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Bromine in PDB 3pvg: Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68)

Enzymatic activity of Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68)

All present enzymatic activity of Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68):
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68), PDB code: 3pvg 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) 69.50 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.876, 60.041, 45.046, 90.00, 103.21, 90.00
R / Rfree (%) 18.2 / 21.1

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68) (pdb code 3pvg). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68), PDB code: 3pvg:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 3pvg

Go back to Bromine Binding Sites List in 3pvg
Bromine binding site 1 out of 4 in the Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1

b:67.3
occ:1.00
 BR13 A:K681 0.0 67.3 1.0
C1 A:K681 1.9 52.4 1.0
C2 A:K681 2.7 51.3 1.0
C6 A:K681 2.9 48.7 1.0
N21 A:K681 3.1 47.5 1.0
BR15 A:K681 3.4 43.2 1.0
O A:HOH606 3.4 45.1 1.0
SD A:MET163 3.7 29.4 1.0
C3 A:K681 4.0 49.2 1.0
CG2 A:VAL45 4.0 23.7 1.0
C5 A:K681 4.2 49.3 1.0
O A:VAL45 4.2 26.6 1.0
C23 A:K681 4.5 51.7 1.0
CB A:VAL45 4.5 26.1 1.0
C4 A:K681 4.7 48.3 1.0
CE A:MET163 4.7 33.1 1.0
C A:VAL45 4.7 25.4 1.0
N25 A:K681 4.8 49.1 1.0
ND2 A:ASN118 5.0 27.9 1.0
CG A:MET163 5.0 21.7 1.0

Bromine binding site 2 out of 4 in 3pvg

Go back to Bromine Binding Sites List in 3pvg
Bromine binding site 2 out of 4 in the Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1

b:43.2
occ:1.00
 BR15 A:K681 0.0 43.2 1.0
C6 A:K681 1.9 48.7 1.0
C1 A:K681 2.9 52.4 1.0
C5 A:K681 2.9 49.3 1.0
O A:VAL116 3.0 33.8 1.0
BR17 A:K681 3.2 59.2 1.0
BR13 A:K681 3.4 67.3 1.0
SD A:MET163 3.7 29.4 1.0
CD1 A:ILE66 3.9 24.0 1.0
C A:VAL116 3.9 32.0 1.0
CG A:MET163 3.9 21.7 1.0
CB A:VAL116 4.1 31.1 1.0
C2 A:K681 4.1 51.3 1.0
CG1 A:ILE66 4.2 25.1 1.0
C4 A:K681 4.2 48.3 1.0
CB A:ASN118 4.3 30.9 1.0
CA A:VAL116 4.4 32.0 1.0
N A:VAL116 4.5 29.1 1.0
C3 A:K681 4.6 49.2 1.0
CB A:MET163 4.7 19.2 1.0
N A:ASN118 4.7 34.1 1.0
CG1 A:VAL116 4.8 34.3 1.0

Bromine binding site 3 out of 4 in 3pvg

Go back to Bromine Binding Sites List in 3pvg
Bromine binding site 3 out of 4 in the Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1

b:59.2
occ:1.00
 BR17 A:K681 0.0 59.2 1.0
C5 A:K681 1.9 49.3 1.0
C6 A:K681 2.9 48.7 1.0
C4 A:K681 2.9 48.3 1.0
BR15 A:K681 3.2 43.2 1.0
BR19 A:K681 3.3 55.9 1.0
CG1 A:ILE66 3.5 25.1 1.0
CG2 A:VAL116 3.9 33.6 1.0
CG2 A:VAL95 4.0 22.2 1.0
CB A:ILE66 4.0 19.9 1.0
CB A:VAL116 4.0 31.1 1.0
CG2 A:ILE174 4.1 15.9 1.0
C1 A:K681 4.2 52.4 1.0
C3 A:K681 4.2 49.2 1.0
N A:VAL116 4.2 29.1 1.0
CG2 A:ILE66 4.2 21.4 1.0
O A:GLU114 4.2 29.3 1.0
CD1 A:ILE66 4.4 24.0 1.0
CG A:MET163 4.7 21.7 1.0
CA A:VAL116 4.7 32.0 1.0
C2 A:K681 4.7 51.3 1.0
O A:VAL116 4.8 33.8 1.0
CB A:PHE113 4.8 18.1 1.0
OE2 A:GLU114 4.8 40.4 1.0

Bromine binding site 4 out of 4 in 3pvg

Go back to Bromine Binding Sites List in 3pvg
Bromine binding site 4 out of 4 in the Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Z. Mays CK2 Alpha Subunit in Complex with the Inhibitor 4,5,6,7-Tetrabromo-1-Carboxymethylbenzimidazole (K68) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1

b:55.9
occ:1.00
 BR19 A:K681 0.0 55.9 1.0
C4 A:K681 1.9 48.3 1.0
O A:HOH439 2.6 23.0 1.0
C5 A:K681 2.9 49.3 1.0
C28 A:K681 2.9 45.8 1.0
C3 A:K681 3.0 49.2 1.0
BR17 A:K681 3.3 59.2 1.0
N25 A:K681 3.4 49.1 1.0
O32 A:K681 3.6 34.2 1.0
CD2 A:PHE113 3.7 17.4 1.0
C30 A:K681 3.8 43.8 1.0
CG A:PHE113 4.0 19.7 1.0
CE2 A:PHE113 4.0 16.4 1.0
CG2 A:ILE66 4.0 21.4 1.0
CG2 A:VAL95 4.1 22.2 1.0
CB A:ILE174 4.1 14.4 1.0
CG2 A:ILE174 4.1 15.9 1.0
C6 A:K681 4.2 48.7 1.0
C2 A:K681 4.3 51.3 1.0
CD1 A:PHE113 4.4 19.7 1.0
CZ A:PHE113 4.4 16.1 1.0
CB A:PHE113 4.5 18.1 1.0
CE1 A:PHE113 4.6 18.3 1.0
CD1 A:ILE174 4.7 15.3 1.0
C1 A:K681 4.7 52.4 1.0
CB A:ILE66 4.7 19.9 1.0
C23 A:K681 4.8 51.7 1.0
O34 A:K681 5.0 45.4 1.0
CG1 A:VAL95 5.0 17.1 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: Wed Jul 10 20:12:34 2024

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