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Palladium in PDB 5yha: Crystal Structure of Pd(Allyl)/Wild Type Polyhedra

Protein crystallography data

The structure of Crystal Structure of Pd(Allyl)/Wild Type Polyhedra, PDB code: 5yha 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) 42.10 / 1.58
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 103.190, 103.190, 103.190, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 19.7

Other elements in 5yha:

The structure of Crystal Structure of Pd(Allyl)/Wild Type Polyhedra also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Palladium Binding Sites:

The binding sites of Palladium atom in the Crystal Structure of Pd(Allyl)/Wild Type Polyhedra (pdb code 5yha). 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)/Wild Type Polyhedra, PDB code: 5yha:
Jump to Palladium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Palladium binding site 1 out of 8 in 5yha

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Palladium binding site 1 out of 8 in the Crystal Structure of Pd(Allyl)/Wild Type Polyhedra


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)/Wild Type Polyhedra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd302

b:36.9
occ:1.00
 PD A:PLL302 0.0 36.9 1.0
C20 A:PLL302 1.9 39.8 1.0
C19 A:PLL302 1.9 35.1 1.0
C21 A:PLL302 2.0 37.9 1.0
SG A:CYS211 2.2 15.4 1.0
PD A:PLL303 3.0 28.1 1.0
CB A:CYS211 3.3 11.5 1.0
C20 A:PLL303 3.5 29.6 1.0
PD A:PD306 3.8 34.1 0.8
N A:CYS211 3.8 8.3 1.0
O A:HOH498 3.9 16.7 1.0
CA A:CYS211 4.1 8.7 1.0
C A:PHE210 4.4 8.0 1.0
C21 A:PLL303 4.5 29.6 1.0
O A:PHE210 4.8 6.9 1.0
C19 A:PLL303 4.8 30.7 1.0
C A:CYS211 4.9 8.2 1.0
O A:CYS211 4.9 8.3 1.0

Palladium binding site 2 out of 8 in 5yha

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Palladium binding site 2 out of 8 in the Crystal Structure of Pd(Allyl)/Wild Type Polyhedra


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)/Wild Type Polyhedra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd303

b:28.1
occ:1.00
 PD A:PLL303 0.0 28.1 1.0
C20 A:PLL303 1.9 29.6 1.0
C21 A:PLL303 1.9 29.6 1.0
C19 A:PLL303 1.9 30.7 1.0
SG A:CYS211 2.4 15.4 1.0
PD A:PLL302 3.0 36.9 1.0
PD A:PD306 3.2 34.1 0.8
CB A:CYS211 3.5 11.5 1.0
C19 A:PLL302 3.7 35.1 1.0
C20 A:PLL302 4.3 39.8 1.0
C21 A:PLL302 4.6 37.9 1.0
CA A:CYS211 4.8 8.7 1.0

Palladium binding site 3 out of 8 in 5yha

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Palladium binding site 3 out of 8 in the Crystal Structure of Pd(Allyl)/Wild Type Polyhedra


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)/Wild Type Polyhedra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd304

b:34.1
occ:1.00
 PD A:PLL304 0.0 34.1 1.0
C20 A:PLL304 1.9 44.8 1.0
C19 A:PLL304 1.9 36.5 1.0
C21 A:PLL304 2.0 40.4 1.0
O A:HOH411 2.2 31.6 1.0
NE2 A:HIS238 2.5 17.9 1.0
CD2 A:HIS238 3.3 15.9 1.0
CE1 A:HIS238 3.6 16.0 1.0
O A:SER239 3.8 13.4 1.0
CG A:HIS238 4.5 13.9 1.0
CE2 A:TYR240 4.6 18.6 1.0
CD2 A:TYR240 4.6 16.2 1.0
ND1 A:HIS238 4.6 15.2 1.0
CZ A:ARG155 4.7 35.6 1.0
NH1 A:ARG155 4.8 39.5 1.0
C A:SER239 4.9 11.8 1.0
NE A:ARG155 4.9 29.4 1.0

