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Ruthenium in PDB 4uwu: Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7)

Enzymatic activity of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7)

All present enzymatic activity of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7):
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7), PDB code: 4uwu was solved by M.F.A.Santos, A.Mukhopadhyay, M.J.Romao, C.C.Romao, T.Santos-Silva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.62 / 1.78
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.660, 78.660, 37.000, 90.00, 90.00, 90.00
R / Rfree (%) 16.13 / 19.522

Other elements in 4uwu:

The structure of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7) (pdb code 4uwu). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 7 binding sites of Ruthenium where determined in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7), PDB code: 4uwu:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6; 7;

Ruthenium binding site 1 out of 7 in 4uwu

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Ruthenium binding site 1 out of 7 in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1136

b:27.3
occ:0.80
 C A:FMT1132 1.9 26.9 0.8
O A:HOH2023 2.0 21.5 0.8
C A:CMO1133 2.1 12.7 0.8
NE2 A:HIS15 2.4 29.9 1.0
O A:HOH2158 2.4 29.7 0.8
O2 A:FMT1132 2.6 23.6 0.8
O1 A:FMT1132 2.7 28.3 0.8
O A:HOH2021 2.8 23.2 0.8
O A:CMO1133 2.9 22.4 0.8
CE1 A:HIS15 3.2 29.5 1.0
CD2 A:HIS15 3.4 29.4 1.0
OD2 A:ASP87 4.1 36.1 1.0
ND1 A:HIS15 4.4 28.9 1.0
CG A:HIS15 4.5 28.8 1.0
CG A:ASP87 4.7 31.6 1.0
CG A:ARG14 4.8 31.4 1.0
OD1 A:ASP87 5.0 29.1 1.0

Ruthenium binding site 2 out of 7 in 4uwu

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Ruthenium binding site 2 out of 7 in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1137

b:23.1
occ:0.70
 OD2 A:ASP119 2.1 30.0 1.0
O A:HOH2151 2.2 17.3 0.7
O A:HOH2160 2.3 16.6 0.7
O A:CMO1134 2.4 29.0 0.7
O A:HOH2150 2.5 26.2 0.7
O A:HOH2149 2.5 17.4 0.7
C A:CMO1134 2.8 19.9 0.7
CG A:ASP119 3.0 26.6 1.0
OD1 A:ASP119 3.2 30.7 1.0
O A:HOH2152 4.0 27.2 1.0
CB A:ASP119 4.5 23.6 1.0
NH2 A:ARG125 4.6 52.4 1.0
CB A:GLN121 4.9 27.1 1.0

Ruthenium binding site 3 out of 7 in 4uwu

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Ruthenium binding site 3 out of 7 in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1138

b:22.4
occ:0.70
 OD2 A:ASP101 2.1 22.3 1.0
O A:HOH2126 2.4 17.8 0.7
O A:HOH2128 2.4 33.0 1.0
O A:HOH2127 2.5 29.3 0.7
RU A:RU1139 2.7 21.8 0.7
CG A:ASP101 2.9 22.1 1.0
O A:HOH2124 3.1 21.1 0.7
OD1 A:ASP101 3.1 23.9 1.0
O A:HOH2162 3.9 25.8 0.7
O A:HOH2163 3.9 25.6 0.7
CB A:ASP101 4.3 20.6 1.0
O A:HOH2060 4.7 32.9 1.0
CD1 A:LEU75 4.8 25.0 1.0
CH2 A:TRP63 5.0 17.8 1.0

Ruthenium binding site 4 out of 7 in 4uwu

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Ruthenium binding site 4 out of 7 in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1139

b:21.8
occ:0.70
 O A:HOH2124 2.1 21.1 0.7
OD1 A:ASP101 2.2 23.9 1.0
O A:HOH2125 2.5 28.6 0.7
O A:HOH2163 2.6 25.6 0.7
RU A:RU1138 2.7 22.4 0.7
O A:HOH2162 2.7 25.8 0.7
CG A:ASP101 3.1 22.1 1.0
O A:HOH2126 3.1 17.8 0.7
OD2 A:ASP101 3.3 22.3 1.0
O A:HOH2127 3.7 29.3 0.7
O A:HOH2121 3.9 22.2 1.0
CB A:ASP101 4.5 20.6 1.0
CA A:ASP101 4.8 19.8 1.0
O A:HOH2128 5.0 33.0 1.0

