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Iodine in PDB 6spw: Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140

Enzymatic activity of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140

All present enzymatic activity of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140:
2.7.11.1;

Protein crystallography data

The structure of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140, PDB code: 6spw was solved by K.Niefind, A.Schnitzler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.59 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.503, 85.171, 90.432, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.6

Other elements in 6spw:

The structure of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 (pdb code 6spw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140, PDB code: 6spw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 6spw

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Iodine binding site 1 out of 12 in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:22.3
occ:1.00
 IAW B:A0Z101 0.0 22.3 1.0
CCO B:A0Z101 2.1 21.4 1.0
CCQ B:A0Z101 3.1 20.9 1.0
CCP B:A0Z101 3.1 28.4 1.0
O A:GLU114 3.3 15.5 1.0
IAY B:A0Z101 3.5 29.0 1.0
IAX B:A0Z101 3.6 26.5 1.0
CD1 A:ILE95 3.8 13.1 1.0
CG2 A:VAL66 3.8 14.4 1.0
CB A:VAL66 3.9 12.2 1.0
CG1 A:VAL66 4.1 12.1 1.0
CG1 A:ILE95 4.2 12.9 1.0
N A:VAL116 4.2 21.1 1.0
CB A:PHE113 4.4 11.2 1.0
CCR B:A0Z101 4.4 36.3 1.0
CG2 A:VAL116 4.4 25.0 1.0
CCS B:A0Z101 4.4 27.3 1.0
C A:GLU114 4.5 16.4 1.0
CB A:VAL116 4.6 26.8 1.0
CA A:HIS115 4.7 20.5 1.0
C A:HIS115 4.7 19.7 1.0
CG2 A:ILE174 5.0 18.5 1.0
CCT B:A0Z101 5.0 30.7 1.0
CG A:PHE113 5.0 12.6 1.0

Iodine binding site 2 out of 12 in 6spw

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Iodine binding site 2 out of 12 in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:26.5
occ:1.00
 IAX B:A0Z101 0.0 26.5 1.0
CCP B:A0Z101 2.1 28.4 1.0
O A:VAL116 3.0 28.4 1.0
CCR B:A0Z101 3.0 36.3 1.0
CCO B:A0Z101 3.0 21.4 1.0
IAZ B:A0Z101 3.5 60.3 1.0
IAW B:A0Z101 3.6 22.3 1.0
C A:VAL116 4.0 25.2 1.0
CB A:VAL116 4.1 26.8 1.0
N A:VAL116 4.1 21.1 1.0
CD1 A:LEU45 4.1 29.1 1.0
SD A:MET163 4.3 36.6 1.0
CA A:VAL116 4.3 22.2 1.0
CCQ B:A0Z101 4.3 20.9 1.0
CG2 A:VAL66 4.4 14.4 1.0
CCT B:A0Z101 4.4 30.7 1.0
O A:HOH732 4.4 49.6 1.0
CG A:MET163 4.6 29.0 1.0
CB A:ASN118 4.8 48.4 1.0
O A:HOH769 4.9 21.4 1.0
CCS B:A0Z101 4.9 27.3 1.0
N A:ASN118 5.0 39.1 1.0
CG1 A:VAL116 5.0 29.1 1.0

Iodine binding site 3 out of 12 in 6spw

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Iodine binding site 3 out of 12 in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:29.0
occ:1.00
 IAY B:A0Z101 0.0 29.0 1.0
CCQ B:A0Z101 2.1 20.9 1.0
O A:HOH737 2.7 14.5 1.0
CCO B:A0Z101 3.0 21.4 1.0
CCS B:A0Z101 3.0 27.3 1.0
CD1 A:PHE113 3.4 16.5 1.0
NBS B:A0Z101 3.5 29.1 1.0
IAW B:A0Z101 3.5 22.3 1.0
CE1 A:PHE113 3.6 12.6 1.0
CG A:PHE113 3.7 12.6 1.0
CZ A:PHE113 4.1 12.7 1.0
CD2 A:PHE113 4.2 10.6 1.0
CB A:PHE113 4.3 11.2 1.0
CCP B:A0Z101 4.3 28.4 1.0
CCT B:A0Z101 4.3 30.7 1.0
CE2 A:PHE113 4.3 11.5 1.0
CG1 A:VAL66 4.4 12.1 1.0
CG1 A:ILE95 4.5 12.9 1.0
CG2 A:ILE174 4.8 18.5 1.0
CBA B:A0Z101 4.8 30.7 1.0
CD A:LYS68 4.8 29.7 1.0
CCR B:A0Z101 4.8 36.3 1.0
CB A:ILE174 4.9 15.6 1.0

