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Ruthenium in PDB 4w96: Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution

Enzymatic activity of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution

All present enzymatic activity of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution, PDB code: 4w96 was solved by H.Tabe, K.Fujita, S.Abe, M.Tsujimoto, T.Kuchimaru, S.Kizaka-Kondo, M.Takano, S.Kitagawa, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.84 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.011, 79.011, 36.994, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.7

Other elements in 4w96:

The structure of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Sodium (Na) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution (pdb code 4w96). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 9 binding sites of Ruthenium where determined in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution, PDB code: 4w96:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Ruthenium binding site 1 out of 9 in 4w96

Go back to Ruthenium Binding Sites List in 4w96
Ruthenium binding site 1 out of 9 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru207

b:38.2
occ:0.70
 RU A:RU1207 0.0 38.2 0.7
C1 A:RU1207 1.9 33.5 0.7
C2 A:RU1207 1.9 38.8 0.7
O A:HOH339 2.0 35.3 0.7
NE2 A:HIS15 2.2 39.0 1.0
CL A:CL208 2.3 49.7 0.7
CL A:CL209 2.4 40.7 0.7
CE1 A:HIS15 3.0 40.4 1.0
O1 A:RU1207 3.1 33.6 0.7
O2 A:RU1207 3.1 42.2 0.7
CD2 A:HIS15 3.3 33.8 1.0
ND1 A:HIS15 4.2 40.0 1.0
OD1 A:ASP87 4.3 37.6 1.0
CG A:HIS15 4.4 34.4 1.0
NH1 A:ARG14 4.7 59.6 1.0

Ruthenium binding site 2 out of 9 in 4w96

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Ruthenium binding site 2 out of 9 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru210

b:29.5
occ:0.50
 OD2 A:ASP18 2.1 40.4 1.0
RU A:RU211 2.6 28.1 0.5
CG A:ASP18 3.0 38.0 1.0
OD1 A:ASP18 3.2 36.7 1.0
CE A:LYS13 3.3 45.2 1.0
NZ A:LYS13 3.5 44.0 1.0
CB A:ASP18 4.5 35.1 1.0
CD A:LYS13 4.8 37.0 1.0
CL A:CL212 4.9 21.0 0.3

Ruthenium binding site 3 out of 9 in 4w96

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Ruthenium binding site 3 out of 9 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru211

b:28.1
occ:0.50
 OD1 A:ASP18 2.1 36.7 1.0
CL A:CL212 2.4 21.0 0.3
RU A:RU210 2.6 29.5 0.5
CG A:ASP18 3.0 38.0 1.0
OD2 A:ASP18 3.1 40.4 1.0
CB A:ASP18 4.5 35.1 1.0
CB A:LEU25 4.9 20.8 1.0

Ruthenium binding site 4 out of 9 in 4w96

Go back to Ruthenium Binding Sites List in 4w96
Ruthenium binding site 4 out of 9 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru213

b:22.5
occ:0.30
 O A:HOH384 2.0 32.0 1.0
O A:HOH397 2.4 21.6 1.0
O A:HOH381 2.4 33.2 1.0
OD2 A:ASP52 2.9 30.4 1.0
O A:HOH386 3.2 30.9 1.0
CG A:ASP52 3.3 20.7 1.0
OD1 A:ASP52 3.4 21.7 1.0
O A:DMF201 3.5 41.6 1.0
O A:HOH382 3.8 25.4 1.0
O A:GLN57 3.9 18.2 1.0
O A:HOH302 4.0 28.2 1.0
O A:HOH364 4.0 25.0 1.0
OE1 A:GLU35 4.3 21.0 1.0
CB A:ASP52 4.4 15.2 1.0
C A:DMF201 4.5 41.0 1.0
CB A:GLN57 4.7 15.9 1.0
ND2 A:ASN46 4.7 31.5 1.0
OE2 A:GLU35 4.9 20.4 1.0
CD A:GLU35 4.9 18.8 1.0
C A:GLN57 5.0 14.9 1.0

Ruthenium binding site 5 out of 9 in 4w96

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Ruthenium binding site 5 out of 9 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 5 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru214

b:45.5
occ:0.30
 RU A:RU215 2.4 25.5 0.1
OD1 A:ASP101 2.4 40.6 1.0
OD2 A:ASP101 2.9 40.5 1.0
CG A:ASP101 3.0 36.6 1.0
CB A:ASP101 4.5 28.8 1.0
O A:ASP101 4.6 30.9 1.0
CD1 A:LEU75 4.9 27.7 1.0

Ruthenium binding site 6 out of 9 in 4w96

Go back to Ruthenium Binding Sites List in 4w96
Ruthenium binding site 6 out of 9 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 6 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru215

b:25.5
occ:0.10
 OD2 A:ASP101 2.2 40.5 1.0
RU A:RU214 2.4 45.5 0.3
CG A:ASP101 3.2 36.6 1.0
OD1 A:ASP101 3.5 40.6 1.0
CB A:ASP101 4.5 28.8 1.0
CH2 A:TRP63 4.8 21.4 1.0
CZ2 A:TRP63 4.8 20.6 1.0
O A:ASP101 5.0 30.9 1.0

Ruthenium binding site 7 out of 9 in 4w96

Go back to Ruthenium Binding Sites List in 4w96
Ruthenium binding site 7 out of 9 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 7 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru216

b:31.8
occ:0.30
 CL A:CL217 2.1 37.8 0.3
OD2 A:ASP119 2.4 38.9 1.0
OD1 A:ASP119 3.0 32.7 1.0
CG A:ASP119 3.1 32.6 1.0
O A:HOH347 4.1 53.0 1.0
OE1 A:GLN121 4.1 48.9 1.0
CB A:ASP119 4.6 25.6 1.0

Ruthenium binding site 8 out of 9 in 4w96

Go back to Ruthenium Binding Sites List in 4w96
Ruthenium binding site 8 out of 9 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 8 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru218

b:27.4
occ:0.30
 OXT A:LEU129 2.5 45.9 1.0
C A:LEU129 3.4 44.8 1.0
O A:LEU129 3.5 47.1 1.0
RU A:RU219 4.2 29.9 0.5
CA A:LEU129 4.9 43.1 1.0
NZ A:LYS13 5.0 44.0 1.0

Ruthenium binding site 9 out of 9 in 4w96

Go back to Ruthenium Binding Sites List in 4w96
Ruthenium binding site 9 out of 9 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 9 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru219

b:29.9
occ:0.50
 O A:LEU129 1.8 47.1 1.0
C A:LEU129 3.1 44.8 1.0
CD A:LYS13 3.6 37.0 1.0
OXT A:LEU129 3.7 45.9 1.0
CA A:LEU129 4.1 43.1 1.0
RU A:RU218 4.2 27.4 0.3
CE A:LYS13 4.2 45.2 1.0
NZ A:LYS13 4.3 44.0 1.0
CG A:LYS13 4.6 33.0 1.0
CB A:LEU129 4.9 42.5 1.0

Reference:

H.Tabe, K.Fujita, S.Abe, M.Tsujimoto, T.Kuchimaru, S.Kizaka-Kondoh, M.Takano, S.Kitagawa, T.Ueno. Preparation of A Cross-Linked Porous Protein Crystal Containing Ru Carbonyl Complexes As A Co-Releasing Extracellular Scaffold Inorg.Chem. V. 54 215 2015.
ISSN: ISSN 0020-1669
PubMed: 25494847
DOI: 10.1021/IC502159X
Page generated: Thu Oct 10 12:56:07 2024

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