Magnesium in PDB 8qf1: Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp

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

All present enzymatic activity of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp:
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 Gtp Analogue Gmppnp, PDB code: 8qf1 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) 58.60 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.628, 71.59, 102.101, 90, 92.09, 90
R / Rfree (%) 21.4 / 23.2

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 Gtp Analogue Gmppnp (pdb code 8qf1). 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 Gtp Analogue Gmppnp, PDB code: 8qf1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8qf1

Go back to Magnesium Binding Sites List in 8qf1
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 Gtp Analogue Gmppnp


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 Gtp Analogue Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:25.4
occ:1.00
OD1 A:ASP176 1.9 19.5 1.0
OD2 A:ASP176 2.0 21.5 1.0
O1B A:GNP401 2.0 29.6 1.0
O A:HOH668 2.1 28.7 1.0
O A:HOH534 2.1 16.8 1.0
O3G A:GNP401 2.1 28.0 1.0
CG A:ASP176 2.2 15.9 1.0
PG A:GNP401 3.3 29.7 1.0
HD2 A:TYR51 3.3 43.7 1.0
PB A:GNP401 3.3 30.6 1.0
N3B A:GNP401 3.6 28.5 1.0
H A:GLY178 3.7 12.2 1.0
CB A:ASP176 3.7 12.4 1.0
O2G A:GNP401 3.8 25.4 1.0
HZ1 A:LYS69 3.8 23.8 1.0
HA3 A:GLY178 3.9 12.2 1.0
MG A:MG403 3.9 18.7 1.0
OD2 A:ASP157 4.0 12.3 1.0
CD2 A:TYR51 4.0 36.4 1.0
HB3 A:ASP176 4.1 14.9 1.0
HB2 A:ASP176 4.2 14.9 1.0
O2B A:GNP401 4.2 33.6 1.0
HG A:LEU179 4.3 17.3 1.0
O A:ASP176 4.3 11.4 1.0
HE2 A:TYR51 4.3 46.3 1.0
HNB3 A:GNP401 4.3 34.2 1.0
HD21 A:ASN162 4.4 11.2 1.0
HB2 A:TYR51 4.4 39.3 1.0
N A:GLY178 4.4 10.2 1.0
HZ2 A:LYS69 4.4 23.8 1.0
HA A:ASP176 4.4 12.6 1.0
O A:HOH622 4.4 27.9 1.0
O1A A:GNP401 4.4 20.7 1.0
O3A A:GNP401 4.4 28.1 1.0
H A:LEU179 4.5 10.9 1.0
CA A:ASP176 4.5 10.5 1.0
NZ A:LYS69 4.5 19.8 1.0
C A:ASP176 4.5 10.8 1.0
CA A:GLY178 4.5 10.2 1.0
O1G A:GNP401 4.5 29.5 1.0
CE2 A:TYR51 4.6 38.5 1.0
PA A:GNP401 4.9 24.1 1.0
N A:LEU179 4.9 9.1 1.0
O A:HOH522 4.9 43.7 1.0
HE3 A:LYS69 5.0 23.6 1.0
O2A A:GNP401 5.0 21.2 1.0
HD12 A:LEU179 5.0 18.5 1.0
C A:GLY178 5.0 9.2 1.0

Magnesium binding site 2 out of 3 in 8qf1

Go back to Magnesium Binding Sites List in 8qf1
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 Gtp Analogue Gmppnp


