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

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

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:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where 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:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl2 b:17.1 occ:1.00 N A:SER139 3.2 4.4 1.0 NE2 A:GLN145 3.4 6.4 1.0 CA A:THR138 3.8 5.8 1.0 OE1 A:GLN145 3.8 7.8 1.0 CB A:SER139 3.9 3.5 1.0 CE2 A:PHE147 3.9 4.7 1.0 CG2 A:THR138 4.0 6.7 1.0 C A:THR138 4.0 6.1 1.0 CD A:GLN145 4.1 6.3 1.0 CA A:SER139 4.2 5.3 1.0 CZ A:PHE147 4.2 6.9 1.0 CB A:THR138 4.5 6.0 1.0 O A:SER137 4.6 9.9 1.0 N A:THR138 5.0 7.3 1.0 OG1 A:THR138 5.0 5.0 1.0

Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl binding site number 2 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:Cl5 b:19.7 occ:1.00 OE1 A:GLU152 2.9 32.5 1.0 O A:HOH24 3.2 4.4 1.0 N A:ARG78 3.2 10.4 1.0 CD A:GLU152 3.3 29.9 1.0 CB A:GLU152 3.6 20.4 1.0 CB A:ARG78 3.6 11.6 1.0 CG A:GLU152 3.6 26.6 1.0 CG A:ARG78 3.7 12.0 1.0 CD A:ARG78 3.9 12.0 1.0 OE1 A:GLN77 4.0 11.1 1.0 CA A:GLN77 4.0 10.7 1.0 OE2 A:GLU152 4.0 32.2 1.0 CA A:ARG78 4.0 11.1 1.0 C A:GLN77 4.1 9.9 1.0 CD A:GLN77 4.2 12.4 1.0 NE2 A:GLN77 4.3 13.3 1.0 O A:LYS76 4.6 13.2 1.0 CD2 A:HIS79 4.6 15.8 1.0 CB A:GLN77 4.7 11.3 1.0 N A:HIS79 4.8 12.0 1.0 CA A:GLU152 4.9 17.7 1.0 C A:ARG78 5.0 11.7 1.0

Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl6 b:19.3 occ:1.00 NZ A:LYS109 3.3 10.8 1.0 CD A:LYS109 4.0 9.7 1.0 CE A:LYS109 4.1 10.7 1.0 O A:HOH198 4.1 30.4 1.0 O A:HOH170 4.8 14.0 1.0 CAN A:FYQ1 4.8 9.5 1.0

Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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 B:Cl170 b:18.9 occ:1.00 N B:SER139 3.2 4.2 1.0 NE2 B:GLN145 3.6 5.8 1.0 CA B:THR138 3.8 6.2 1.0 CB B:SER139 3.9 4.9 1.0 CE2 B:PHE147 3.9 5.0 1.0 CG2 B:THR138 4.0 6.1 1.0 OE1 B:GLN145 4.0 9.2 1.0 C B:THR138 4.0 5.9 1.0 CA B:SER139 4.2 5.8 1.0 CD B:GLN145 4.2 6.1 1.0 CZ B:PHE147 4.2 6.5 1.0 CB B:THR138 4.5 6.2 1.0 O B:SER137 4.6 8.1 1.0 OG1 B:THR138 4.9 5.7 1.0 N B:THR138 4.9 6.7 1.0

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