0
CG A:HIS272 4.3 21.2 1.0
C6N A:NAD401 4.3 19.1 1.0
CB A:ASP194 4.4 22.6 1.0
CG A:HIS258 4.4 21.7 1.0
ND1 A:HIS258 4.5 23.2 1.0
O A:ASP194 4.6 20.6 1.0
CD2 A:HIS198 4.7 19.1 1.0
CG A:ASN276 4.7 24.5 1.0
O A:HOH789 4.7 26.8 1.0
O A:HOH749 4.8 32.6 1.0
OD1 A:ASN276 4.9 23.1 1.0
CA A:ASP194 4.9 18.8 1.0
C4N A:NAD401 5.0 19.2 1.0

Reference:

T.R.Zachman-Brockmeyer, J.B.Thoden, H.M.Holden. Structures of Kdnb and Kdna From Shewanella Oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-D-Manno-Octulosonic Acid. Biochemistry V. 55 4485 2016.
ISSN: ISSN 0006-2960
PubMed: 27275764
DOI: 10.1021/ACS.BIOCHEM.6B00439
Page generated: Sun Oct 27 20:12:23 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy