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Magnesium in PDB 5kb5: Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate

Enzymatic activity of Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate

All present enzymatic activity of Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate:
2.7.1.20;

Protein crystallography data

The structure of Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate, PDB code: 5kb5 was solved by R.R.Oliveira, R.M.Neto, C.C.Polo, C.C.C.Tonoli, M.T.Murakami, K.G.Franchini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.63 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.264, 73.559, 84.330, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20

Other elements in 5kb5:

The structure of Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate (pdb code 5kb5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate, PDB code: 5kb5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5kb5

Go back to Magnesium Binding Sites List in 5kb5
Magnesium binding site 1 out of 2 in the Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:24.2
occ:1.00
O A:HOH554 2.0 29.4 1.0
O A:HOH517 2.3 25.3 1.0
O A:HOH514 2.3 23.8 1.0
O2B A:ADP402 2.3 18.9 1.0
O A:HOH555 2.4 25.2 1.0
PB A:ADP402 3.5 18.4 1.0
O3B A:ADP402 3.9 17.8 1.0
O A:HOH527 3.9 16.9 1.0
O A:HOH607 3.9 37.5 1.0
O1B A:ADP402 4.0 19.4 1.0
O A:HOH608 4.1 22.4 1.0
OE2 A:GLU242 4.2 26.3 1.0
O A:SER214 4.2 17.0 1.0
OE1 A:GLU242 4.4 21.9 1.0
O A:HOH519 4.4 19.2 1.0
OD1 A:ASP316 4.5 18.2 1.0
CA A:GLY315 4.5 14.4 1.0
O5' A:ADN401 4.6 20.3 1.0
NH1 A:ARG148 4.6 33.6 1.0
O A:HOH563 4.6 26.2 1.0
O3A A:ADP402 4.7 16.5 1.0
CD A:GLU242 4.7 21.1 1.0
ND2 A:ASN239 4.8 21.0 1.0
OD1 A:ASN212 4.8 16.0 1.0
C A:GLY315 4.8 14.2 1.0
NE2 A:GLN54 4.9 27.8 1.0
N A:ASP316 4.9 14.6 1.0
N A:GLY315 5.0 14.3 1.0

Magnesium binding site 2 out of 2 in 5kb5

Go back to Magnesium Binding Sites List in 5kb5
Magnesium binding site 2 out of 2 in the Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:31.6
occ:1.00
O A:HOH534 2.2 23.1 1.0
O A:HOH568 2.2 44.3 1.0
O1A A:ADP402 2.3 16.6 1.0
O A:HOH538 2.3 31.3 1.0
O A:HOH522 2.5 19.0 1.0
O A:HOH512 3.6 44.2 1.0
O1B A:ADP402 3.7 19.4 1.0
PA A:ADP402 3.7 17.4 1.0
OG1 A:THR311 4.1 20.7 1.0
CB A:THR311 4.2 19.9 1.0
O3B A:ADP402 4.2 17.8 1.0
PB A:ADP402 4.2 18.4 1.0
ND2 A:ASN52 4.3 29.7 1.0
O5' A:ADP402 4.3 15.6 1.0
O3A A:ADP402 4.3 16.5 1.0
N7 A:ADP402 4.4 17.6 1.0
OD1 A:ASN52 4.5 28.2 1.0
C8 A:ADP402 4.6 17.4 1.0
NH1 A:ARG148 4.7 33.6 1.0
CG2 A:THR311 4.7 21.7 1.0
O A:THR311 4.8 17.2 1.0
O2A A:ADP402 4.8 15.3 1.0
CG A:ASN52 4.8 28.4 1.0
O A:GLY146 4.9 27.1 1.0
CZ A:ARG148 4.9 30.6 1.0
O A:HOH616 5.0 33.8 1.0

Reference:

R.R.Oliveira, R.M.Neto, C.C.Polo, C.C.C.Tonoli, M.T.Murakami, K.G.Franchini. Crystal Structure of the Adenosine Kinase From Mus Musculus in Complex with Adenosine and Adenosine-Diphosphate To Be Published.
Page generated: Sun Sep 29 18:55:41 2024

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