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Palladium in PDB 4q9x: Mtfp* PDCL2 Soak

Protein crystallography data

The structure of Mtfp* PDCL2 Soak, PDB code: 4q9x was solved by J.Fischer, F.Quitterer, M.Groll, J.Eppinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.470, 83.630, 37.820, 90.00, 112.01, 90.00
R / Rfree (%) 17.6 / 21.7

Other elements in 4q9x:

The structure of Mtfp* PDCL2 Soak also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Palladium Binding Sites:

The binding sites of Palladium atom in the Mtfp* PDCL2 Soak (pdb code 4q9x). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 8 binding sites of Palladium where determined in the Mtfp* PDCL2 Soak, PDB code: 4q9x:
Jump to Palladium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Palladium binding site 1 out of 8 in 4q9x

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Palladium binding site 1 out of 8 in the Mtfp* PDCL2 Soak


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 1 of Mtfp* PDCL2 Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd901

b:45.8
occ:1.00
 OE1 A:GLU123 2.0 40.9 1.0
O A:HOH1011 2.3 43.4 1.0
NZ A:LYS102 2.7 44.9 1.0
NZ A:LYS121 2.8 49.6 1.0
CD A:GLU123 2.9 39.8 1.0
OE2 A:GLU123 3.2 42.1 1.0
CE A:LYS121 3.3 45.2 1.0
CE A:LYS102 3.4 43.5 1.0
CD A:LYS121 3.5 40.2 1.0
CD A:LYS102 3.5 40.4 1.0
CG A:GLU123 4.3 38.2 1.0
CG A:LYS121 4.5 35.9 1.0
CG A:LYS102 4.8 36.1 1.0

Palladium binding site 2 out of 8 in 4q9x

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Palladium binding site 2 out of 8 in the Mtfp* PDCL2 Soak


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 2 of Mtfp* PDCL2 Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd902

b:56.3
occ:1.00
 O A:HOH1052 2.2 49.6 1.0
OD2 A:ASP7 2.4 48.0 1.0
O A:HOH1050 2.5 52.9 1.0
CL A:CL908 2.6 58.0 1.0
NZ A:LYS32 2.8 52.7 1.0
OD1 A:ASP7 2.8 49.5 1.0
CG A:ASP7 3.0 47.5 1.0
CE A:LYS32 3.2 53.8 1.0
CD A:LYS32 3.4 51.2 1.0
CG A:LYS32 4.1 47.2 1.0
CB A:ASP7 4.5 43.3 1.0
O A:PRO6 4.6 43.8 1.0

Palladium binding site 3 out of 8 in 4q9x

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Palladium binding site 3 out of 8 in the Mtfp* PDCL2 Soak


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 3 of Mtfp* PDCL2 Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd903

b:81.3
occ:1.00
 OE1 A:GLU43 2.2 54.8 1.0
NZ A:LYS45 2.8 54.4 1.0
CE A:LYS45 3.0 51.8 1.0
CD A:GLU43 3.4 49.9 1.0
OE2 A:GLU43 3.9 58.0 1.0
CD A:LYS45 4.2 49.0 1.0
CG A:GLU43 4.6 43.2 1.0
OE1 A:GLU26 4.6 50.0 1.0
CB A:GLU43 4.7 39.1 1.0

Palladium binding site 4 out of 8 in 4q9x

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Palladium binding site 4 out of 8 in the Mtfp* PDCL2 Soak


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 4 of Mtfp* PDCL2 Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd904

b:0.3
occ:1.00
 OE1 A:GLU164 2.2 54.1 1.0
CD A:GLU164 3.1 59.2 1.0
NZ A:LYS135 3.2 54.3 1.0
OE2 A:GLU164 3.4 64.6 1.0
CE A:LYS135 3.7 59.6 1.0
CD A:LYS135 4.5 57.6 1.0
CG A:GLU164 4.5 54.0 1.0

Palladium binding site 5 out of 8 in 4q9x

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Palladium binding site 5 out of 8 in the Mtfp* PDCL2 Soak


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 5 of Mtfp* PDCL2 Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd906

b:49.0
occ:0.50
 O A:HOH1046 2.1 72.9 1.0
NZ A:LYS154 2.8 55.1 1.0
O A:HOH1045 2.9 50.2 1.0
CD A:LYS154 3.1 50.2 1.0
CE A:LYS154 3.3 53.4 1.0
CG A:LYS154 4.6 45.9 1.0
NZ A:LYS174 4.6 48.4 1.0
OH A:TYR147 4.8 58.3 1.0

Palladium binding site 6 out of 8 in 4q9x

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Palladium binding site 6 out of 8 in the Mtfp* PDCL2 Soak


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 6 of Mtfp* PDCL2 Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd907

b:93.7
occ:1.00
 NZ A:LYS11 3.0 57.7 1.0
CE A:LYS11 3.0 54.1 1.0
CD A:LYS11 3.2 48.7 1.0
CG A:LYS11 4.4 45.7 1.0
OE2 A:GLU110 4.5 63.7 1.0

Palladium binding site 7 out of 8 in 4q9x

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Palladium binding site 7 out of 8 in the Mtfp* PDCL2 Soak


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 7 of Mtfp* PDCL2 Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd905

b:62.2
occ:0.50
 OE1 A:GLU117 2.0 59.7 1.0
CD A:GLU117 3.2 48.8 1.0
O A:HOH1056 3.7 48.8 1.0
OE2 A:GLU117 3.7 51.9 1.0
OH A:TYR119 3.8 51.7 1.0
OE2 A:GLU15 4.1 58.1 1.0
CD A:LYS13 4.3 42.0 1.0
CG A:GLU117 4.3 38.9 1.0
CD A:GLU15 4.3 49.7 1.0
CE A:LYS13 4.4 46.5 1.0
NZ A:LYS13 4.4 52.1 1.0
CZ A:TYR119 4.6 46.2 1.0
OE1 A:GLU15 4.8 52.7 1.0
CE1 A:TYR119 4.8 46.5 1.0
CG A:GLU15 4.8 41.6 1.0

Palladium binding site 8 out of 8 in 4q9x

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Palladium binding site 8 out of 8 in the Mtfp* PDCL2 Soak


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 8 of Mtfp* PDCL2 Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd914

b:56.5
occ:0.50
 SD A:MET132 3.0 62.3 1.0
CG A:MET132 3.8 51.7 1.0
CB A:MET132 4.1 48.5 1.0
O A:PRO51 4.5 46.0 1.0
CE A:MET132 4.7 59.1 1.0
ND2 A:ASN19 4.8 40.5 1.0
CA A:MET132 4.9 44.3 1.0

Reference:

J.Fischer, F.Quitterer, M.Groll, J.Eppinger. Mtfp*: An Imperishable and Versatile Protein Host For Anchoring Diverse Ligands and Organocatalysts To Be Published.
Page generated: Thu Oct 10 10:20:15 2024

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