Atomistry » Ruthenium » PDB 5iu5-6bo1 » 5ob8
Atomistry »
  Ruthenium »
    PDB 5iu5-6bo1 »
      5ob8 »

Ruthenium in PDB 5ob8: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl):
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl), PDB code: 5ob8 was solved by N.Pontillo, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.56 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.573, 78.573, 36.664, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 23

Other elements in 5ob8:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) (pdb code 5ob8). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl), PDB code: 5ob8:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5ob8

Go back to Ruthenium Binding Sites List in 5ob8
Ruthenium binding site 1 out of 2 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru206

b:43.4
occ:0.80
 RU1 A:9QB206 0.0 43.4 0.8
C2 A:9QB206 1.6 38.2 0.8
C1 A:9QB206 1.8 45.9 0.8
O5 A:9QB206 2.1 41.3 0.8
NE2 A:HIS15 2.2 37.9 1.0
CL1 A:9QB206 2.3 48.8 0.8
O4 A:9QB206 2.3 35.5 0.8
O2 A:9QB206 2.5 32.5 0.8
O1 A:9QB206 2.7 38.6 0.8
CE1 A:HIS15 3.1 49.2 1.0
CD2 A:HIS15 3.2 37.0 1.0
OD1 A:ASP87 3.6 54.9 1.0
ND1 A:HIS15 4.2 41.5 1.0
O A:HOH303 4.3 51.7 1.0
CG A:HIS15 4.3 38.8 1.0
CG A:ARG14 4.7 48.1 1.0
CG A:ASP87 4.9 47.7 1.0

Ruthenium binding site 2 out of 2 in 5ob8

Go back to Ruthenium Binding Sites List in 5ob8
Ruthenium binding site 2 out of 2 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru207

b:56.7
occ:0.40
 RU A:RU2207 0.0 56.7 0.4
C2 A:RU2207 1.9 47.9 0.4
OD2 A:ASP18 2.3 52.2 1.0
O3 A:RU2207 2.3 49.2 0.4
O5 A:RU2207 2.4 50.4 0.4
O1 A:RU2207 2.4 44.8 0.4
O4 A:RU2207 2.4 48.5 0.4
O2 A:RU2207 3.0 41.5 0.4
CG A:ASP18 3.0 44.8 1.0
OD1 A:ASP18 3.1 43.3 1.0
NZ A:LYS13 4.0 41.2 0.5
CE A:LYS13 4.3 41.8 0.5
CB A:ASP18 4.5 42.9 1.0
ND2 A:ASN19 4.7 62.3 1.0

Reference:

N.Pontillo, G.Ferraro, L.Messori, G.Tamasi, A.Merlino. Ru-Based Co Releasing Molecules with Azole Ligands: Interaction with Proteins and the Co Release Mechanism Disclosed By X-Ray Crystallography. Dalton Trans V. 46 9621 2017.
ISSN: ESSN 1477-9234
PubMed: 28702564
DOI: 10.1039/C7DT01991B
Page generated: Thu Oct 10 13:01:35 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy