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: Wed Dec 16 06:26:35 2020

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