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Potassium in PDB 4cfs: Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine

Enzymatic activity of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine

All present enzymatic activity of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine:
1.13.11.48;

Protein crystallography data

The structure of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine, PDB code: 4cfs was solved by S.Bui, R.A.Steiner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.45 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.730, 166.850, 167.740, 90.00, 90.00, 90.00
R / Rfree (%) 16.287 / 19.841

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine (pdb code 4cfs). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine, PDB code: 4cfs:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4cfs

Go back to Potassium Binding Sites List in 4cfs
Potassium binding site 1 out of 4 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1276

b:34.0
occ:1.00
 O A:ALA235 2.6 39.5 1.0
O A:PHE241 2.6 24.8 1.0
O A:HOH2149 2.6 33.0 1.0
O A:HIS238 3.0 35.3 1.0
O A:HOH2147 3.0 33.8 1.0
O A:HOH2060 3.4 24.3 1.0
C A:ALA235 3.6 37.7 1.0
O A:PRO239 3.6 29.8 1.0
C A:PRO239 3.8 31.3 1.0
CA A:PRO239 3.8 35.0 1.0
C A:PHE241 3.8 25.9 1.0
C A:HIS238 3.9 35.0 1.0
CA A:ALA235 3.9 34.4 1.0
CB A:ALA235 4.0 34.8 1.0
N A:PRO239 4.3 35.3 1.0
N A:PHE241 4.3 28.3 1.0
O D:HOH2112 4.4 39.0 1.0
CA A:PHE241 4.6 25.8 1.0
N A:TRP240 4.6 30.3 1.0
N A:GLU236 4.7 39.4 1.0
N A:SER242 4.8 25.2 1.0
OD2 D:ASP158 4.9 31.7 1.0

Potassium binding site 2 out of 4 in 4cfs

Go back to Potassium Binding Sites List in 4cfs
Potassium binding site 2 out of 4 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1276

b:25.6
occ:1.00
 O B:PHE241 2.5 17.3 1.0
O B:HOH2159 2.6 27.2 1.0
O B:ALA235 2.7 25.9 1.0
O B:HIS238 2.9 29.5 1.0
O B:HOH2050 3.1 29.1 1.0
O B:HOH2154 3.3 27.1 1.0
O B:PRO239 3.6 18.9 1.0
C B:ALA235 3.6 24.6 1.0
C B:PHE241 3.7 18.2 1.0
C B:PRO239 3.8 23.6 1.0
CA B:PRO239 3.9 26.4 1.0
C B:HIS238 3.9 27.7 1.0
CA B:ALA235 3.9 22.6 1.0
CB B:ALA235 4.0 23.1 1.0
N B:PHE241 4.2 19.8 1.0
N B:PRO239 4.3 27.9 1.0
CA B:PHE241 4.4 17.8 1.0
N B:TRP240 4.6 23.1 1.0
N B:SER242 4.7 17.3 1.0
N B:GLU236 4.8 25.7 1.0
CA B:SER242 4.9 16.9 1.0
CB B:PHE241 4.9 19.0 1.0
C B:TRP240 5.0 20.6 1.0

Potassium binding site 3 out of 4 in 4cfs

Go back to Potassium Binding Sites List in 4cfs
Potassium binding site 3 out of 4 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1276

b:31.6
occ:1.00
 O A:HOH2099 2.3 38.4 1.0
O C:PHE241 2.6 25.2 1.0
O C:HOH2116 2.8 22.0 1.0
O C:ALA235 2.8 32.0 1.0
O C:HOH2117 2.9 29.0 1.0
O C:HIS238 3.2 36.3 1.0
O A:HOH2031 3.3 31.9 1.0
O C:PRO239 3.5 27.9 1.0
C C:ALA235 3.7 28.1 1.0
C C:PHE241 3.8 27.2 1.0
C C:PRO239 3.8 30.9 1.0
CA C:PRO239 3.9 32.5 1.0
CA C:ALA235 4.1 24.5 1.0
C C:HIS238 4.1 33.5 1.0
CB C:ALA235 4.1 24.1 1.0
N C:PHE241 4.3 26.6 1.0
OD2 A:ASP158 4.3 29.0 1.0
N C:PRO239 4.4 34.1 1.0
O A:HOH2083 4.5 20.3 0.5
CA C:PHE241 4.6 25.2 1.0
N C:TRP240 4.7 28.1 1.0
N C:SER242 4.7 25.9 1.0
CA C:SER242 4.9 26.8 1.0
CB A:ASP158 4.9 26.4 1.0
N C:GLU236 4.9 32.3 1.0

Potassium binding site 4 out of 4 in 4cfs

Go back to Potassium Binding Sites List in 4cfs
Potassium binding site 4 out of 4 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) Catalytically Inactive H251A Variant Complexed with Its Natural Substrate 1-H-3- Hydroxy-4-Oxoquinaldine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1276

b:28.6
occ:1.00
 O D:HOH2164 2.5 33.0 1.0
O D:PHE241 2.6 21.2 1.0
O D:ALA235 2.8 26.4 1.0
O D:HOH2166 2.8 48.2 1.0
O D:HOH2161 2.9 29.9 1.0
O D:HIS238 3.0 31.7 1.0
O D:HOH2162 3.2 38.4 1.0
O D:PRO239 3.5 28.1 1.0
C D:ALA235 3.7 26.5 1.0
C D:PRO239 3.7 27.1 1.0
C D:PHE241 3.8 22.8 1.0
CA D:PRO239 3.8 28.4 1.0
C D:HIS238 3.9 28.1 1.0
CA D:ALA235 4.0 25.9 1.0
CB D:ALA235 4.1 24.3 1.0
N D:PHE241 4.3 23.0 1.0
N D:PRO239 4.3 28.2 1.0
O D:HOH2165 4.4 30.0 1.0
CA D:PHE241 4.5 21.8 1.0
N D:TRP240 4.6 26.8 1.0
N D:SER242 4.7 21.9 1.0
N D:GLU236 4.8 29.6 1.0
CA D:SER242 4.9 22.7 1.0

Reference:

A.Hernandez-Ortega, M.G.Quesne, S.Bui, D.P.Heuts, R.A.Steiner, D.J.Heyes, S.P.De Visser, N.S.Scrutton. Origin of the Proton-Transfer Step in the Cofactor-Free 1-H- 3-Hydroxy-4-Oxoquinaldine 2,4- Dioxygenase: Effect of the Basicity of An Active Site His Residue. J.Biol.Chem. V. 289 8620 2014.
ISSN: ISSN 0021-9258
PubMed: 24482238
DOI: 10.1074/JBC.M113.543033
Page generated: Mon Aug 12 10:24:06 2024

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