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Zinc in PDB 4md9: Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336)

Enzymatic activity of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336)

All present enzymatic activity of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336):
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336), PDB code: 4md9 was solved by G.Lolli, A.Ranchio, R.Battistutta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 181.72 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 283.924, 115.707, 208.223, 90.00, 119.22, 90.00
R / Rfree (%) 22.9 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336) (pdb code 4md9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336), PDB code: 4md9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4md9

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Zinc binding site 1 out of 8 in the Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:58.3
occ:1.00
 SG A:CYS109 2.2 63.5 1.0
SG A:CYS140 2.3 62.5 1.0
SG A:CYS114 2.3 67.6 1.0
SG A:CYS137 2.3 65.2 1.0
CB A:CYS137 3.2 61.8 1.0
CB A:CYS140 3.3 60.0 1.0
CB A:CYS109 3.3 63.2 1.0
CB A:CYS114 3.4 71.6 1.0
N A:CYS140 3.7 67.0 1.0
CA A:CYS140 4.0 63.0 1.0
OH A:TYR144 4.1 61.5 1.0
NH1 A:ARG111 4.1 63.4 1.0
CB A:ARG111 4.2 60.6 1.0
CE1 A:TYR144 4.3 60.9 1.0
CZ A:TYR144 4.6 58.8 1.0
CA A:CYS137 4.6 65.3 1.0
CB A:LYS139 4.6 62.0 1.0
CD A:ARG111 4.7 60.1 1.0
C A:LYS139 4.7 67.6 1.0
CA A:CYS109 4.7 63.5 1.0
CA A:CYS114 4.8 71.8 1.0
CG A:ARG111 4.9 59.8 1.0
C A:CYS140 4.9 61.5 1.0

Zinc binding site 2 out of 8 in 4md9

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Zinc binding site 2 out of 8 in the Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:66.6
occ:1.00
 SG B:CYS109 2.1 61.7 1.0
SG B:CYS137 2.3 70.2 1.0
SG B:CYS114 2.3 65.5 1.0
SG B:CYS140 2.7 68.6 1.0
CB B:CYS137 3.2 69.0 1.0
CB B:CYS109 3.3 65.5 1.0
CB B:CYS114 3.3 72.6 1.0
CB B:CYS140 3.4 66.1 1.0
N B:CYS140 3.8 72.3 1.0
OH B:TYR144 4.1 61.9 1.0
CA B:CYS140 4.2 67.8 1.0
CB B:ARG111 4.3 68.0 1.0
CE1 B:TYR144 4.3 58.7 1.0
NH1 B:ARG111 4.5 62.8 1.0
CZ B:TYR144 4.6 60.2 1.0
CB B:LYS139 4.6 76.9 1.0
CA B:CYS109 4.7 66.8 1.0
CA B:CYS137 4.7 65.8 1.0
CA B:CYS114 4.8 75.3 1.0
CD B:ARG111 4.9 67.9 1.0
C B:LYS139 4.9 74.7 1.0

Zinc binding site 3 out of 8 in 4md9

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Zinc binding site 3 out of 8 in the Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:63.8
occ:1.00
 SG C:CYS137 2.2 77.2 1.0
SG C:CYS109 2.3 59.4 1.0
SG C:CYS140 2.3 65.0 1.0
SG C:CYS114 2.5 59.5 1.0
CB C:CYS140 3.1 61.9 1.0
CB C:CYS137 3.2 68.3 1.0
CB C:CYS109 3.4 59.6 1.0
CB C:CYS114 3.5 65.0 1.0
N C:CYS140 3.6 64.5 1.0
CA C:CYS140 3.9 61.1 1.0
OH C:TYR144 4.2 63.6 1.0
CB C:ARG111 4.2 64.3 1.0
NH1 C:ARG111 4.2 72.5 1.0
CE1 C:TYR144 4.5 59.1 1.0
CD C:ARG111 4.5 64.7 1.0
CB C:LYS139 4.5 70.7 1.0
C C:LYS139 4.6 67.5 1.0
CA C:CYS137 4.6 67.8 1.0
CZ C:TYR144 4.7 60.8 1.0
CA C:CYS109 4.8 62.7 1.0
CG C:ARG111 4.8 64.1 1.0
N C:LYS139 4.9 66.4 1.0
CA C:CYS114 4.9 66.2 1.0
CA C:LYS139 4.9 67.5 1.0
C C:CYS140 4.9 57.9 1.0
C C:CYS137 5.0 65.5 1.0

