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Chlorine 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:

Zinc (Zn) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the X-Ray Structure of Kdnb, 3-Deoxy-Alpha-D-Manno-Octulosonate 8-Oxidase, From Shewanella Oneidensis, PDB code: 5k8c:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5k8c

Go back to Chlorine Binding Sites List in 5k8c
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl404

b:25.9
occ:1.00
O A:HOH931 3.0 31.1 1.0
O A:HOH911 3.0 30.1 1.0
N A:HIS271 3.2 19.3 1.0
CD2 A:HIS271 3.5 21.2 1.0
CG2 A:ILE274 3.7 16.1 1.0
CD1 A:TYR270 3.8 19.8 1.0
CA A:TYR270 3.8 19.9 1.0
CB A:HIS271 3.8 19.9 1.0
CG A:HIS271 3.9 21.0 1.0
C A:TYR270 4.0 19.9 1.0
CA A:HIS271 4.1 19.1 1.0
O A:GLY269 4.3 23.0 1.0
CE1 A:TYR270 4.5 20.6 1.0
CB A:TYR270 4.5 20.6 1.0
CG A:TYR270 4.5 20.1 1.0
NE2 A:HIS271 4.6 23.2 1.0
O A:HOH739 4.8 23.3 1.0
N A:TYR270 4.9 21.5 1.0
CD1 A:ILE274 5.0 20.2 1.0
CB A:ILE274 5.0 16.8 1.0

Chlorine binding site 2 out of 2 in 5k8c

Go back to Chlorine Binding Sites List in 5k8c
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl binding site number 2 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:Cl406

b:33.9
occ:1.00
O A:HOH660 2.6 30.0 1.0
NE2 A:GLN75 3.1 24.0 1.0
O A:HOH850 3.2 43.6 1.0
CG A:GLN75 4.0 27.3 1.0
CD A:GLN75 4.0 26.2 1.0
CD2 A:LEU79 4.0 24.8 1.0
N A:ASN66 4.1 19.1 1.0
CG1 A:VAL65 4.2 18.5 1.0
CA A:VAL65 4.2 16.9 1.0
CD1 A:LEU79 4.3 23.5 1.0
CG A:LEU79 4.5 21.5 1.0
O A:TRP64 4.5 18.9 1.0
CB A:VAL65 4.6 16.8 1.0
O A:ASN66 4.7 20.5 1.0
C A:VAL65 4.7 17.0 1.0
CG2 A:VAL65 4.8 16.4 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: Sat Dec 12 11:55:41 2020

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