Palladium in PDB 5yhb: Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194

The structure of Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194, PDB code: 5yhb was solved by S.Abe, K.Atsumi, K.Yamashita, K.Hirata, H.Mori, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.20 / 2.08
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	105.920, 105.920, 105.920, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 24.4

The binding sites of Palladium atom in the Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194 (pdb code 5yhb). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 8 binding sites of Palladium where determined in the Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194, PDB code: 5yhb:
Jump to Palladium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Palladium binding site 1 out of 8 in the Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 1 of Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194 within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd301 b:43.7 occ:1.00 NE2 A:HIS183 2.3 33.5 1.0 O A:HOH420 2.4 24.0 1.0 CD2 A:HIS183 3.0 32.4 1.0 CE1 A:HIS183 3.4 34.5 1.0 CD1 A:TYR57 3.6 31.7 1.0 CE1 A:TYR57 4.2 32.3 1.0 CG A:HIS183 4.2 31.7 1.0 ND2 A:ASN185 4.3 54.8 1.0 ND1 A:HIS183 4.4 36.3 1.0 CG A:ASN185 4.4 51.8 1.0 CB A:ASN185 4.4 48.0 1.0 CG A:TYR57 4.5 31.3 1.0 CB A:TYR57 4.7 28.9 1.0

Palladium binding site 2 out of 8 in the Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 2 of Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194 within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd302 b:50.8 occ:0.78 OE1 A:GLU219 2.3 54.6 1.0 NE2 A:HIS223 2.4 47.8 1.0 CD2 A:HIS223 3.2 46.1 1.0 CE1 A:HIS223 3.2 49.0 1.0 CD A:GLU219 3.2 47.1 1.0 CG A:GLU219 3.6 46.0 1.0 ND1 A:HIS223 4.1 48.5 1.0 CG A:HIS223 4.2 44.9 1.0 OE2 A:GLU219 4.3 56.8 1.0 CB A:GLU219 4.9 38.6 1.0

Palladium binding site 3 out of 8 in the Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 3 of Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194 within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd303 b:49.1 occ:1.00 O A:HOH419 2.3 35.3 1.0 ND1 A:HIS223 2.4 48.5 1.0 CE1 A:HIS223 3.1 49.0 1.0 CG A:HIS223 3.1 44.9 1.0 CB A:HIS223 3.6 34.7 1.0 CA A:HIS223 3.6 33.3 1.0 NE2 A:HIS223 3.9 47.8 1.0 CD2 A:HIS223 4.0 46.1 1.0 O A:ASN222 4.2 29.1 1.0 O A:HIS223 4.3 31.9 1.0 C A:HIS223 4.4 31.0 1.0 N A:HIS223 4.5 29.6 1.0 C A:ASN222 4.7 30.3 1.0

Palladium binding site 4 out of 8 in the Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 4 of Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194 within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd304 b:55.8 occ:0.40 SG A:CYS211 2.3 59.2 1.0 NH2 A:ARG209 2.6 55.1 1.0 PD A:PD305 2.7 52.6 0.4 CB A:CYS211 3.2 37.7 1.0 NH1 A:ARG209 3.2 51.6 1.0 CZ A:ARG209 3.3 55.5 1.0 PD A:PD306 4.0 55.8 0.4 NE A:ARG209 4.6 54.1 1.0 CA A:CYS211 4.7 37.2 1.0

Palladium binding site 5 out of 8 in the Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 5 of Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194 within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd305 b:52.6 occ:0.40 SG A:CYS211 2.5 59.2 1.0 PD A:PD304 2.7 55.8 0.4 CB A:CYS211 3.1 37.7 1.0 C A:CYS211 3.8 32.4 1.0 CA A:CYS211 4.1 37.2 1.0 O A:CYS211 4.1 33.5 1.0 N A:ASN212 4.1 31.4 1.0 PD A:PD306 4.3 55.8 0.4 CA A:ASN212 4.5 36.0 1.0 O A:HOH401 4.8 21.6 1.0 NH2 A:ARG209 4.9 55.1 1.0 N A:CYS211 4.9 33.3 1.0

Palladium binding site 6 out of 8 in the Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 6 of Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194 within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd306 b:55.8 occ:0.40 O A:HOH401 2.0 21.6 1.0 SG A:CYS211 2.3 59.2 1.0 NH1 A:ARG209 2.6 51.6 1.0 N A:CYS211 3.4 33.3 1.0 CB A:CYS211 3.6 37.7 1.0 CZ A:ARG209 3.9 55.5 1.0 PD A:PD304 4.0 55.8 0.4 CA A:CYS211 4.0 37.2 1.0 C A:PHE210 4.1 32.4 1.0 PD A:PD305 4.3 52.6 0.4 CA A:PHE210 4.4 33.6 1.0 O A:CYS211 4.4 33.5 1.0 NH2 A:ARG209 4.5 55.1 1.0 C A:CYS211 4.6 32.4 1.0 O A:ARG209 4.8 38.0 1.0 NE A:ARG209 4.9 54.1 1.0 N A:PHE210 5.0 32.5 1.0

Palladium binding site 7 out of 8 in the Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 7 of Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194 within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd307 b:57.2 occ:0.40 ND1 A:HIS238 2.6 35.0 1.0 CE1 A:HIS238 3.5 32.7 1.0 CG A:HIS238 3.5 29.6 1.0 CA A:HIS238 3.7 26.4 1.0 CB A:HIS238 3.8 27.2 1.0 N A:HIS238 4.4 26.8 1.0 O A:ASN237 4.5 26.1 1.0 NE2 A:HIS238 4.6 37.0 1.0 CD2 A:HIS238 4.7 32.5 1.0 C A:ASN237 4.7 28.8 1.0 O A:ASN236 4.8 29.7 1.0 C A:HIS238 5.0 24.4 1.0

Palladium binding site 8 out of 8 in the Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 8 of Crystal Structure of Pd(Allyl)/Polyhedra Mutant with Deletion of GLY192-ALA194 within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd308 b:35.3 occ:1.00 PD A:PLL308 0.0 35.3 1.0 C19 A:PLL308 1.9 36.9 1.0 C20 A:PLL308 1.9 42.3 1.0 C21 A:PLL308 2.0 38.1 1.0 NE2 A:HIS238 2.3 37.0 1.0 CD2 A:HIS238 3.2 32.5 1.0 CE1 A:HIS238 3.3 32.7 1.0 O A:SER239 3.6 26.9 1.0 CG A:HIS238 4.3 29.6 1.0 ND1 A:HIS238 4.3 35.0 1.0 NH2 A:ARG155 4.4 53.0 1.0 C A:SER239 4.8 23.5 1.0 NE A:ARG155 4.8 43.3 1.0 CZ A:ARG155 4.9 44.5 1.0

S.Abe, K.Atsumi, K.Yamashita, K.Hirata, H.Mori, T.Ueno. Structure of in Cell Protein Crystals Containing Organometallic Complexes. Phys Chem Chem Phys V. 20 2986 2018.
ISSN: ESSN 1463-9084
PubMed: 29138769
DOI: 10.1039/C7CP06651A