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Iodine in PDB 3kxn: Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88)

Enzymatic activity of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88)

All present enzymatic activity of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88):
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88), PDB code: 3kxn was solved by E.Papinutto, C.Franchin, R.Battistutta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.01 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.839, 60.901, 46.015, 90.00, 103.37, 90.00
R / Rfree (%) 20.7 / 26.4

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88) (pdb code 3kxn). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88), PDB code: 3kxn:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 3kxn

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Iodine binding site 1 out of 8 in the Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:53.4
occ:0.50
 I13 A:K8X1 0.0 53.4 0.5
I17 A:K8X1 1.2 55.0 0.5
C5 A:K8X1 1.4 52.3 0.5
C4 A:K8X1 1.9 50.0 0.5
C1 A:K8X1 2.1 52.4 0.5
I19 A:K8X1 2.4 42.1 0.5
C6 A:K8X1 2.7 54.2 0.5
C6 A:K8X1 3.0 53.6 0.5
C2 A:K8X1 3.0 53.1 0.5
C3 A:K8X1 3.3 51.4 0.5
N21 A:K8X1 3.4 51.5 0.5
I15 A:K8X1 3.5 49.4 0.5
CG1 A:ILE66 3.6 25.0 1.0
C1 A:K8X1 3.8 57.6 0.5
I15 A:K8X1 3.8 50.8 0.5
C2 A:K8X1 4.0 55.3 0.5
CG A:MET163 4.2 28.6 1.0
O A:GLU114 4.2 31.0 1.0
CB A:ILE66 4.3 23.7 1.0
N A:VAL116 4.3 28.0 1.0
CB A:VAL116 4.3 29.3 1.0
C5 A:K8X1 4.3 55.4 0.5
CG2 A:ILE66 4.3 22.1 1.0
C3 A:K8X1 4.3 55.2 0.5
N25 A:K8X1 4.4 51.6 0.5
CD1 A:ILE66 4.4 25.8 1.0
CG2 A:VAL116 4.6 29.3 1.0
CG2 A:ILE174 4.7 24.6 1.0
C23 A:K8X1 4.8 54.2 0.5
CG2 A:VAL95 4.8 25.1 1.0
CA A:VAL116 4.8 29.9 1.0
C4 A:K8X1 4.9 57.4 0.5
SD A:MET163 4.9 31.2 1.0
O A:VAL116 4.9 31.9 1.0
CB A:MET163 4.9 22.7 1.0

Iodine binding site 2 out of 8 in 3kxn

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Iodine binding site 2 out of 8 in the Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:74.7
occ:0.50
 I13 A:K8X1 0.0 74.7 0.5
C23 A:K8X1 1.0 54.2 0.5
N25 A:K8X1 2.0 53.5 0.5
C1 A:K8X1 2.1 57.6 0.5
N21 A:K8X1 2.3 51.5 0.5
C6 A:K8X1 3.0 54.2 0.5
C2 A:K8X1 3.0 55.3 0.5
C3 A:K8X1 3.1 55.2 0.5
C2 A:K8X1 3.2 53.1 0.5
O A:HOH479 3.4 13.9 1.0
N21 A:K8X1 3.4 53.4 0.5
I15 A:K8X1 3.5 50.8 0.5
CD1 A:ILE174 3.6 18.7 1.0
CG2 A:VAL53 3.9 26.3 1.0
CE A:LYS68 4.3 31.8 1.0
C5 A:K8X1 4.3 52.3 0.5
C3 A:K8X1 4.3 51.4 0.5
C4 A:K8X1 4.4 57.4 0.5
CD A:LYS68 4.4 27.2 1.0
CG1 A:VAL53 4.6 27.2 1.0
C1 A:K8X1 4.6 52.4 0.5
CG1 A:ILE174 4.8 24.0 1.0
C23 A:K8X1 4.8 53.6 0.5
CB A:ILE174 4.8 22.6 1.0
NZ A:LYS68 4.8 35.5 1.0
CB A:ASP175 4.8 25.9 1.0
C4 A:K8X1 4.9 50.0 0.5
CB A:VAL53 4.9 25.5 1.0
CG A:LYS68 4.9 26.6 1.0
N A:ASP175 5.0 23.5 1.0
CG A:ASP175 5.0 32.5 1.0