Zinc binding site 4 out of 8 in 4md9

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Zinc binding site 4 out of 8 in the Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:63.5
occ:1.00
 SG D:CYS109 2.2 55.6 1.0
SG D:CYS114 2.4 61.2 1.0
SG D:CYS137 2.4 71.4 1.0
SG D:CYS140 2.6 63.3 1.0
CB D:CYS137 3.2 69.2 1.0
CB D:CYS140 3.3 65.9 1.0
CB D:CYS114 3.3 64.7 1.0
CB D:CYS109 3.4 58.2 1.0
N D:CYS140 3.7 73.3 1.0
NH1 D:ARG111 3.9 74.6 1.0
OH D:TYR144 4.1 68.4 1.0
CA D:CYS140 4.1 69.4 1.0
CE1 D:TYR144 4.3 67.7 1.0
CB D:ARG111 4.3 73.0 1.0
CZ D:TYR144 4.6 67.7 1.0
CB D:LYS139 4.6 70.2 1.0
CA D:CYS137 4.7 68.2 1.0
CA D:CYS109 4.7 60.5 1.0
CD D:ARG111 4.8 73.1 1.0
CA D:CYS114 4.8 68.0 1.0
C D:LYS139 4.8 73.1 1.0

Zinc binding site 5 out of 8 in 4md9

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Zinc binding site 5 out of 8 in the Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn301

b:70.1
occ:1.00
 SG I:CYS137 2.3 81.4 1.0
SG I:CYS109 2.4 72.8 1.0
SG I:CYS114 2.4 72.5 1.0
SG I:CYS140 2.5 80.3 1.0
CB I:CYS114 3.3 74.4 1.0
CB I:CYS140 3.3 83.0 1.0
CB I:CYS137 3.3 81.0 1.0
CB I:CYS109 3.5 74.0 1.0
N I:CYS140 3.5 84.7 1.0
OH I:TYR144 3.8 79.1 1.0
CA I:CYS140 4.0 84.4 1.0
CB I:LYS139 4.2 84.3 1.0
CB I:ARG111 4.3 81.0 1.0
CE1 I:TYR144 4.3 78.7 1.0
CD I:ARG111 4.5 84.0 1.0
CZ I:TYR144 4.5 79.5 1.0
NH1 I:ARG111 4.5 92.2 1.0
C I:LYS139 4.5 86.2 1.0
CG I:ARG111 4.7 84.1 1.0
CA I:CYS137 4.7 77.0 1.0
CA I:LYS139 4.7 83.3 1.0
CA I:CYS114 4.7 75.5 1.0
N I:LYS139 4.8 78.4 1.0
CA I:CYS109 4.9 74.7 1.0
C I:CYS137 5.0 77.8 1.0

Zinc binding site 6 out of 8 in 4md9

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Zinc binding site 6 out of 8 in the Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:77.1
occ:1.00
 SG J:CYS140 2.4 80.4 1.0
SG J:CYS114 2.4 90.2 1.0
SG J:CYS109 2.4 67.0 1.0
SG J:CYS137 2.4 95.5 1.0
CB J:CYS140 3.1 77.5 1.0
CB J:CYS137 3.3 85.4 1.0
CB J:CYS114 3.5 89.2 1.0
N J:CYS140 3.5 80.1 1.0
CB J:CYS109 3.6 74.1 1.0
CA J:CYS140 3.9 77.3 1.0
NH1 J:ARG111 4.1 80.6 1.0
OH J:TYR144 4.1 82.6 1.0
CB J:ARG111 4.2 85.2 1.0
CE1 J:TYR144 4.3 76.3 1.0
CD J:ARG111 4.5 82.1 1.0
CB J:LYS139 4.6 81.6 1.0
CZ J:TYR144 4.6 78.2 1.0
C J:LYS139 4.7 83.3 1.0
CA J:CYS137 4.7 81.0 1.0
CG J:ARG111 4.8 82.8 1.0
C J:CYS140 4.8 76.9 1.0
CA J:CYS114 4.9 86.7 1.0
N J:MET141 5.0 75.4 1.0
CA J:CYS109 5.0 76.6 1.0
CA J:LYS139 5.0 81.0 1.0