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 Gtp Analogue Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:18.7
occ:1.00
OD1 A:ASN162 2.0 11.7 1.0
O1A A:GNP401 2.1 20.7 1.0
OD2 A:ASP176 2.1 21.5 1.0
O A:HOH663 2.1 22.6 1.0
O2G A:GNP401 2.1 25.4 1.0
HNB3 A:GNP401 2.4 34.2 1.0
N3B A:GNP401 2.5 28.5 1.0
PG A:GNP401 2.8 29.7 1.0
HD21 A:ASN162 3.0 11.2 1.0
CG A:ASP176 3.0 15.9 1.0
CG A:ASN162 3.0 9.4 1.0
HB2 A:ASP176 3.1 14.9 1.0
HB3 A:ASP176 3.4 14.9 1.0
CB A:ASP176 3.4 12.4 1.0
ND2 A:ASN162 3.4 9.3 1.0
PA A:GNP401 3.5 24.1 1.0
O3G A:GNP401 3.6 28.0 1.0
H5'2 A:GNP401 3.6 29.4 1.0
PB A:GNP401 3.7 30.6 1.0
MG A:MG402 3.9 25.4 1.0
O1B A:GNP401 3.9 29.6 1.0
HE3 A:LYS159 4.0 14.7 1.0
O3A A:GNP401 4.0 28.1 1.0
HE2 A:LYS159 4.0 14.7 1.0
O1G A:GNP401 4.1 29.5 1.0
OD1 A:ASP176 4.2 19.5 1.0
HZ1 A:LYS159 4.2 18.1 1.0
HD22 A:ASN162 4.2 11.2 1.0
HO3' A:GNP401 4.2 27.9 1.0
HA A:ASN162 4.3 10.6 1.0
O2A A:GNP401 4.3 21.2 1.0
HB3 A:HIS161 4.3 16.8 1.0
O3' A:GNP401 4.4 23.3 1.0
CB A:ASN162 4.4 8.9 1.0
CE A:LYS159 4.4 12.3 1.0
C5' A:GNP401 4.4 24.5 1.0
O5' A:GNP401 4.4 23.1 1.0
H3' A:GNP401 4.5 29.4 1.0
OD2 A:ASP157 4.5 12.3 1.0
O A:HIS161 4.6 10.8 1.0
HA3 A:GLY49 4.7 42.0 1.0
O A:HOH534 4.7 16.8 1.0
HD11 A:ILE175 4.7 8.6 1.0
CA A:ASN162 4.8 8.8 1.0
HB3 A:ASN162 4.8 10.7 1.0
NZ A:LYS159 4.8 15.1 1.0
HG13 A:ILE175 4.8 9.1 1.0
CA A:ASP176 4.9 10.5 1.0
C3' A:GNP401 4.9 24.5 1.0
C A:HIS161 4.9 10.6 1.0
O A:HOH522 4.9 43.7 1.0
N A:ASN162 5.0 9.8 1.0
HD12 A:ILE175 5.0 8.6 1.0

Magnesium binding site 3 out of 3 in 8qf1

Go back to Magnesium Binding Sites List in 8qf1
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 Gtp Analogue Gmppnp


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 Gtp Analogue Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:36.1
occ:1.00
OD2 B:ASP176 2.1 33.9 1.0
OD1 B:ASN162 2.2 29.7 1.0
O B:HOH637 2.6 56.5 1.0
HD21 B:ASN162 3.0 33.2 1.0
CG B:ASP176 3.1 32.0 1.0
CG B:ASN162 3.1 25.9 1.0
HB2 B:ASP176 3.3 32.8 1.0
ND2 B:ASN162 3.4 27.6 1.0
HB3 B:ASP176 3.4 32.8 1.0
HE1 B:HIS161 3.5 40.7 1.0
CB B:ASP176 3.5 27.4 1.0
ND1 B:HIS161 3.6 34.1 1.0
HE3 B:LYS159 3.8 29.7 1.0
CE1 B:HIS161 3.8 33.9 1.0
HZ3 B:LYS159 4.0 32.8 1.0
HE2 B:LYS159 4.1 29.7 1.0
OD1 B:ASP176 4.3 32.8 1.0
HD22 B:ASN162 4.3 33.2 1.0
CE B:LYS159 4.3 24.8 1.0
OD2 B:ASP157 4.4 23.0 1.0
CB B:ASN162 4.5 24.1 1.0
HA B:ASN162 4.6 27.7 1.0
NZ B:LYS159 4.6 27.3 1.0
CG B:HIS161 4.8 30.1 1.0
HB3 B:ASN162 4.8 28.9 1.0
HB3 B:HIS161 4.9 29.8 1.0
O B:HOH625 4.9 40.1 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: Fri Oct 4 16:41:37 2024

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