Iodine binding site 3 out of 8 in 3kxn

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Iodine binding site 3 out of 8 in the Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:49.4
occ:0.50
 I15 A:K8X1 0.0 49.4 0.5
I19 A:K8X1 1.1 42.1 0.5
C6 A:K8X1 2.1 53.6 0.5
C4 A:K8X1 2.8 50.0 0.5
O A:VAL116 2.9 31.9 1.0
C1 A:K8X1 3.0 52.4 0.5
C5 A:K8X1 3.0 55.4 0.5
N25 A:K8X1 3.3 51.6 0.5
C3 A:K8X1 3.3 51.4 0.5
I17 A:K8X1 3.5 58.1 0.5
I13 A:K8X1 3.5 53.4 0.5
CB A:ASN118 3.8 34.9 1.0
SD A:MET163 3.8 31.2 1.0
C A:VAL116 3.9 30.2 1.0
C5 A:K8X1 4.0 52.3 0.5
CD1 A:ILE66 4.3 25.8 1.0
N A:ASN118 4.3 34.6 1.0
C4 A:K8X1 4.3 57.4 0.5
C2 A:K8X1 4.3 53.1 0.5
CB A:VAL116 4.3 29.3 1.0
CG A:MET163 4.4 28.6 1.0
N A:VAL116 4.5 28.0 1.0
CA A:VAL116 4.5 29.9 1.0
I17 A:K8X1 4.6 55.0 0.5
CG1 A:ILE66 4.6 25.0 1.0
C23 A:K8X1 4.6 53.6 0.5
C2 A:K8X1 4.7 55.3 0.5
CA A:ASN118 4.7 33.7 1.0
CG A:ASN118 4.8 32.6 1.0
C3 A:K8X1 4.9 55.2 0.5
CG1 A:VAL116 4.9 29.3 1.0
CB A:MET163 4.9 22.7 1.0
O A:HOH480 4.9 20.9 1.0
N A:ASN117 4.9 32.4 1.0

Iodine binding site 4 out of 8 in 3kxn

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Iodine binding site 4 out of 8 in the Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:50.8
occ:0.50
 I15 A:K8X1 0.0 50.8 0.5
C6 A:K8X1 2.1 54.2 0.5
N21 A:K8X1 2.4 51.5 0.5
C1 A:K8X1 3.0 57.6 0.5
C5 A:K8X1 3.0 52.3 0.5
O A:HOH479 3.1 13.9 1.0
C23 A:K8X1 3.2 54.2 0.5
CD2 A:PHE113 3.2 26.8 1.0
CE2 A:PHE113 3.4 29.8 1.0
I17 A:K8X1 3.5 55.0 0.5
I13 A:K8X1 3.5 74.7 0.5
C2 A:K8X1 3.6 53.1 0.5
CG A:PHE113 3.6 25.9 1.0
CG2 A:VAL95 3.8 25.1 1.0
I13 A:K8X1 3.8 53.4 0.5
CZ A:PHE113 3.9 30.1 1.0
CG2 A:ILE174 4.1 24.6 1.0
CD1 A:PHE113 4.1 28.4 1.0
CB A:ILE174 4.1 22.6 1.0
C1 A:K8X1 4.2 52.4 0.5
CE1 A:PHE113 4.2 26.3 1.0
CB A:PHE113 4.3 26.2 1.0
C4 A:K8X1 4.3 50.0 0.5
C2 A:K8X1 4.3 55.3 0.5
N25 A:K8X1 4.4 53.5 0.5
C3 A:K8X1 4.6 55.2 0.5
CD1 A:ILE174 4.7 18.7 1.0
CG1 A:VAL95 4.7 25.0 1.0
CG2 A:ILE66 4.8 22.1 1.0
CB A:VAL95 4.8 25.0 1.0
C3 A:K8X1 4.9 51.4 0.5

