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Chlorine in PDB 5m56: Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21)

Enzymatic activity of Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21)

All present enzymatic activity of Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21):
2.7.11.1;

Protein crystallography data

The structure of Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21), PDB code: 5m56 was solved by K.Niefind, N.Bischoff, S.M.Yarmoluk, V.G.Bdzhola, A.G.Golub, A.O.Balanda, A.O.Prykhod'ko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.81 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.341, 87.620, 72.977, 90.00, 109.69, 90.00
R / Rfree (%) 16.4 / 20.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21) (pdb code 5m56). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21), PDB code: 5m56:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5m56

Go back to Chlorine Binding Sites List in 5m56
Chlorine binding site 1 out of 6 in the Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:36.0
occ:1.00
 CL5 A:7FC401 0.0 36.0 1.0
C15 A:7FC401 1.7 34.3 1.0
C11 A:7FC401 2.7 33.1 1.0
C12 A:7FC401 2.7 27.9 1.0
OH A:TYR116 3.5 38.0 1.0
NH1 B:ARG44 3.6 44.3 1.0
CZ B:ARG44 3.6 46.7 1.0
NE B:ARG44 3.7 46.5 1.0
CD B:ARG44 3.7 41.2 1.0
N A:ASN119 3.9 26.4 1.0
O A:ILE117 4.0 29.5 1.0
O A:HOH511 4.0 44.8 1.0
C17 A:7FC401 4.0 30.1 1.0
C22 A:7FC401 4.0 25.5 1.0
CZ A:TYR116 4.1 32.6 1.0
CE1 A:TYR116 4.1 24.6 1.0
O A:HOH554 4.1 34.4 1.0
CB A:ASN119 4.2 27.3 1.0
O A:ASN119 4.2 28.0 1.0
NH2 B:ARG44 4.3 48.2 1.0
O A:HOH655 4.4 38.9 1.0
CD2 A:LEU46 4.4 23.4 1.0
CA A:ASN119 4.5 27.5 1.0
C23 A:7FC401 4.5 24.6 1.0
C A:ASN119 4.8 33.1 1.0
C A:ASN118 4.8 30.5 1.0
CD1 A:LEU46 4.8 24.2 1.0
CA A:ASN118 4.9 30.8 1.0

Chlorine binding site 2 out of 6 in 5m56

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Chlorine binding site 2 out of 6 in the Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:34.1
occ:1.00
 CL6 A:7FC401 0.0 34.1 1.0
C17 A:7FC401 1.7 30.1 1.0
C11 A:7FC401 2.7 33.1 1.0
C23 A:7FC401 2.7 24.6 1.0
O13 A:7FC401 3.0 24.2 1.0
CB A:LEU46 3.9 30.3 1.0
C22 A:7FC401 4.0 25.5 1.0
C15 A:7FC401 4.0 34.3 1.0
NH2 A:ARG48 4.2 66.2 1.0
O A:HOH655 4.2 38.9 1.0
O A:LEU46 4.2 42.8 1.0
C20 A:7FC401 4.3 24.6 1.0
SD A:MET164 4.3 33.4 1.0
NE A:ARG48 4.4 67.0 1.0
O A:HOH554 4.4 34.4 1.0
C09 A:7FC401 4.5 22.3 1.0
C12 A:7FC401 4.5 27.9 1.0
CD1 A:LEU46 4.5 24.2 1.0
CE A:MET164 4.6 24.1 1.0
C A:LEU46 4.6 37.0 1.0
CZ A:ARG48 4.7 64.8 1.0
CG1 A:VAL54 4.8 30.6 1.0
CG A:LEU46 4.8 28.4 1.0
CA A:LEU46 4.9 31.0 1.0
C18 A:7FC401 4.9 23.6 1.0

Chlorine binding site 3 out of 6 in 5m56

Go back to Chlorine Binding Sites List in 5m56
Chlorine binding site 3 out of 6 in the Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:42.4
occ:1.00
 N A:ARG279 3.1 33.9 1.0
O A:HOH622 3.6 37.3 1.0
CA A:SER278 3.7 35.6 1.0
CB A:SER278 3.8 40.2 1.0
C A:SER278 3.9 34.2 1.0
CB A:ARG279 3.9 32.5 1.0
O A:HOH598 4.0 35.8 1.0
CA A:ARG279 4.1 32.8 1.0
O A:ARG279 4.5 40.0 1.0
C A:ARG279 4.8 33.4 1.0
N A:SER278 5.0 38.8 1.0