Iodine binding site 4 out of 12 in 6spw

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Iodine binding site 4 out of 12 in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:60.3
occ:1.00
 IAZ B:A0Z101 0.0 60.3 1.0
CCR B:A0Z101 2.2 36.3 1.0
O A:HOH769 2.3 21.4 1.0
CCP B:A0Z101 3.1 28.4 1.0
CCT B:A0Z101 3.1 30.7 1.0
CBL B:A0Z101 3.4 38.9 1.0
IAX B:A0Z101 3.5 26.5 1.0
NDB B:A0Z101 3.6 32.4 1.0
SD A:MET163 3.9 36.6 1.0
CB A:LEU45 4.3 24.0 1.0
CCS B:A0Z101 4.4 27.3 1.0
CCO B:A0Z101 4.4 21.4 1.0
O A:HOH732 4.5 49.6 1.0
CD1 A:LEU45 4.7 29.1 1.0
CBI B:A0Z101 4.8 48.6 1.0
CE A:MET163 4.8 36.6 1.0
O A:LEU45 4.9 34.8 1.0
CBA B:A0Z101 4.9 30.7 1.0
CCQ B:A0Z101 4.9 20.9 1.0
CG1 A:VAL53 5.0 18.7 1.0

Iodine binding site 5 out of 12 in 6spw

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Iodine binding site 5 out of 12 in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I101

b:25.1
occ:1.00
 IAW C:A0Z101 0.0 25.1 1.0
CCO C:A0Z101 2.1 22.0 1.0
CCQ C:A0Z101 3.0 20.6 1.0
CCP C:A0Z101 3.0 25.2 1.0
IAX C:A0Z101 3.5 27.5 1.0
IAY C:A0Z101 3.6 22.9 1.0
CG2 A:VAL101 3.6 16.6 1.0
CB A:ALA110 4.0 14.5 1.0
OE1 A:GLN36 4.1 45.4 1.0
CG1 A:VAL67 4.2 21.7 1.0
CCR C:A0Z101 4.3 39.9 1.0
CB A:GLN36 4.3 26.1 1.0
CCS C:A0Z101 4.4 24.5 1.0
CB A:VAL101 4.8 16.2 1.0
CA A:GLN36 4.9 20.6 1.0
CCT C:A0Z101 4.9 31.9 1.0
O A:GLN36 4.9 18.3 1.0

Iodine binding site 6 out of 12 in 6spw

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Iodine binding site 6 out of 12 in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I101

b:27.5
occ:1.00
 IAX C:A0Z101 0.0 27.5 1.0
CCP C:A0Z101 2.2 25.2 1.0
CCO C:A0Z101 3.1 22.0 1.0
CCR C:A0Z101 3.1 39.9 1.0
O A:THR108 3.3 21.9 1.0
IAZ C:A0Z101 3.3 66.4 1.0
IAW C:A0Z101 3.5 25.1 1.0
CG2 A:THR108 4.2 25.8 1.0
C A:THR108 4.2 21.1 1.0
CB A:THR108 4.3 27.7 1.0
CB A:ALA110 4.3 14.5 1.0
CG2 A:ILE69 4.3 27.4 1.0
N A:ASP103 4.3 24.3 1.0
CB A:ASP103 4.3 27.1 1.0
CCQ C:A0Z101 4.4 20.6 1.0
CCT C:A0Z101 4.4 31.9 1.0
OE1 A:GLN36 4.4 45.4 1.0
O A:PRO109 4.5 20.8 1.0
C A:PRO109 4.6 18.2 1.0
CG1 A:ILE69 4.6 22.7 1.0
CD1 A:ILE69 4.8 28.5 1.0
N A:ALA110 4.9 16.0 1.0
CA A:THR108 4.9 25.4 1.0
CA A:ASP103 4.9 25.2 1.0
CCS C:A0Z101 4.9 24.5 1.0
N A:PRO109 5.0 20.8 1.0

Iodine binding site 7 out of 12 in 6spw

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Iodine binding site 7 out of 12 in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I101

b:22.9
occ:1.00
 IAY C:A0Z101 0.0 22.9 1.0
CCQ C:A0Z101 2.1 20.6 1.0
CCS C:A0Z101 3.0 24.5 1.0
CCO C:A0Z101 3.1 22.0 1.0
O A:TYR39 3.2 16.9 1.0
NBS C:A0Z101 3.4 23.6 1.0
IAW C:A0Z101 3.6 25.1 1.0
O A:HOH573 3.6 31.0 1.0
C A:TYR39 3.7 15.2 1.0
CB A:TYR39 4.0 13.3 1.0
CA A:GLN40 4.1 12.6 1.0
CD2 A:LEU41 4.1 16.9 1.0
N A:GLN40 4.2 13.6 1.0
N A:LEU41 4.2 13.9 1.0
CG A:LEU41 4.2 16.6 1.0
CCT C:A0Z101 4.3 31.9 1.0
CCP C:A0Z101 4.3 25.2 1.0
C A:GLN40 4.4 17.3 1.0
CA A:TYR39 4.5 13.8 1.0
O A:GLN36 4.5 18.3 1.0
CBA C:A0Z101 4.7 26.8 1.0
CCR C:A0Z101 4.8 39.9 1.0