Iodine binding site 5 out of 8 in 3kxn

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Iodine binding site 5 out of 8 in the Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:58.1
occ:0.50
 I17 A:K8X1 0.0 58.1 0.5
C5 A:K8X1 2.1 55.4 0.5
O A:HOH480 2.2 20.9 1.0
N25 A:K8X1 2.3 51.6 0.5
C23 A:K8X1 2.8 53.6 0.5
C4 A:K8X1 3.0 57.4 0.5
C6 A:K8X1 3.0 53.6 0.5
I15 A:K8X1 3.5 49.4 0.5
I19 A:K8X1 3.5 65.4 0.5
C3 A:K8X1 3.5 51.4 0.5
O A:VAL45 4.0 31.4 1.0
SD A:MET163 4.1 31.2 1.0
ND2 A:ASN118 4.1 33.0 1.0
N21 A:K8X1 4.1 53.4 0.5
CB A:VAL45 4.1 30.7 1.0
CG2 A:VAL45 4.2 28.1 1.0
I19 A:K8X1 4.2 42.1 0.5
C4 A:K8X1 4.3 50.0 0.5
C1 A:K8X1 4.3 52.4 0.5
C3 A:K8X1 4.3 55.2 0.5
CB A:ASN118 4.4 34.9 1.0
C2 A:K8X1 4.5 55.3 0.5
CG A:ASN118 4.7 32.6 1.0
C A:VAL45 4.7 30.6 1.0
CE A:MET163 4.8 29.5 1.0
C2 A:K8X1 4.9 53.1 0.5

Iodine binding site 6 out of 8 in 3kxn

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Iodine binding site 6 out of 8 in the Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:55.0
occ:0.50
 I17 A:K8X1 0.0 55.0 0.5
I13 A:K8X1 1.2 53.4 0.5
C5 A:K8X1 2.1 52.3 0.5
C4 A:K8X1 3.0 50.0 0.5
C6 A:K8X1 3.0 54.2 0.5
C1 A:K8X1 3.2 52.4 0.5
O A:GLU114 3.3 31.0 1.0
I15 A:K8X1 3.5 50.8 0.5
I19 A:K8X1 3.5 42.1 0.5
CG1 A:ILE66 3.7 25.0 1.0
C2 A:K8X1 3.8 53.1 0.5
CG2 A:VAL95 3.9 25.1 1.0
N21 A:K8X1 3.9 51.5 0.5
CB A:ILE66 4.1 23.7 1.0
C6 A:K8X1 4.2 53.6 0.5
N A:VAL116 4.3 28.0 1.0
CB A:PHE113 4.3 26.2 1.0
C1 A:K8X1 4.3 57.6 0.5
C3 A:K8X1 4.3 51.4 0.5
CG2 A:VAL116 4.4 29.3 1.0
CG2 A:ILE66 4.4 22.1 1.0
CB A:VAL116 4.5 29.3 1.0
C A:GLU114 4.5 29.1 1.0
I15 A:K8X1 4.6 49.4 0.5
CG2 A:ILE174 4.6 24.6 1.0
CG A:GLU114 4.7 24.6 1.0
CG A:PHE113 4.8 25.9 1.0
CD1 A:ILE66 4.8 25.8 1.0
C2 A:K8X1 4.9 55.3 0.5
CA A:TYR115 4.9 27.1 1.0
C A:TYR115 4.9 27.1 1.0
CA A:VAL116 5.0 29.9 1.0