Zinc binding site 7 out of 8 in 4md9

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Zinc binding site 7 out of 8 in the Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn301

b:73.7
occ:1.00
 SG N:CYS114 2.3 79.0 1.0
SG N:CYS137 2.5 88.2 1.0
SG N:CYS109 2.6 68.6 1.0
SG N:CYS140 2.7 85.2 1.0
CB N:CYS140 3.2 83.5 1.0
CB N:CYS114 3.3 80.9 1.0
CB N:CYS137 3.4 88.8 1.0
CB N:CYS109 3.6 74.4 1.0
N N:CYS140 3.6 84.1 1.0
OH N:TYR144 4.0 76.6 1.0
CA N:CYS140 4.0 82.7 1.0
CB N:ARG111 4.1 91.8 1.0
CD N:ARG111 4.1 88.7 1.0
NH1 N:ARG111 4.3 96.9 1.0
CB N:LYS139 4.4 86.3 1.0
CE1 N:TYR144 4.4 72.4 1.0
CG N:ARG111 4.6 91.5 1.0
CZ N:TYR144 4.6 73.3 1.0
CA N:CYS114 4.7 86.7 1.0
C N:LYS139 4.7 86.2 1.0
CA N:CYS137 4.9 90.1 1.0
CA N:LYS139 5.0 87.0 1.0

Zinc binding site 8 out of 8 in 4md9

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Zinc binding site 8 out of 8 in the Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Symmetric CK2 Holoenzyme with Mutated Alpha Subunit (F121E Truncated at Aa 336) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn301

b:59.6
occ:1.00
 SG O:CYS140 2.3 82.7 1.0
SG O:CYS114 2.3 81.9 1.0
SG O:CYS137 2.3 0.0 1.0
SG O:CYS109 2.5 73.7 1.0
CB O:CYS140 3.2 79.4 1.0
CB O:CYS137 3.2 91.3 1.0
CB O:CYS114 3.3 84.9 1.0
N O:CYS140 3.6 84.6 1.0
CB O:CYS109 3.6 73.2 1.0
CA O:CYS140 4.0 79.2 1.0
CB O:ARG111 4.2 73.3 1.0
OH O:TYR144 4.2 77.7 1.0
CE1 O:TYR144 4.3 76.1 1.0
CD O:ARG111 4.4 72.8 1.0
NH1 O:ARG111 4.4 72.2 1.0
CB O:LYS139 4.5 79.6 1.0
CG O:ARG111 4.6 71.8 1.0
C O:LYS139 4.6 83.6 1.0
CZ O:TYR144 4.7 77.8 1.0
CA O:CYS137 4.7 86.3 1.0
CA O:CYS114 4.7 86.1 1.0
N O:LYS139 4.9 76.9 1.0
CA O:LYS139 4.9 78.9 1.0
C O:CYS140 5.0 74.0 1.0
CA O:CYS109 5.0 75.8 1.0

Reference:

G.Lolli, A.Ranchio, R.Battistutta. Active Form of the Protein Kinase CK2 Alpha 2 Beta 2 Holoenzyme Is A Strong Complex with Symmetric Architecture. Acs Chem.Biol. V. 9 366 2014.
ISSN: ISSN 1554-8929
PubMed: 24175891
DOI: 10.1021/CB400771Y
Page generated: Sun Oct 27 02:22:24 2024

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