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Magnesium in PDB 8qcg: Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp

Enzymatic activity of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp

All present enzymatic activity of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp:
2.7.11.1;

Protein crystallography data

The structure of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp, PDB code: 8qcg was solved by C.Werner, D.Lindenblatt, K.Niefind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.04 / 1.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.599, 71.852, 101.984, 90, 92.42, 90
R / Rfree (%) 15.1 / 17

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp (pdb code 8qcg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp, PDB code: 8qcg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8qcg

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Magnesium binding site 1 out of 3 in the Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:21.8
occ:1.00
 O2G A:ANP401 1.8 31.6 1.0
O1A A:ANP401 1.8 19.7 1.0
OD2 A:ASP176 2.0 18.5 1.0
OD1 A:ASN162 2.2 10.1 1.0
PG A:ANP401 2.7 42.1 1.0
O A:HOH521 2.9 28.3 1.0
HB2 A:ASP176 2.9 14.1 1.0
N3B A:ANP401 2.9 37.1 1.0
CG A:ASP176 3.0 15.4 1.0
HNB1 A:ANP401 3.2 44.5 1.0
PA A:ANP401 3.2 17.2 1.0
HD21 A:ASN162 3.2 11.3 1.0
CG A:ASN162 3.2 8.2 1.0
CB A:ASP176 3.3 11.8 1.0
HB3 A:ASP176 3.4 14.1 1.0
O1G A:ANP401 3.4 38.4 1.0
ND2 A:ASN162 3.6 9.4 1.0
PB A:ANP401 3.7 28.9 1.0
O2A A:ANP401 3.8 15.0 1.0
O1B A:ANP401 3.8 17.9 1.0
O3A A:ANP401 3.9 20.1 1.0
O3G A:ANP401 4.0 47.2 1.0
OD1 A:ASP176 4.1 17.9 1.0
H5'2 A:ANP401 4.1 17.9 1.0
HE3 A:LYS159 4.2 20.4 1.0
O A:HOH564 4.3 32.0 1.0
O5' A:ANP401 4.3 16.0 1.0
HA A:ASN162 4.3 9.3 1.0
HD22 A:ASN162 4.4 11.3 1.0
O A:HOH865 4.4 35.9 1.0
CB A:ASN162 4.5 7.6 1.0
HE2 A:LYS159 4.6 20.4 1.0
HD11 A:ILE175 4.6 10.7 1.0
HZ3 A:LYS159 4.7 26.8 1.0
HG13 A:ILE175 4.7 9.4 1.0
HD12 A:ILE175 4.7 10.7 1.0
HB2 A:HIS161 4.7 17.5 1.0
OD2 A:ASP157 4.7 13.0 1.0
C5' A:ANP401 4.7 14.9 1.0
O A:HIS161 4.8 12.0 1.0
CA A:ASP176 4.8 9.9 1.0
HZ2 A:LYS69 4.8 33.3 1.0
CE A:LYS159 4.8 17.0 1.0
HB3 A:ASN162 4.9 9.1 1.0
CA A:ASN162 4.9 7.8 1.0
HA A:ASP176 4.9 11.8 1.0