Chlorine binding site 4 out of 6 in 5m56

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Chlorine binding site 4 out of 6 in the Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:32.3
occ:1.00
 CL5 B:7FC401 0.0 32.3 1.0
C15 B:7FC401 1.7 28.6 1.0
C11 B:7FC401 2.7 33.7 1.0
C12 B:7FC401 2.7 23.3 1.0
NE A:ARG44 3.3 47.7 1.0
CZ A:ARG44 3.5 46.1 1.0
NH2 A:ARG44 3.6 44.1 1.0
OH B:TYR116 3.6 41.5 1.0
O B:HOH591 3.7 42.2 1.0
N B:ASN119 3.8 32.9 1.0
CD A:ARG44 4.0 48.7 1.0
C17 B:7FC401 4.0 34.4 1.0
O B:ILE117 4.0 28.2 1.0
C22 B:7FC401 4.0 24.3 1.0
O B:ASN119 4.0 33.6 1.0
O B:HOH521 4.1 34.0 1.0
CZ B:TYR116 4.1 33.5 1.0
CE1 B:TYR116 4.1 36.8 1.0
CB B:ASN119 4.2 26.7 1.0
NH1 A:ARG44 4.3 48.8 1.0
CD2 B:LEU46 4.4 33.4 1.0
CA B:ASN119 4.4 26.3 1.0
C23 B:7FC401 4.5 26.2 1.0
C B:ASN119 4.7 30.7 1.0
O B:HOH640 4.8 48.2 1.0
C B:ASN118 4.8 30.3 1.0
CA B:ASN118 4.8 30.2 1.0
CD1 B:LEU46 4.8 30.2 1.0

Chlorine binding site 5 out of 6 in 5m56

Go back to Chlorine Binding Sites List in 5m56
Chlorine binding site 5 out of 6 in the Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:41.0
occ:1.00
 CL6 B:7FC401 0.0 41.0 1.0
C17 B:7FC401 1.7 34.4 1.0
C11 B:7FC401 2.7 33.7 1.0
C23 B:7FC401 2.7 26.2 1.0
O13 B:7FC401 3.0 25.9 1.0
O B:GLY47 3.3 50.5 1.0
CD B:ARG48 3.4 46.4 1.0
O1 B:GOL403 3.4 60.5 1.0
O B:HOH640 3.7 48.2 1.0
CB B:LEU46 4.0 29.5 1.0
C22 B:7FC401 4.0 24.3 1.0
C15 B:7FC401 4.0 28.6 1.0
SD B:MET164 4.2 32.1 1.0
C1 B:GOL403 4.2 58.3 1.0
C20 B:7FC401 4.3 26.0 1.0
NH1 B:ARG48 4.3 41.3 1.0
CG B:ARG48 4.4 50.6 1.0
NE B:ARG48 4.4 44.6 1.0
C B:GLY47 4.4 50.5 1.0
C09 B:7FC401 4.5 21.3 1.0
C12 B:7FC401 4.5 23.3 1.0
CE B:MET164 4.5 27.8 1.0
CD1 B:LEU46 4.5 30.2 1.0
CG1 B:VAL54 4.7 26.3 1.0
CZ B:ARG48 4.8 45.5 1.0
O B:HOH521 4.8 34.0 1.0
C B:LEU46 4.8 32.4 1.0
CG B:LEU46 4.8 31.2 1.0
C18 B:7FC401 4.9 23.1 1.0
N B:GLY47 5.0 34.5 1.0

Chlorine binding site 6 out of 6 in 5m56

Go back to Chlorine Binding Sites List in 5m56
Chlorine binding site 6 out of 6 in the Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Monoclinic Complex Structure of Human Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA') with the Inhibitor 4'-Carboxy-6,8-Chloro- Flavonol (FLC21) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:52.3
occ:1.00
 N B:HIS235 3.1 38.7 1.0
O B:HOH553 3.1 39.7 1.0
O B:PHE233 3.5 36.4 1.0
NH1 B:ARG245 3.6 65.7 1.0
CD B:ARG245 3.7 49.2 1.0
CB B:ARG245 3.7 37.2 1.0
O B:HOH685 3.7 49.0 1.0
CA B:PHE234 3.8 34.1 1.0
CG B:ARG245 3.8 42.2 1.0
C B:PHE234 3.9 34.1 1.0
CA B:HIS235 4.0 33.4 1.0
NH2 B:ARG230 4.0 60.8 1.0
CB B:HIS235 4.0 35.7 1.0
C B:HIS235 4.3 34.5 1.0
O B:HIS235 4.4 33.3 1.0
C B:PHE233 4.4 30.0 1.0
CZ B:ARG245 4.6 63.6 1.0
N B:PHE234 4.6 32.7 1.0
NE B:ARG245 4.6 59.9 1.0
CA B:ARG245 4.7 34.7 1.0
CZ B:ARG230 4.8 62.9 1.0
CB B:PHE234 4.8 28.8 1.0
CD1 B:PHE234 4.9 27.2 1.0
O B:ARG245 5.0 30.2 1.0

Reference:

K.Niefind, N.Bischoff, A.G.Golub, V.G.Bdzhola, A.O.Balanda, A.O.Prykhod'ko, S.M.Yarmoluk. Structural Hypervariability of the Two Human Protein Kinase CK2 Catalytic Subunit Paralogs Revealed By Complex Structures with A Flavonol- and A Thieno[2,3-D]Pyrimidine-Based Inhibitor. Pharmaceuticals V. 10 2017.
ISSN: ESSN 1424-8247
PubMed: 28085026
DOI: 10.3390/PH10010009
Page generated: Fri Jul 26 12:29:19 2024

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