Ruthenium binding site 5 out of 7 in 4uwu

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Ruthenium binding site 5 out of 7 in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 5 of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1140

b:23.1
occ:0.50
 O A:HOH2025 1.9 21.4 0.5
OD1 A:ASP18 2.3 32.0 1.0
O A:HOH2164 2.3 20.5 0.5
O A:HOH2026 2.5 31.0 1.0
RU A:RU1141 2.5 25.4 0.5
O A:HOH2165 2.8 30.0 0.5
OD2 A:ASP18 2.9 33.4 1.0
CG A:ASP18 3.0 32.8 1.0
O A:HOH2028 3.1 16.9 0.5
O A:HOH2027 3.7 22.1 0.5
O A:HOH2166 3.8 20.7 0.5
CB A:ASP18 4.5 26.8 1.0
O A:HOH2018 4.9 13.8 0.5
CB A:LEU25 5.0 16.0 1.0

Ruthenium binding site 6 out of 7 in 4uwu

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Ruthenium binding site 6 out of 7 in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 6 of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1141

b:25.4
occ:0.50
 O A:HOH2028 2.2 16.9 0.5
OD2 A:ASP18 2.3 33.4 1.0
O A:HOH2018 2.4 13.8 0.5
O A:HOH2027 2.4 22.1 0.5
RU A:RU1140 2.5 23.1 0.5
O A:HOH2166 2.5 20.7 0.5
O A:HOH2025 3.0 21.4 0.5
CG A:ASP18 3.3 32.8 1.0
O A:HOH2164 3.6 20.5 0.5
OD1 A:ASP18 3.7 32.0 1.0
O A:HOH2165 3.9 30.0 0.5
CE A:LYS13 4.0 36.4 1.0
NZ A:LYS13 4.3 39.4 1.0
CB A:ASP18 4.7 26.8 1.0
O A:HOH2026 4.9 31.0 1.0
CD A:LYS13 5.0 30.5 1.0

Ruthenium binding site 7 out of 7 in 4uwu

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Ruthenium binding site 7 out of 7 in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 7 of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1142

b:42.1
occ:0.40
 C A:CMO1135 1.9 10.0 0.4
OD2 A:ASP52 2.1 25.1 1.0
O A:HOH2084 2.2 5.2 0.4
O A:HOH2059 2.2 8.2 0.4
O A:CMO1135 2.8 11.0 0.4
CG A:ASP52 3.0 17.4 1.0
O A:HOH2132 3.4 24.8 1.0
OD1 A:ASP52 3.4 14.5 1.0
O A:HOH2086 3.9 15.0 1.0
O A:HOH2058 4.0 24.4 1.0
O A:HOH2083 4.1 41.1 1.0
O A:GLN57 4.2 11.3 1.0
CB A:ASP52 4.2 11.6 1.0
O A:HOH2057 4.3 29.0 1.0
OD1 A:ASN46 4.3 25.4 1.0
OE1 A:GLU35 4.6 12.8 1.0
CB A:GLN57 4.9 10.3 1.0

Reference:

J.Seixas, M.F.A.Santos, A.Mukhopadhyay, A.C.Coelho, P.M.Reis, L.F.Veiros, A.R.Marques, N.Penacho, A.M.L.Goncalves, M.J Romao, G.J.L.Bernardes, T.Santos-Silva, C.C.Romao. A Contribution to the Rational Design of Ru(Co) 3CI2L Complexes For in Vivo Delivery of Co Dalton Trans 2014.
ISSN: ESSN 1477-9234
PubMed: 25427784
DOI: 10.1039/C4DT02966F
Page generated: Thu Oct 10 12:56:01 2024

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