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Chlorine in PDB 4yo4: Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine

Enzymatic activity of Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine

All present enzymatic activity of Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine, PDB code: 4yo4 was solved by V.L.Grum-Tokars, S.M.Roy, G.Minasov, W.F.Anderson, D.M.Watterson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.48 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.004, 62.523, 88.537, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine (pdb code 4yo4). 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 DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine, PDB code: 4yo4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 4yo4

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Chlorine binding site 1 out of 7 in the Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine


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 DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:55.5
occ:1.00
 NH2 A:ARG63 3.5 26.4 1.0
O A:HOH540 3.5 40.2 1.0
NE A:ARG63 3.6 23.8 1.0
NZ A:LYS175 3.9 62.5 1.0
CZ A:ARG63 4.0 23.6 1.0
O A:HOH512 4.2 25.9 1.0
CD A:LYS175 4.6 53.6 1.0
CD2 A:HIS166 4.8 18.1 1.0
CD A:ARG63 4.8 22.0 1.0
OE2 A:GLU59 4.9 41.8 1.0
CE A:LYS175 4.9 58.2 1.0
OE2 A:GLU173 4.9 44.4 1.0

Chlorine binding site 2 out of 7 in 4yo4

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Chlorine binding site 2 out of 7 in the Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine


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 DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:20.5
occ:0.70
 CL A:CL302 0.0 20.5 0.7
CL A:CL302 1.5 17.4 0.3
N A:ASP161 3.2 15.8 1.0
O A:HOH487 3.3 19.8 1.0
O A:HOH602 3.3 32.9 1.0
NZ A:LYS42 3.3 22.6 1.0
C9 A:4FT307 3.4 26.5 1.0
CA A:ASP161 3.4 17.2 1.0
CD A:LYS42 3.8 19.8 1.0
CD1 A:LEU93 3.9 19.1 1.0
C8 A:4FT307 4.0 25.5 1.0
CE A:LYS42 4.0 22.6 1.0
CB A:ASP161 4.1 20.0 1.0
CB A:ILE160 4.3 15.8 1.0
C10 A:4FT307 4.3 26.5 1.0
C A:ILE160 4.4 15.7 1.0
CD1 A:ILE160 4.6 19.3 1.0
CG A:ASP161 4.6 24.2 1.0
C A:ASP161 4.6 16.3 1.0
N A:PHE162 4.7 15.8 1.0
OE2 A:GLU64 4.7 20.1 1.0
OD1 A:ASP161 4.7 22.6 1.0
CA A:ILE160 4.8 15.2 1.0
CG1 A:ILE160 4.9 16.6 1.0
CG A:LYS42 5.0 17.7 1.0

Chlorine binding site 3 out of 7 in 4yo4

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Chlorine binding site 3 out of 7 in the Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine


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 DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:17.4
occ:0.30
 CL A:CL302 0.0 17.4 0.3
CL A:CL302 1.5 20.5 0.7
O A:HOH487 2.9 19.8 1.0
N A:ASP161 3.1 15.8 1.0
CD1 A:LEU93 3.5 19.1 1.0
C9 A:4FT307 3.6 26.5 1.0
CA A:ASP161 3.8 17.2 1.0
CB A:ILE160 3.8 15.8 1.0
C A:ILE160 4.1 15.7 1.0
CG2 A:ILE77 4.1 19.7 1.0
C10 A:4FT307 4.1 26.5 1.0
CA A:ILE160 4.1 15.2 1.0
CD2 A:LEU93 4.5 20.4 1.0
NZ A:LYS42 4.5 22.6 1.0
CG2 A:ILE160 4.6 16.8 1.0
C8 A:4FT307 4.6 25.5 1.0
CG A:LEU93 4.6 17.2 1.0
N A:PHE162 4.6 15.8 1.0
O A:HOH602 4.7 32.9 1.0
CD A:LYS42 4.8 19.8 1.0
CG1 A:ILE77 4.8 22.9 1.0
CB A:ILE77 4.8 19.6 1.0
C A:ASP161 4.8 16.3 1.0
CB A:ASP161 4.8 20.0 1.0
CG1 A:ILE160 4.9 16.6 1.0
CD1 A:ILE160 4.9 19.3 1.0

Chlorine binding site 4 out of 7 in 4yo4

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Chlorine binding site 4 out of 7 in the Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine


