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Ruthenium in PDB 4uwn: Lysozyme Soaked with A Ruthenium Based Corm with A Methione Oxide Ligand (Complex 6B)

Enzymatic activity of Lysozyme Soaked with A Ruthenium Based Corm with A Methione Oxide Ligand (Complex 6B)

All present enzymatic activity of Lysozyme Soaked with A Ruthenium Based Corm with A Methione Oxide Ligand (Complex 6B):
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Soaked with A Ruthenium Based Corm with A Methione Oxide Ligand (Complex 6B), PDB code: 4uwn 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) 56.52 / 1.67
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.930, 79.930, 36.890, 90.00, 90.00, 90.00
R / Rfree (%) 16.575 / 21.153

Other elements in 4uwn:

The structure of Lysozyme Soaked with A Ruthenium Based Corm with A Methione Oxide Ligand (Complex 6B) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Ruthenium Binding Sites:

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

Ruthenium binding site 1 out of 4 in 4uwn

Go back to Ruthenium Binding Sites List in 4uwn
Ruthenium binding site 1 out of 4 in the Lysozyme Soaked with A Ruthenium Based Corm with A Methione Oxide Ligand (Complex 6B)


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 Methione Oxide Ligand (Complex 6B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1132

b:38.2
occ:1.00
C A:CMO1136 2.0 23.1 1.0
NE2 A:HIS15 2.3 32.3 1.0
O A:HOH2019 2.3 29.3 1.0
O A:HOH2020 2.4 42.2 1.0
O A:HOH2017 2.5 42.4 1.0
O A:HOH2145 2.7 49.2 1.0
O A:CMO1136 2.8 38.2 1.0
CE1 A:HIS15 3.2 31.8 1.0
CD2 A:HIS15 3.2 31.9 1.0
ND1 A:HIS15 4.3 31.2 1.0
CG A:HIS15 4.4 31.2 1.0
OD1 A:ASP87 4.7 33.6 1.0

Ruthenium binding site 2 out of 4 in 4uwn

Go back to Ruthenium Binding Sites List in 4uwn
Ruthenium binding site 2 out of 4 in the Lysozyme Soaked with A Ruthenium Based Corm with A Methione Oxide Ligand (Complex 6B)


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 Methione Oxide Ligand (Complex 6B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1133

b:32.6
occ:0.65
C A:CMO1137 1.7 29.2 0.7
OD2 A:ASP18 2.2 35.6 1.0
O A:HOH2022 2.2 37.5 0.7
O A:HOH2015 2.5 24.7 0.7
O A:HOH2146 2.5 40.0 0.7
O A:CMO1137 2.7 29.4 0.7
CG A:ASP18 2.9 31.7 1.0
OD1 A:ASP18 3.0 31.3 1.0
NZ A:LYS13 4.0 42.2 1.0
CB A:ASP18 4.4 30.5 1.0
CE A:LYS13 4.8 40.4 1.0

Ruthenium binding site 3 out of 4 in 4uwn

Go back to Ruthenium Binding Sites List in 4uwn
Ruthenium binding site 3 out of 4 in the Lysozyme Soaked with A Ruthenium Based Corm with A Methione Oxide Ligand (Complex 6B)


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 Methione Oxide Ligand (Complex 6B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1134

b:35.2
occ:0.50
OD2 A:ASP52 2.2 23.6 1.0
O A:HOH2147 2.3 19.5 0.5
O A:HOH2071 2.4 27.5 0.5
O A:HOH2043 2.7 16.3 0.5
CG A:ASP52 3.2 20.4 1.0
OD1 A:ASP52 3.4 19.2 1.0
OD1 A:ASN46 3.8 28.6 1.0
O A:HOH2117 3.8 31.6 1.0
O A:HOH2072 3.9 20.5 1.0
CB A:ASP52 4.4 14.8 1.0
O A:HOH2042 4.4 31.1 1.0
O A:HOH2041 4.4 39.8 1.0
CG A:ASN46 4.5 29.1 1.0
ND2 A:ASN46 4.6 29.8 1.0
O A:GLN57 4.8 14.4 1.0

Ruthenium binding site 4 out of 4 in 4uwn

Go back to Ruthenium Binding Sites List in 4uwn
Ruthenium binding site 4 out of 4 in the Lysozyme Soaked with A Ruthenium Based Corm with A Methione Oxide Ligand (Complex 6B)


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 Methione Oxide Ligand (Complex 6B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1135

b:51.3
occ:0.50
O A:HOH2136 2.0 33.0 0.5
OD2 A:ASP119 2.1 45.8 1.0
O A:HOH2134 2.4 24.9 0.5
O A:HOH2148 2.5 29.5 0.5
CG A:ASP119 3.0 40.3 1.0
OD1 A:ASP119 3.1 44.6 1.0
CB A:ASP119 4.5 35.3 1.0
OE1 A:GLN121 4.8 56.2 0.0

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: Wed Dec 16 02:08:23 2020

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