Iodine binding site 8 out of 12 in 6spw

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Iodine binding site 8 out of 12 in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I101

b:66.4
occ:1.00
 IAZ C:A0Z101 0.0 66.4 1.0
CCR C:A0Z101 2.1 39.9 1.0
O A:HOH780 2.8 34.3 1.0
O A:HOH725 2.9 49.6 1.0
CCP C:A0Z101 3.0 25.2 1.0
CCT C:A0Z101 3.2 31.9 1.0
IAX C:A0Z101 3.3 27.5 1.0
CBI C:A0Z101 3.4 34.0 1.0
CBL C:A0Z101 3.5 32.4 1.0
NDB C:A0Z101 3.7 29.3 1.0
CCO C:A0Z101 4.3 22.0 1.0
CCS C:A0Z101 4.4 24.5 1.0
CB A:THR108 4.5 27.7 1.0
CG2 A:THR108 4.6 25.8 1.0
CBF C:A0Z101 4.6 35.5 1.0
CG2 A:ILE69 4.7 27.4 1.0
OG A:SER106 4.7 30.4 1.0
CD1 A:ILE69 4.8 28.5 1.0
CB A:ASP103 4.9 27.1 1.0
CCQ C:A0Z101 4.9 20.6 1.0
OG1 A:THR108 4.9 31.5 1.0

Iodine binding site 9 out of 12 in 6spw

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Iodine binding site 9 out of 12 in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I101

b:33.5
occ:1.00
 IAW D:A0Z101 0.0 33.5 1.0
CCO D:A0Z101 2.1 25.3 1.0
CCP D:A0Z101 3.1 20.8 1.0
CCQ D:A0Z101 3.1 20.7 1.0
IAY D:A0Z101 3.5 32.0 1.0
IAX D:A0Z101 3.5 20.9 1.0
O A:ILE272 4.3 29.6 1.0
CCR D:A0Z101 4.4 21.6 1.0
CCS D:A0Z101 4.4 21.9 1.0
O A:HOH572 4.5 30.4 1.0
CB A:ILE272 4.5 26.2 1.0
CCT D:A0Z101 4.9 21.7 1.0

Iodine binding site 10 out of 12 in 6spw

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Iodine binding site 10 out of 12 in the Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Protein Kinase CK2 Catalytic Subunit with the CK2BETA- Competitive Bisubstrate Inhibitor ARC3140 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I101

b:20.9
occ:1.00
 IAX D:A0Z101 0.0 20.9 1.0
CCP D:A0Z101 2.1 20.8 1.0
OD1 A:ASP240 3.0 18.5 1.0
CCO D:A0Z101 3.1 25.3 1.0
CCR D:A0Z101 3.1 21.6 1.0
IAW D:A0Z101 3.5 33.5 1.0
IAZ D:A0Z101 3.5 20.8 1.0
CG A:ASP240 3.7 17.1 1.0
CB A:ASP240 3.8 15.0 1.0
CA A:ASP240 3.9 14.9 1.0
CG2 A:VAL243 4.2 15.3 1.0
NH2 A:ARG244 4.2 26.2 1.0
CCQ D:A0Z101 4.4 20.7 1.0
CCT D:A0Z101 4.4 21.7 1.0
CB A:VAL243 4.4 14.0 1.0
CD1 A:ILE272 4.4 33.4 1.0
N A:ASP240 4.5 14.9 1.0
CG1 A:VAL243 4.6 16.1 1.0
OD2 A:ASP240 4.7 21.1 1.0
CCS D:A0Z101 4.9 21.9 1.0

Reference:

K.Niefind, A.Schnitzler, A.Uri, M.Pietsch, J.Jose, C.Nienberg, M.Steinkrueger, K.Viht. Unexpected CK2 Beta-Antagonistic Functionality of Bisubstrate Inhibitors Targeting Protein Kinase CK2 Bioorg.Chem. 2020.
ISSN: ISSN 0045-2068
DOI: 10.1016/J.BIOORG.2020.103608
Page generated: Fri Aug 8 22:13:56 2025

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