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Chlorine in PDB 5ukf: Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor

Enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor

All present enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor, PDB code: 5ukf was solved by R.M.Counago, C.Wells, W.Zuercher, T.M.Willson, C.Bountra, A.M.Edwards, P.Arruda, O.Gileadi, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.19 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.138, 96.051, 192.741, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor (pdb code 5ukf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor, PDB code: 5ukf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5ukf

Go back to Chlorine Binding Sites List in 5ukf
Chlorine binding site 1 out of 7 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:89.5
occ:1.00
 NH2 A:ARG148 3.3 62.1 1.0
NE2 A:HIS258 3.4 64.7 1.0
NH1 A:ARG148 3.5 55.8 1.0
CE1 A:HIS258 3.8 64.3 1.0
CZ A:ARG148 3.8 73.5 1.0
CD2 A:HIS258 4.6 61.2 1.0

Chlorine binding site 2 out of 7 in 5ukf

Go back to Chlorine Binding Sites List in 5ukf
Chlorine binding site 2 out of 7 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:87.0
occ:1.00
 NH1 B:ARG241 3.6 33.6 1.0
NH2 B:ARG279 4.1 44.0 1.0
NH2 B:ARG241 4.1 31.6 1.0
O B:HOH557 4.1 52.3 1.0
O B:HOH552 4.1 53.6 1.0
CZ B:ARG241 4.3 51.5 1.0
NH1 B:ARG279 4.6 46.6 1.0
CZ B:ARG279 4.7 61.4 1.0

Chlorine binding site 3 out of 7 in 5ukf

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Chlorine binding site 3 out of 7 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:0.5
occ:1.00
 NE2 C:HIS171 3.3 46.9 1.0
NE2 C:GLN95 3.4 39.5 1.0
O C:HOH620 3.7 75.1 1.0
CD2 C:HIS171 3.9 46.4 1.0
CG C:GLN95 3.9 49.3 1.0
O C:HOH517 4.1 55.8 1.0
CD C:GLN95 4.2 53.9 1.0
CE1 C:HIS171 4.4 46.4 1.0
O C:HOH631 4.8 63.4 1.0

Chlorine binding site 4 out of 7 in 5ukf

Go back to Chlorine Binding Sites List in 5ukf
Chlorine binding site 4 out of 7 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:81.1
occ:1.00
 NE2 D:HIS258 3.2 52.3 1.0
NH2 D:ARG148 3.7 45.5 1.0
CE1 D:HIS258 4.0 52.3 1.0
CD2 D:HIS258 4.2 50.4 1.0
NH1 D:ARG148 4.4 37.1 1.0
CZ D:ARG148 4.6 53.7 1.0

Chlorine binding site 5 out of 7 in 5ukf

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Chlorine binding site 5 out of 7 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl404

b:72.4
occ:1.00
 NH2 D:ARG89 3.4 64.2 1.0
NH1 D:ARG89 3.5 47.0 1.0
CZ D:ARG89 3.9 65.7 1.0
NZ D:LYS85 3.9 0.5 1.0
CE D:LYS85 4.0 98.5 1.0
O D:HOH588 4.5 49.5 1.0
NH1 D:ARG203 4.6 52.1 1.0
CD D:ARG203 4.8 48.0 1.0

Chlorine binding site 6 out of 7 in 5ukf

Go back to Chlorine Binding Sites List in 5ukf
Chlorine binding site 6 out of 7 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl405

b:86.2
occ:1.00
 O D:HOH557 3.3 66.9 1.0
NE2 D:HIS171 3.5 41.8 1.0
NZ D:LYS98 3.7 99.0 1.0
NE2 D:GLN95 3.9 44.4 1.0
CG D:GLN95 3.9 60.0 1.0
CD2 D:HIS171 4.1 40.8 1.0
CD D:GLN95 4.4 66.7 1.0
CB D:GLN95 4.4 53.7 1.0
CE1 D:HIS171 4.7 39.3 1.0
CA D:GLN95 4.9 54.9 1.0

Chlorine binding site 7 out of 7 in 5ukf

Go back to Chlorine Binding Sites List in 5ukf
Chlorine binding site 7 out of 7 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Human Vaccinia-Related Kinase 1 Bound to An Oxindole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl406

b:82.6
occ:1.00
 NH1 D:ARG241 3.4 31.1 1.0
O D:HOH555 3.7 41.5 1.0
NH2 D:ARG241 3.8 29.0 1.0
O D:HOH605 4.0 72.5 1.0
CZ D:ARG241 4.1 41.3 1.0
NH2 D:ARG279 4.4 53.0 1.0
O D:HOH553 4.5 66.8 1.0

Reference:

R.M.Counago, C.K.Allerston, P.Savitsky, H.Azevedo, P.H.Godoi, C.I.Wells, A.Mascarello, F.H.De Souza Gama, K.B.Massirer, W.J.Zuercher, C.R.W.Guimaraes, O.Gileadi. Structural Characterization of Human Vaccinia-Related Kinases (Vrk) Bound to Small-Molecule Inhibitors Identifies Different P-Loop Conformations. Sci Rep V. 7 7501 2017.
ISSN: ESSN 2045-2322
PubMed: 28790404
DOI: 10.1038/S41598-017-07755-Y
Page generated: Fri Jul 26 18:08:35 2024

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