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Magnesium in PDB 3imd: Crystal Structure of the GRB2 SH2 Domain in Complex with A Flexible Ac-Py-Q-N-NH2 Tripeptide Mimic

Protein crystallography data

The structure of Crystal Structure of the GRB2 SH2 Domain in Complex with A Flexible Ac-Py-Q-N-NH2 Tripeptide Mimic, PDB code: 3imd was solved by J.H.Clements, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.239, 42.243, 110.384, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.7

Other elements in 3imd:

The structure of Crystal Structure of the GRB2 SH2 Domain in Complex with A Flexible Ac-Py-Q-N-NH2 Tripeptide Mimic also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the GRB2 SH2 Domain in Complex with A Flexible Ac-Py-Q-N-NH2 Tripeptide Mimic (pdb code 3imd). 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 Crystal Structure of the GRB2 SH2 Domain in Complex with A Flexible Ac-Py-Q-N-NH2 Tripeptide Mimic, PDB code: 3imd:

Magnesium binding site 1 out of 1 in 3imd

Go back to Magnesium Binding Sites List in 3imd
Magnesium binding site 1 out of 1 in the Crystal Structure of the GRB2 SH2 Domain in Complex with A Flexible Ac-Py-Q-N-NH2 Tripeptide Mimic


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 GRB2 SH2 Domain in Complex with A Flexible Ac-Py-Q-N-NH2 Tripeptide Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4

b:25.7
occ:1.00
ND2 A:ASN129 2.7 3.7 1.0
OD2 A:ASP133 3.0 9.3 1.0
CE1 A:HIS58 3.1 9.6 1.0
O A:HOH213 3.5 9.2 1.0
CG A:ASN129 3.6 6.3 1.0
NE2 A:HIS58 3.6 8.8 1.0
OD1 A:ASN129 3.6 5.7 1.0
CG A:ASP133 3.9 7.7 1.0
OD1 A:ASP133 4.0 9.0 1.0
ND1 A:HIS58 4.1 9.8 1.0
O A:HOH174 4.5 19.1 1.0
CD2 A:HIS58 4.8 10.5 1.0

Reference:

J.E.Delorbe, J.H.Clements, M.G.Teresk, A.P.Benfield, H.R.Plake, L.E.Millspaugh, S.F.Martin. Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization. J.Am.Chem.Soc. V. 131 16758 2009.
ISSN: ISSN 0002-7863
PubMed: 19886660
DOI: 10.1021/JA904698Q
Page generated: Mon Dec 14 08:17:18 2020

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