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Platinum in PDB 1qyy: Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-Alpha at 2.8 Angstrom Resolution

Protein crystallography data

The structure of Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-Alpha at 2.8 Angstrom Resolution, PDB code: 1qyy was solved by K.I.Varughese, Z.M.Ruggeri, R.Celikel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.610, 113.820, 56.210, 90.00, 95.21, 90.00
R / Rfree (%) 21.9 / 28.2

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-Alpha at 2.8 Angstrom Resolution (pdb code 1qyy). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 3 binding sites of Platinum where determined in the Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-Alpha at 2.8 Angstrom Resolution, PDB code: 1qyy:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in 1qyy

Go back to Platinum Binding Sites List in 1qyy
Platinum binding site 1 out of 3 in the Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-Alpha at 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-Alpha at 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt505

b:30.0
occ:1.00
NE2 A:HIS86 2.3 28.3 1.0
CE1 A:HIS86 2.8 28.3 1.0
CE1 A:PHE109 3.5 23.6 1.0
CD1 A:PHE109 3.5 23.6 1.0
CD2 A:HIS86 3.6 28.3 1.0
ND1 A:HIS86 4.1 28.3 1.0
CG A:HIS86 4.5 28.3 1.0
CZ A:PHE109 4.5 23.6 1.0
CG A:PHE109 4.6 23.6 1.0
CG G:PRO260 4.7 52.3 1.0
CE2 G:PHE254 4.7 38.5 1.0

Platinum binding site 2 out of 3 in 1qyy

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Platinum binding site 2 out of 3 in the Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-Alpha at 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-Alpha at 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt506

b:27.7
occ:1.00
O A:HOH507 2.4 10.8 1.0
ND1 A:HIS195 2.5 42.2 1.0
CG A:HIS195 2.9 42.2 1.0
CB A:HIS195 3.0 42.2 1.0
CA A:HIS195 3.4 48.3 1.0
CE1 A:HIS195 3.4 42.2 1.0
CA A:GLU172 3.6 50.0 1.0
O A:GLU172 3.6 50.0 1.0
CB A:GLU172 3.7 42.9 1.0
CD2 A:HIS195 3.9 42.2 1.0
C A:GLU172 4.0 50.0 1.0
NE2 A:HIS195 4.2 42.2 1.0
N A:LEU196 4.2 44.1 1.0
C A:HIS195 4.4 48.3 1.0
N A:HIS195 4.4 48.3 1.0
O A:LEU171 4.8 36.4 1.0
N A:GLU172 4.9 50.0 1.0
CG A:GLU172 4.9 42.9 1.0

Platinum binding site 3 out of 3 in 1qyy

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Platinum binding site 3 out of 3 in the Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-Alpha at 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-Alpha at 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Pt602

b:31.0
occ:1.00
NE2 G:HIS86 2.2 25.1 1.0
CD2 G:HIS86 3.2 25.1 1.0
CE1 G:HIS86 3.2 25.1 1.0
CE1 G:PHE109 3.5 28.8 1.0
CD1 G:PHE109 3.6 28.8 1.0
ND1 G:HIS86 4.3 25.1 1.0
CG G:HIS86 4.3 25.1 1.0
CZ G:PHE109 4.4 28.8 1.0
CG G:PHE109 4.6 28.8 1.0

Reference:

K.I.Varughese, Z.M.Ruggeri, R.Celikel. Platinum-Induced Space-Group Transformation in Crystals of the Platelet Glycoprotein Ib Alpha N-Terminal Domain. Acta Crystallogr.,Sect.D V. 60 405 2004.
ISSN: ISSN 0907-4449
PubMed: 14993663
DOI: 10.1107/S0907444903026805
Page generated: Wed Dec 16 02:03:47 2020

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