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Zinc in PDB 4md7: Crystal Structure of Full-Length Symmetric CK2 Holoenzyme

Enzymatic activity of Crystal Structure of Full-Length Symmetric CK2 Holoenzyme

All present enzymatic activity of Crystal Structure of Full-Length Symmetric CK2 Holoenzyme:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Full-Length Symmetric CK2 Holoenzyme, PDB code: 4md7 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) 181.83 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 142.316, 57.958, 186.188, 90.00, 102.42, 90.00
R / Rfree (%) 23.3 / 26.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Full-Length Symmetric CK2 Holoenzyme (pdb code 4md7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Full-Length Symmetric CK2 Holoenzyme, PDB code: 4md7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4md7

Go back to Zinc Binding Sites List in 4md7
Zinc binding site 1 out of 4 in the Crystal Structure of Full-Length Symmetric CK2 Holoenzyme


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 Full-Length Symmetric CK2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:14.6
occ:1.00
SG A:CYS109 2.1 23.2 1.0
SG A:CYS140 2.2 17.6 1.0
SG A:CYS114 2.3 16.3 1.0
SG A:CYS137 2.3 16.6 1.0
CB A:CYS137 3.1 15.7 1.0
CB A:CYS114 3.2 17.8 1.0
CB A:CYS109 3.3 21.3 1.0
CB A:CYS140 3.3 19.1 1.0
N A:CYS140 3.8 19.6 1.0
CB A:ARG111 4.0 31.9 1.0
OH A:TYR144 4.1 20.0 1.0
CA A:CYS140 4.2 20.2 1.0
CE1 A:TYR144 4.2 19.9 1.0
NH1 A:ARG111 4.2 36.1 1.0
CD A:ARG111 4.3 36.6 1.0
CZ A:TYR144 4.6 19.8 1.0
CA A:CYS137 4.6 15.7 1.0
CG A:ARG111 4.6 35.3 1.0
CA A:CYS114 4.6 19.7 1.0
CA A:CYS109 4.7 21.2 1.0
CB A:LYS139 4.9 19.7 1.0
C A:LYS139 4.9 19.6 1.0

Zinc binding site 2 out of 4 in 4md7

Go back to Zinc Binding Sites List in 4md7
Zinc binding site 2 out of 4 in the Crystal Structure of Full-Length Symmetric CK2 Holoenzyme


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 Full-Length Symmetric CK2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:17.9
occ:1.00
SG B:CYS109 2.2 21.6 1.0
SG B:CYS114 2.2 21.9 1.0
SG B:CYS137 2.3 22.4 1.0
SG B:CYS140 2.3 21.2 1.0
CB B:CYS137 3.1 22.0 1.0
CB B:CYS114 3.2 23.6 1.0
CB B:CYS140 3.2 22.2 1.0
CB B:CYS109 3.3 22.8 1.0
N B:CYS140 3.7 23.4 1.0
CA B:CYS140 4.1 23.0 1.0
CB B:ARG111 4.1 20.9 1.0
OH B:TYR144 4.2 21.9 1.0
CE1 B:TYR144 4.3 22.3 1.0
NH1 B:ARG111 4.3 22.3 1.0
CD B:ARG111 4.4 20.2 1.0
CA B:CYS137 4.6 22.1 1.0
CA B:CYS114 4.6 24.9 1.0
CZ B:TYR144 4.7 22.0 1.0
CA B:CYS109 4.7 23.6 1.0
CB B:LYS139 4.7 26.2 1.0
CG B:ARG111 4.7 20.4 1.0
C B:LYS139 4.8 24.5 1.0
C B:CYS140 4.9 22.7 1.0
O B:CYS137 4.9 21.6 1.0
C B:CYS137 4.9 22.1 1.0

Zinc binding site 3 out of 4 in 4md7

Go back to Zinc Binding Sites List in 4md7
Zinc binding site 3 out of 4 in the Crystal Structure of Full-Length Symmetric CK2 Holoenzyme


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 Full-Length Symmetric CK2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:32.4
occ:1.00
SG C:CYS140 2.1 38.5 1.0
SG C:CYS114 2.3 40.4 1.0
SG C:CYS109 2.3 37.2 1.0
SG C:CYS137 2.4 40.3 1.0
CB C:CYS137 3.1 40.6 1.0
CB C:CYS140 3.1 40.2 1.0
CB C:CYS114 3.4 42.1 1.0
CB C:CYS109 3.4 38.2 1.0
N C:CYS140 3.7 40.6 1.0
CA C:CYS140 4.0 40.7 1.0
OH C:TYR144 4.0 47.2 1.0
CB C:ARG111 4.1 40.6 1.0
CE1 C:TYR144 4.2 47.2 1.0
NH1 C:ARG111 4.3 42.0 1.0
CD C:ARG111 4.3 40.2 1.0
CZ C:TYR144 4.5 47.5 1.0
CA C:CYS137 4.5 40.5 1.0
CG C:ARG111 4.6 40.6 1.0
CA C:CYS114 4.7 44.4 1.0
CB C:LYS139 4.8 42.4 1.0
C C:LYS139 4.8 41.5 1.0
CA C:CYS109 4.8 39.1 1.0
C C:CYS140 4.8 40.5 1.0
O C:CYS137 4.9 41.5 1.0
C C:CYS137 4.9 41.0 1.0

Zinc binding site 4 out of 4 in 4md7

Go back to Zinc Binding Sites List in 4md7
Zinc binding site 4 out of 4 in the Crystal Structure of Full-Length Symmetric CK2 Holoenzyme


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 Full-Length Symmetric CK2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:36.7
occ:1.00
SG D:CYS140 2.2 43.2 1.0
SG D:CYS109 2.2 41.9 1.0
SG D:CYS114 2.3 40.4 1.0
SG D:CYS137 2.3 43.7 1.0
CB D:CYS137 3.1 43.4 1.0
CB D:CYS114 3.2 42.8 1.0
CB D:CYS140 3.3 44.1 1.0
CB D:CYS109 3.3 41.6 1.0
N D:CYS140 3.7 44.8 1.0
CA D:CYS140 4.1 44.5 1.0
CB D:ARG111 4.1 41.4 1.0
OH D:TYR144 4.1 47.8 1.0
CE1 D:TYR144 4.2 48.5 1.0
NH1 D:ARG111 4.3 40.0 1.0
CD D:ARG111 4.3 39.7 1.0
CA D:CYS137 4.5 43.0 1.0
CZ D:TYR144 4.6 48.4 1.0
CG D:ARG111 4.7 41.0 1.0
CA D:CYS114 4.7 44.7 1.0
CA D:CYS109 4.7 41.7 1.0
CB D:LYS139 4.7 47.0 1.0
C D:LYS139 4.8 45.5 1.0
C D:CYS137 4.9 42.9 1.0
O D:CYS137 4.9 42.2 1.0
C D:CYS140 5.0 45.0 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: Wed Dec 16 05:34:40 2020

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