Magnesium binding site 2 out of 3 in 8qcg

Go back to Magnesium Binding Sites List in 8qcg
Magnesium binding site 2 out of 3 in the Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:30.9
occ:1.00
 O3G B:ANP401 2.0 37.9 1.0
O2A B:ANP401 2.0 32.9 1.0
OD1 B:ASN162 2.1 15.5 1.0
OD2 B:ASP176 2.2 31.0 1.0
O B:HOH511 2.6 40.1 1.0
PG B:ANP401 2.9 43.4 1.0
N3B B:ANP401 2.9 43.9 1.0
HB2 B:ASP176 3.0 21.5 1.0
CG B:ASP176 3.1 26.5 1.0
HNB1 B:ANP401 3.1 52.7 1.0
CG B:ASN162 3.2 13.0 1.0
HD21 B:ASN162 3.2 17.2 1.0
CB B:ASP176 3.4 17.9 1.0
PA B:ANP401 3.5 30.6 1.0
HB3 B:ASP176 3.5 21.5 1.0
ND2 B:ASN162 3.6 14.4 1.0
H5'1 B:ANP401 3.7 37.8 1.0
PB B:ANP401 3.8 40.7 1.0
O1B B:ANP401 3.8 40.6 1.0
O2G B:ANP401 3.8 38.6 1.0
O3A B:ANP401 4.0 37.9 1.0
HE3 B:LYS159 4.0 27.3 1.0
MG B:MG403 4.1 34.9 1.0
O1G B:ANP401 4.1 48.2 1.0
OD1 B:ASP176 4.2 28.4 1.0
HA B:ASN162 4.3 14.1 1.0
HE2 B:LYS159 4.3 27.3 1.0
HZ3 B:LYS159 4.3 33.9 1.0
O1A B:ANP401 4.4 32.7 1.0
HD22 B:ASN162 4.4 17.2 1.0
O5' B:ANP401 4.4 29.7 1.0
C5' B:ANP401 4.5 31.5 1.0
CB B:ASN162 4.5 12.3 1.0
CE B:LYS159 4.6 22.7 1.0
HB2 B:HIS161 4.6 24.7 1.0
O B:HIS161 4.7 16.9 1.0
O B:HOH678 4.7 48.3 1.0
HD11 B:ILE175 4.7 16.8 1.0
OD2 B:ASP157 4.7 15.6 1.0
H3' B:ANP401 4.8 38.6 1.0
HD12 B:ILE175 4.8 16.8 1.0
HG13 B:ILE175 4.8 15.8 1.0
CA B:ASN162 4.8 11.8 1.0
CA B:ASP176 4.9 14.2 1.0
HB3 B:ASN162 4.9 14.8 1.0
NZ B:LYS159 4.9 28.3 1.0
O3' B:ANP401 5.0 34.0 1.0
C B:HIS161 5.0 14.6 1.0

Magnesium binding site 3 out of 3 in 8qcg

Go back to Magnesium Binding Sites List in 8qcg
Magnesium binding site 3 out of 3 in the Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Atp Analogue Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:34.9
occ:1.00
 OD1 B:ASP176 1.9 28.4 1.0
O B:HOH710 2.1 36.6 1.0
OD2 B:ASP176 2.1 31.0 1.0
O2G B:ANP401 2.1 38.6 1.0
O B:HOH587 2.1 31.1 1.0
O1B B:ANP401 2.1 40.6 1.0
CG B:ASP176 2.3 26.5 1.0
PG B:ANP401 3.2 43.4 1.0
PB B:ANP401 3.4 40.7 1.0
O3G B:ANP401 3.6 37.9 1.0
H B:GLY178 3.7 17.6 1.0
CB B:ASP176 3.8 17.9 1.0
HA3 B:GLY178 3.8 19.7 1.0
N3B B:ANP401 3.8 43.9 1.0
HZ2 B:LYS69 4.0 36.9 1.0
OD2 B:ASP157 4.0 15.6 1.0
MG B:MG402 4.1 30.9 1.0
HB3 B:ASP176 4.1 21.5 1.0
HB2 B:ASP176 4.2 21.5 1.0
HG B:LEU179 4.3 21.6 1.0
O2B B:ANP401 4.3 46.0 1.0
O B:HOH621 4.3 35.3 0.6
N B:GLY178 4.4 14.7 1.0
HD21 B:ASN162 4.4 17.2 1.0
HA B:ASP176 4.4 17.0 1.0
O B:ASP176 4.4 15.4 1.0
H B:LEU179 4.5 16.5 1.0
CA B:GLY178 4.5 16.4 1.0
O B:HOH618 4.5 35.2 1.0
O1G B:ANP401 4.5 48.2 1.0
O2A B:ANP401 4.5 32.9 1.0
CA B:ASP176 4.5 14.2 1.0
C B:ASP176 4.6 14.2 1.0
HNB1 B:ANP401 4.6 52.7 1.0
O3A B:ANP401 4.6 37.9 1.0
HZ3 B:LYS69 4.8 36.9 1.0
NZ B:LYS69 4.8 30.7 1.0
N B:LEU179 4.8 13.8 1.0
HB2 B:TYR51 4.9 64.8 1.0
C B:GLY178 4.9 14.9 1.0

Reference:

C.Werner, D.Lindenblatt, K.Viht, A.Uri, K.Niefind. Discovery and Exploration of Protein Kinase CK2 Binding Sites Using CK2ALPHA CYS336SER As An Exquisite Crystallographic Tool Kinases Phosphatases 2023.
DOI: 10.3390/KINASESPHOSPHATASES1040018
Page generated: Thu Dec 28 10:07:03 2023

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