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 DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:58.2
occ:0.60
 CL A:CL303 0.0 58.2 0.6
CL A:CL303 1.6 53.0 0.4
N A:GLN23 3.1 40.1 1.0
O A:HOH620 3.2 44.8 0.5
N A:PHE24 3.2 37.3 1.0
CA A:GLY22 3.5 40.0 1.0
C A:GLY22 3.5 39.8 1.0
O A:HOH620 3.6 34.1 0.5
N A:ALA25 3.7 31.1 1.0
CA A:GLN23 4.0 43.4 1.0
C A:GLN23 4.0 42.3 1.0
O A:HOH613 4.1 36.5 1.0
CA A:PHE24 4.1 36.6 1.0
C A:PHE24 4.3 32.9 1.0
CB A:ALA25 4.3 27.4 1.0
CB A:GLN23 4.3 47.9 1.0
CB A:PHE24 4.4 40.6 1.0
O A:GLY22 4.4 42.5 1.0
N A:GLY22 4.5 38.8 1.0
CA A:ALA25 4.5 26.0 1.0
O A:HOH614 4.5 28.4 0.5
O A:ALA25 4.6 29.0 1.0
CD2 A:PHE24 4.8 47.9 1.0
O A:HOH425 4.8 38.2 1.0

Chlorine binding site 5 out of 7 in 4yo4

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Chlorine binding site 5 out of 7 in the Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine


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 DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:53.0
occ:0.40
 CL A:CL303 0.0 53.0 0.4
CL A:CL303 1.6 58.2 0.6
O A:HOH620 3.0 44.8 0.5
O A:HOH614 3.1 28.4 0.5
O A:HOH425 3.7 38.2 1.0
O A:HOH620 3.9 34.1 0.5
CA A:GLY22 4.0 40.0 1.0
CB A:ALA25 4.0 27.4 1.0
O A:HOH613 4.2 36.5 1.0
N A:ALA25 4.4 31.1 1.0
N A:GLN23 4.4 40.1 1.0
C A:GLY22 4.5 39.8 1.0
N A:GLY22 4.7 38.8 1.0
OD2 A:ASP161 4.7 28.8 1.0
N A:PHE24 4.7 37.3 1.0
CA A:ALA25 4.7 26.0 1.0
O A:ALA25 4.8 29.0 1.0
O A:HOH602 4.9 32.9 1.0

Chlorine binding site 6 out of 7 in 4yo4

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Chlorine binding site 6 out of 7 in the Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine


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 DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:36.2
occ:0.70
 CL A:CL304 0.0 36.2 0.7
CL A:CL304 2.0 34.0 0.3
O A:HOH581 3.3 35.0 1.0
N A:GLY16 3.9 24.4 1.0
CD A:LYS29 3.9 31.8 1.0
CG A:LYS29 3.9 25.4 1.0
CA A:GLY16 4.0 24.8 1.0
O A:LYS29 4.0 19.4 1.0
CA A:CYS30 4.1 18.3 1.0
C A:LYS29 4.2 19.6 1.0
C A:CYS30 4.2 18.5 1.0
N A:CYS30 4.2 17.4 1.0
C A:THR15 4.3 25.9 1.0
CB A:LYS29 4.3 22.4 1.0
N A:ARG31 4.4 18.5 1.0
O A:ASP14 4.4 23.8 1.0
O A:CYS30 4.5 18.2 1.0
CB A:ARG31 4.6 18.2 1.0
O A:THR15 4.7 28.8 1.0
CA A:THR15 4.9 23.9 1.0
CA A:LYS29 4.9 20.1 1.0

Chlorine binding site 7 out of 7 in 4yo4

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Chlorine binding site 7 out of 7 in the Crystal Structure of DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine


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 DAPK1 Catalytic Domain in Complex with the Hinge Binding Fragment Phthalazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:34.0
occ:0.30
 CL A:CL304 0.0 34.0 0.3
CL A:CL304 2.0 36.2 0.7
O A:ASP14 3.5 23.8 1.0
C A:THR15 3.5 25.9 1.0
O A:THR15 3.6 28.8 1.0
N A:GLY16 3.8 24.4 1.0
C A:ASP14 3.8 22.9 1.0
CA A:THR15 4.1 23.9 1.0
CA A:GLY16 4.1 24.8 1.0
N A:THR15 4.1 23.5 1.0
CB A:ASP14 4.2 24.6 1.0
CB A:ARG31 4.3 18.2 1.0
N A:ARG31 4.4 18.5 1.0
O A:HOH581 4.5 35.0 1.0
CA A:CYS30 4.6 18.3 1.0
CA A:ASP14 4.7 23.7 1.0
C A:CYS30 4.7 18.5 1.0
O A:LYS29 4.8 19.4 1.0

Reference:

V.L.Grum-Tokars, G.Minasov, S.M.Roy, W.F.Anderson, D.M.Watterson. Crystal Structure of DAPK1 Catalytic Domain in Complex with Hinge Binding Fragments To Be Published.
Page generated: Sat Dec 12 11:26:05 2020

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