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Magnesium in PDB 5r9a: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha:
2.7.11.24;

Protein crystallography data

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha, PDB code: 5r9a was solved by G.F.De Nicola, C.E.Nichols, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.94 / 1.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.600, 86.390, 125.640, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 20.8

Other elements in 5r9a:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha (pdb code 5r9a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha, PDB code: 5r9a:

Magnesium binding site 1 out of 1 in 5r9a

Go back to Magnesium Binding Sites List in 5r9a
Magnesium binding site 1 out of 1 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:34.2
occ:1.00
 O A:HOH579 2.0 31.7 1.0
O A:HOH575 2.0 33.7 1.0
O A:HOH521 2.1 35.6 1.0
O A:HOH580 2.1 36.5 1.0
OD1 A:ASN155 2.2 28.2 1.0
OD2 A:ASP168 2.2 37.7 1.0
CG A:ASP168 3.3 38.5 1.0
CG A:ASN155 3.3 25.4 1.0
CB A:ASP168 3.7 27.1 1.0
ND2 A:ASN155 3.8 25.5 1.0
O A:SER154 4.1 27.4 1.0
O1 A:SO4411 4.1 45.3 0.7
O3 A:SO4411 4.1 51.9 0.7
OD1 A:ASP168 4.4 38.0 1.0
OG A:SER154 4.5 23.6 1.0
CB A:ASN155 4.5 20.9 1.0
S A:SO4411 4.5 55.7 0.7
C A:SER154 4.6 26.6 1.0
CA A:ASN155 4.6 22.4 1.0
O2 A:SO4411 4.7 48.7 0.7
N A:ASN155 4.8 19.8 1.0
CE A:LYS152 5.0 27.4 1.0
CB A:SER154 5.0 23.5 1.0

Reference:

C.Nichols, J.Ng, A.Keshu, G.Kelly, M.R.Conte, M.S.Marber, F.Fraternali, G.F.De Nicola. Mining the Pdb For Tractable Cases Where X-Ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated By IL1 Beta-IL1R and P38 Alpha-TAB1 Complexes. J.Med.Chem. V. 63 7559 2020.
ISSN: ISSN 0022-2623
PubMed: 32543856
DOI: 10.1021/ACS.JMEDCHEM.0C00403
Page generated: Tue Aug 12 18:44:47 2025

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