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Magnesium in PDB 3n84: Crystal Structure of the GRB2 SH2 Domain in Complex with A 23-Membered Macrocyclic Ligand Having the Sequence Pyvnvp

Protein crystallography data

The structure of Crystal Structure of the GRB2 SH2 Domain in Complex with A 23-Membered Macrocyclic Ligand Having the Sequence Pyvnvp, PDB code: 3n84 was solved by J.H.Clements, S.F.Martin, 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 C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.223, 141.320, 62.452, 90.00, 89.99, 90.00
R / Rfree (%) 18 / 22.3

Other elements in 3n84:

The structure of Crystal Structure of the GRB2 SH2 Domain in Complex with A 23-Membered Macrocyclic Ligand Having the Sequence Pyvnvp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the GRB2 SH2 Domain in Complex with A 23-Membered Macrocyclic Ligand Having the Sequence Pyvnvp (pdb code 3n84). 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 23-Membered Macrocyclic Ligand Having the Sequence Pyvnvp, PDB code: 3n84:

Magnesium binding site 1 out of 1 in 3n84

Go back to Magnesium Binding Sites List in 3n84
Magnesium binding site 1 out of 1 in the Crystal Structure of the GRB2 SH2 Domain in Complex with A 23-Membered Macrocyclic Ligand Having the Sequence Pyvnvp


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 23-Membered Macrocyclic Ligand Having the Sequence Pyvnvp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg8

b:13.8
occ:1.00
O C:HOH727 3.1 29.5 1.0
N C:VAL122 3.3 11.9 1.0
N C:VAL123 3.3 11.1 1.0
O C:HOH728 3.3 35.9 1.0
O C:HOH165 3.4 14.7 1.0
NH2 C:ARG142 3.4 22.8 1.0
CG2 C:VAL123 3.6 16.2 1.0
CB C:TRP121 3.7 10.4 1.0
CB C:VAL122 3.7 14.5 1.0
CA C:VAL122 3.8 12.8 1.0
O C:HOH725 3.9 41.5 1.0
CB C:VAL123 4.0 13.7 1.0
C C:VAL122 4.0 12.3 1.0
NE C:ARG142 4.1 24.9 1.0
CZ C:ARG142 4.2 25.0 1.0
CA C:VAL123 4.2 13.1 1.0
O C:HOH166 4.3 13.1 1.0
C C:TRP121 4.3 11.9 1.0
CA C:TRP121 4.6 11.3 1.0
CG C:TRP121 4.6 10.4 1.0
CG2 C:VAL122 4.6 16.5 1.0
CD1 C:TRP121 4.8 8.4 1.0
CG1 C:VAL122 4.8 17.2 1.0

Reference:

J.E.Delorbe, J.H.Clements, B.B.Whiddon, S.F.Martin. Thermodynamic and Structural Effects of Macrocyclization As A Constraining Method in Protein-Ligand Interactions. Acs Med.Chem.Lett. V. 1 448 2010.
ISSN: ISSN 1948-5875
PubMed: 21116482
DOI: 10.1021/ML100142Y
Page generated: Mon Dec 14 08:27:57 2020

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