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Magnesium in PDB 7dmc: Dipyridamole Binds to the N-Terminal Domain of Human HSP90A

Protein crystallography data

The structure of Dipyridamole Binds to the N-Terminal Domain of Human HSP90A, PDB code: 7dmc was solved by L.Shi, C.Zhou, Y.Zhong, J.Gao, H.Zhou, N.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.95 / 2.34
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.489, 89.937, 99.067, 90, 90, 90
R / Rfree (%) 20.3 / 24.4

Other elements in 7dmc:

The structure of Dipyridamole Binds to the N-Terminal Domain of Human HSP90A also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dipyridamole Binds to the N-Terminal Domain of Human HSP90A (pdb code 7dmc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dipyridamole Binds to the N-Terminal Domain of Human HSP90A, PDB code: 7dmc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7dmc

Go back to Magnesium Binding Sites List in 7dmc
Magnesium binding site 1 out of 2 in the Dipyridamole Binds to the N-Terminal Domain of Human HSP90A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dipyridamole Binds to the N-Terminal Domain of Human HSP90A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:50.9
occ:1.00
O A:ILE91 2.9 35.5 1.0
MG A:MG305 2.9 49.2 1.0
OD2 A:ASP93 3.2 34.1 1.0
CG2 A:VAL186 3.3 33.0 1.0
OG A:SER52 3.4 35.6 1.0
O A:THR184 3.4 32.3 1.0
C A:ILE91 3.7 35.8 1.0
CG2 A:ILE91 3.7 38.5 1.0
N A:VAL186 3.8 33.8 1.0
C A:THR184 3.8 37.9 1.0
CG2 A:THR184 3.9 37.3 1.0
CB A:VAL186 4.0 33.4 1.0
CB A:THR184 4.0 37.7 1.0
CG A:ASP93 4.1 33.5 1.0
CB A:ILE91 4.2 35.7 1.0
N A:ASP93 4.2 35.9 1.0
N A:LYS185 4.3 39.1 1.0
C A:LYS185 4.4 39.2 1.0
C10 A:H9F301 4.4 41.7 1.0
N A:VAL92 4.4 35.3 1.0
CA A:LYS185 4.5 38.7 1.0
C7 A:H9F301 4.5 38.7 1.0
C A:VAL92 4.5 37.6 1.0
CA A:THR184 4.5 36.8 1.0
C9 A:H9F301 4.5 48.1 1.0
O2 A:H9F301 4.5 33.0 1.0
CA A:VAL186 4.5 33.9 1.0
CA A:VAL92 4.5 35.5 1.0
CA A:ILE91 4.6 35.3 1.0
CB A:ASP93 4.7 33.2 1.0
CB A:SER52 4.8 36.1 1.0
OD1 A:ASP93 4.9 34.7 1.0

Magnesium binding site 2 out of 2 in 7dmc

Go back to Magnesium Binding Sites List in 7dmc
Magnesium binding site 2 out of 2 in the Dipyridamole Binds to the N-Terminal Domain of Human HSP90A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dipyridamole Binds to the N-Terminal Domain of Human HSP90A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:49.2
occ:1.00
O1 A:H9F301 2.6 30.8 1.0
O A:LEU48 2.9 33.8 1.0
MG A:MG304 2.9 50.9 1.0
OG A:SER52 3.2 35.6 1.0
C8 A:H9F301 3.5 34.4 1.0
C7 A:H9F301 3.5 38.7 1.0
C A:LEU48 3.6 33.0 1.0
CG2 A:VAL186 3.7 33.0 1.0
CB A:LEU48 3.7 36.0 1.0
CA A:LEU48 3.8 36.0 1.0
CG2 A:ILE91 3.9 38.5 1.0
C10 A:H9F301 4.1 41.7 1.0
N5 A:H9F301 4.2 43.9 1.0
CB A:SER52 4.2 36.1 1.0
N A:SER52 4.3 34.4 1.0
C9 A:H9F301 4.4 48.1 1.0
CB A:ASN51 4.4 36.9 1.0
CD2 A:LEU48 4.5 35.5 1.0
CB A:VAL186 4.5 33.4 1.0
OD2 A:ASP93 4.5 34.1 1.0
CB A:ILE91 4.5 35.7 1.0
CA A:SER52 4.6 36.3 1.0
CG A:LEU48 4.7 36.4 1.0
N A:ILE49 4.8 30.4 1.0
C A:ASN51 5.0 33.2 1.0

Reference:

J.Gao, C.Zhou. Development of A Filter Tips-Based Affinity Selection Mass Spectrometry Microreactor For Rapid and High-Efficient Compound Screening To Be Published.
Page generated: Fri Dec 17 10:30:51 2021

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