Iodine binding site 7 out of 8 in 3kxn

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Iodine binding site 7 out of 8 in the Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:65.4
occ:0.50
 I19 A:K8X1 0.0 65.4 0.5
C23 A:K8X1 1.5 53.6 0.5
C4 A:K8X1 2.1 57.4 0.5
N21 A:K8X1 2.1 53.4 0.5
N25 A:K8X1 2.8 51.6 0.5
C5 A:K8X1 3.0 55.4 0.5
C3 A:K8X1 3.0 55.2 0.5
C2 A:K8X1 3.4 55.3 0.5
N25 A:K8X1 3.4 53.5 0.5
I17 A:K8X1 3.5 58.1 0.5
CA A:GLY46 3.6 30.1 1.0
C3 A:K8X1 3.7 51.4 0.5
O A:HOH472 3.7 38.0 1.0
O A:VAL45 3.7 31.4 1.0
N A:GLY46 4.2 30.0 1.0
C A:VAL45 4.2 30.6 1.0
C6 A:K8X1 4.3 53.6 0.5
C2 A:K8X1 4.3 53.1 0.5
CG1 A:VAL53 4.6 27.2 1.0
C A:GLY46 4.6 30.5 1.0
C1 A:K8X1 4.6 57.6 0.5
CB A:VAL53 4.7 25.5 1.0
CG2 A:VAL45 4.8 28.1 1.0
C23 A:K8X1 4.8 54.2 0.5
C1 A:K8X1 4.9 52.4 0.5
N A:ARG47 4.9 30.1 1.0
CG2 A:VAL53 4.9 26.3 1.0

Iodine binding site 8 out of 8 in 3kxn

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Iodine binding site 8 out of 8 in the Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Z. Mays CK2 Kinase Alpha Subunit in Complex with the Inhibitor Tetraiodobenzimidazole (K88) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:42.1
occ:0.50
 I19 A:K8X1 0.0 42.1 0.5
I15 A:K8X1 1.1 49.4 0.5
C6 A:K8X1 2.0 53.6 0.5
C4 A:K8X1 2.1 50.0 0.5
C1 A:K8X1 2.4 52.4 0.5
I13 A:K8X1 2.4 53.4 0.5
C5 A:K8X1 3.0 52.3 0.5
C3 A:K8X1 3.0 51.4 0.5
O A:VAL116 3.2 31.9 1.0
C5 A:K8X1 3.2 55.4 0.5
N25 A:K8X1 3.4 51.6 0.5
I17 A:K8X1 3.5 55.0 0.5
C2 A:K8X1 3.8 53.1 0.5
CG1 A:ILE66 3.9 25.0 1.0
CD1 A:ILE66 3.9 25.8 1.0
N A:VAL116 3.9 28.0 1.0
CB A:VAL116 4.0 29.3 1.0
C A:VAL116 4.0 30.2 1.0
SD A:MET163 4.0 31.2 1.0
CA A:VAL116 4.2 29.9 1.0
CG A:MET163 4.2 28.6 1.0
I17 A:K8X1 4.2 58.1 0.5
C6 A:K8X1 4.3 54.2 0.5
C2 A:K8X1 4.3 55.3 0.5
C4 A:K8X1 4.3 57.4 0.5
C3 A:K8X1 4.6 55.2 0.5
CB A:ASN118 4.6 34.9 1.0
CB A:MET163 4.8 22.7 1.0
C23 A:K8X1 4.8 53.6 0.5
CG1 A:VAL116 4.8 29.3 1.0
N21 A:K8X1 4.8 51.5 0.5
C1 A:K8X1 4.9 57.6 0.5
CG2 A:VAL116 5.0 29.3 1.0

Reference:

S.Sarno, E.Papinutto, C.Franchin, J.Bain, M.Elliott, F.Meggio, Z.Kazimierczuk, A.Orzeszko, G.Zanotti, R.Battistutta, L.A.Pinna. Atp Site-Directed Inhibitors of Protein Kinase CK2: An Update. Curr Top Med Chem V. 11 1340 2011.
ISSN: ISSN 1568-0266
PubMed: 21513497
Page generated: Sun Aug 11 15:35:38 2024

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