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Palladium in PDB 3esc: Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid

Enzymatic activity of Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid

All present enzymatic activity of Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid:
3.1.1.74;

Protein crystallography data

The structure of Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid, PDB code: 3esc was solved by L.Rutten, J.P.B.A.Mannie, M.Lutz, P.Gros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.00 / 1.20
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 83.949, 83.949, 55.771, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 19.4

Other elements in 3esc:

The structure of Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Palladium Binding Sites:

The binding sites of Palladium atom in the Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid (pdb code 3esc). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 2 binding sites of Palladium where determined in the Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid, PDB code: 3esc:
Jump to Palladium binding site number: 1; 2;

Palladium binding site 1 out of 2 in 3esc

Go back to Palladium Binding Sites List in 3esc
Palladium binding site 1 out of 2 in the Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 1 of Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd215

b:12.9
occ:0.65
PD1 A:SXC215 0.0 12.9 0.7
PD1 A:SXC215 1.5 10.2 0.3
C1 A:SXC215 2.0 9.7 0.7
C1 A:SXC215 2.1 10.3 0.3
S2 A:SXC215 2.3 23.4 0.7
S1 A:SXC215 2.3 14.8 0.7
S2 A:SXC215 2.4 7.8 0.3
BR1 A:SXC215 2.4 36.3 0.7
C12 A:SXC215 2.6 32.0 0.3
C6 A:SXC215 2.9 12.3 0.3
C10 A:SXC215 3.0 9.9 0.3
C2 A:SXC215 3.0 11.2 0.7
S1 A:SXC215 3.0 18.1 0.3
C6 A:SXC215 3.0 9.5 0.7
C2 A:SXC215 3.1 9.7 0.3
C12 A:SXC215 3.2 25.9 0.7
C7 A:SXC215 3.2 10.5 0.7
C10 A:SXC215 3.3 14.0 0.7
C9 A:SXC215 3.3 15.6 0.7
C9 A:SXC215 3.3 40.4 0.3
BR1 A:SXC215 3.4 62.2 0.3
C7 A:SXC215 3.4 9.0 0.3
CG A:LEU81 4.0 42.8 1.0
C5 A:SXC215 4.2 13.6 0.3
CD2 A:LEU81 4.3 23.3 1.0
C3 A:SXC215 4.3 6.9 0.7
C3 A:SXC215 4.4 11.6 0.3
C5 A:SXC215 4.4 7.3 0.7
CB A:LEU81 4.5 20.8 1.0
C4 A:SXC215 4.7 9.7 0.3
C4 A:SXC215 4.8 6.6 0.7

Palladium binding site 2 out of 2 in 3esc

Go back to Palladium Binding Sites List in 3esc
Palladium binding site 2 out of 2 in the Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 2 of Cut-2A; Ncn-Pt-Pincer-Cutinase Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd215

b:10.2
occ:0.35
PD1 A:SXC215 0.0 10.2 0.3
PD1 A:SXC215 1.5 12.9 0.7
C1 A:SXC215 2.0 10.3 0.3
C1 A:SXC215 2.1 9.7 0.7
S2 A:SXC215 2.3 7.8 0.3
S1 A:SXC215 2.3 18.1 0.3
BR1 A:SXC215 2.4 62.2 0.3
S2 A:SXC215 2.5 23.4 0.7
S1 A:SXC215 2.9 14.8 0.7
C2 A:SXC215 3.0 11.2 0.7
C6 A:SXC215 3.0 12.3 0.3
C2 A:SXC215 3.0 9.7 0.3
C6 A:SXC215 3.0 9.5 0.7
C7 A:SXC215 3.2 10.5 0.7
C7 A:SXC215 3.2 9.0 0.3
C10 A:SXC215 3.2 9.9 0.3
C10 A:SXC215 3.2 14.0 0.7
C9 A:SXC215 3.2 40.4 0.3
BR1 A:SXC215 3.2 36.3 0.7
C12 A:SXC215 3.3 32.0 0.3
C9 A:SXC215 3.3 15.6 0.7
C12 A:SXC215 4.0 25.9 0.7
C3 A:SXC215 4.2 6.9 0.7
C5 A:SXC215 4.2 13.6 0.3
C5 A:SXC215 4.2 7.3 0.7
C3 A:SXC215 4.3 11.6 0.3
C4 A:SXC215 4.7 6.6 0.7
C4 A:SXC215 4.8 9.7 0.3
O A:HOH565 4.9 50.0 0.3

Reference:

L.Rutten, B.Wieczorek, J.P.B.A.Mannie, C.A.Kruithof, H.P.Dijkstra, M.R.Egmond, M.Lutz, R.J.M.Klein Gebbink, P.Gros, G.Van Koten. Solid-State Structural Characterization of Cutinase-Ece-Pincer-Metal Hybrids Chemistry V. 15 4270 2009.
ISSN: ISSN 0947-6539
PubMed: 19219875
DOI: 10.1002/CHEM.200801995
Page generated: Wed Dec 16 02:02:47 2020

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