Palladium binding site 4 out of 8 in 5yha

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Palladium binding site 4 out of 8 in the Crystal Structure of Pd(Allyl)/Wild Type Polyhedra


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)/Wild Type Polyhedra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd305

b:28.0
occ:0.40
 ND1 A:HIS76 2.5 30.8 1.0
CG A:HIS76 3.3 28.9 1.0
CE1 A:HIS76 3.3 32.2 1.0
CB A:HIS76 3.6 25.4 1.0
OD1 A:ASP78 4.2 33.9 1.0
CD2 A:HIS76 4.3 34.1 1.0
NE2 A:HIS76 4.3 34.4 1.0
NH2 A:ARG72 4.3 26.6 1.0
O A:HIS76 4.4 18.9 1.0
C A:HIS76 4.6 20.1 1.0
CA A:HIS76 4.7 23.3 1.0

Palladium binding site 5 out of 8 in 5yha

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Palladium binding site 5 out of 8 in the Crystal Structure of Pd(Allyl)/Wild Type Polyhedra


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)/Wild Type Polyhedra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd306

b:34.1
occ:0.80
 SG A:CYS211 2.2 15.4 1.0
PD A:PLL303 3.2 28.1 1.0
O A:CYS211 3.5 8.3 1.0
CB A:CYS211 3.7 11.5 1.0
PD A:PLL302 3.8 36.9 1.0
C A:CYS211 3.8 8.2 1.0
CA A:CYS211 4.2 8.7 1.0
N A:ASN212 4.4 7.3 1.0
O A:HOH498 4.5 16.7 1.0
C19 A:PLL303 4.6 30.7 1.0
C21 A:PLL303 4.7 29.6 1.0
CA A:ASN212 4.8 7.3 1.0
N A:CYS211 4.8 8.3 1.0
C20 A:PLL303 4.8 29.6 1.0
OE2 A:GLU73 4.9 31.4 1.0

Palladium binding site 6 out of 8 in 5yha

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Palladium binding site 6 out of 8 in the Crystal Structure of Pd(Allyl)/Wild Type Polyhedra


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)/Wild Type Polyhedra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd307

b:54.0
occ:0.50
 NE2 A:HIS170 2.3 22.3 1.0
CD2 A:HIS170 3.3 24.4 1.0
CE1 A:HIS170 3.3 21.9 1.0
ND1 A:HIS170 4.4 19.0 1.0
CG A:HIS170 4.4 21.9 1.0
CG A:PRO169 4.7 17.9 1.0

Palladium binding site 7 out of 8 in 5yha

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Palladium binding site 7 out of 8 in the Crystal Structure of Pd(Allyl)/Wild Type Polyhedra


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)/Wild Type Polyhedra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd308

b:45.9
occ:0.80
 O A:HOH509 2.4 18.8 1.0
SG A:CYS204 2.5 41.2 1.0
CB A:CYS204 3.3 24.4 1.0
NZ A:LYS58 3.5 28.7 1.0
CE A:LYS58 4.2 24.2 1.0
CA A:CYS204 4.6 19.1 1.0

Palladium binding site 8 out of 8 in 5yha

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Palladium binding site 8 out of 8 in the Crystal Structure of Pd(Allyl)/Wild Type Polyhedra


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)/Wild Type Polyhedra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd309

b:46.5
occ:0.50
 ND1 A:HIS238 2.7 15.2 1.0
CG A:HIS238 3.6 13.9 1.0
CE1 A:HIS238 3.7 16.0 1.0
CB A:HIS238 3.8 12.8 1.0
CA A:HIS238 3.9 11.5 1.0
O A:HOH495 4.1 23.2 1.0
N A:HIS238 4.5 11.3 1.0
O A:ASN237 4.8 13.0 1.0
NE2 A:HIS238 4.8 17.9 1.0
O A:ASN236 4.8 12.0 1.0
CD2 A:HIS238 4.8 15.9 1.0
C A:ASN237 4.9 13.1 1.0

Reference:

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
Page generated: Thu Oct 10 10:21:33 2024

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