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Ruthenium in PDB 4w94: Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2

Enzymatic activity of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2

All present enzymatic activity of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 5MM [Ru(Co)3CL2]2:
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, PDB code: 4w94 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) 30.80 / 1.55
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.034, 79.034, 36.920, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.2

Other elements in 4w94:

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

Chlorine (Cl) 9 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 (pdb code 4w94). 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, PDB code: 4w94:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Ruthenium binding site 1 out of 9 in 4w94

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru206

b:39.4
occ:0.75
 RU A:RU1206 0.0 39.4 0.8
C2 A:RU1206 1.9 35.2 0.8
C1 A:RU1206 1.9 39.5 0.8
O A:HOH301 2.0 38.4 0.8
CL A:CL208 2.3 46.3 0.8
NE2 A:HIS15 2.3 39.7 1.0
CL A:CL207 2.5 50.8 0.8
O2 A:RU1206 3.0 35.1 0.8
O1 A:RU1206 3.0 40.1 0.8
CE1 A:HIS15 3.2 38.6 1.0
CD2 A:HIS15 3.4 32.3 1.0
OD2 A:ASP87 3.9 46.8 1.0
ND1 A:HIS15 4.4 38.8 1.0
CG A:HIS15 4.5 35.8 1.0
CG A:ASP87 4.8 38.1 1.0

Ruthenium binding site 2 out of 9 in 4w94

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru209

b:25.7
occ:0.50
 RU A:RU1209 0.0 25.7 0.5
C2 A:RU1209 1.9 25.3 0.5
C1 A:RU1209 1.9 24.2 0.5
OD1 A:ASP18 2.1 32.1 1.0
CL A:CL211 2.4 26.5 0.5
CL A:CL210 2.5 41.0 0.5
RU A:RU1212 2.6 27.9 0.5
C2 A:RU1212 2.9 28.2 0.5
O1 A:RU1209 3.0 33.9 0.5
O2 A:RU1209 3.0 28.9 0.5
CG A:ASP18 3.0 36.6 1.0
OD2 A:ASP18 3.2 37.6 1.0
C1 A:RU1212 3.2 27.8 0.5
CL A:CL213 3.4 43.3 0.5
O2 A:RU1212 3.5 34.5 0.5
O1 A:RU1212 4.1 27.8 0.5
CB A:ASP18 4.5 31.6 1.0
CB A:LEU25 4.9 21.1 1.0

Ruthenium binding site 3 out of 9 in 4w94

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru212

b:27.9
occ:0.50
 RU A:RU1212 0.0 27.9 0.5
C1 A:RU1212 1.9 27.8 0.5
C2 A:RU1212 1.9 28.2 0.5
CL A:CL213 1.9 43.3 0.5
OD2 A:ASP18 2.1 37.6 1.0
RU A:RU1209 2.6 25.7 0.5
O A:HOH330 2.6 31.4 1.0
O1 A:RU1212 3.0 27.8 0.5
O2 A:RU1212 3.0 34.5 0.5
CG A:ASP18 3.0 36.6 1.0
OD1 A:ASP18 3.2 32.1 1.0
C1 A:RU1209 3.2 24.2 0.5
C2 A:RU1209 3.4 25.3 0.5
CL A:CL210 3.7 41.0 0.5
CE A:LYS13 4.0 45.9 1.0
O1 A:RU1209 4.1 33.9 0.5
NZ A:LYS13 4.1 51.7 1.0
O2 A:RU1209 4.2 28.9 0.5
RU A:RU220 4.5 29.3 0.3
CB A:ASP18 4.5 31.6 1.0
CD A:LYS13 4.5 39.2 1.0
CL A:CL211 4.9 26.5 0.5

Ruthenium binding site 4 out of 9 in 4w94

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru214

b:29.4
occ:0.35
 O A:HOH398 2.0 31.1 1.0
O A:HOH410 2.4 24.8 1.0
O A:HOH399 2.5 34.1 1.0
OD2 A:ASP52 2.7 30.4 1.0
O A:HOH380 3.2 31.3 1.0
CG A:ASP52 3.2 22.6 1.0
O A:DMF201 3.3 40.0 1.0
OD1 A:ASP52 3.4 21.8 1.0
O A:GLN57 3.8 19.0 1.0
O A:HOH379 3.9 24.6 1.0
O A:HOH304 3.9 27.1 1.0
O A:HOH378 4.0 26.3 1.0
C A:DMF201 4.4 40.3 1.0
OE1 A:GLU35 4.4 22.3 1.0
CB A:ASP52 4.4 16.5 1.0
CB A:GLN57 4.6 16.1 1.0
ND2 A:ASN46 4.7 29.1 1.0
C A:GLN57 4.9 16.6 1.0
OE2 A:GLU35 5.0 20.4 1.0

Ruthenium binding site 5 out of 9 in 4w94

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru215

b:33.7
occ:0.10
 OD1 A:ASP101 2.4 43.1 1.0
CG A:ASP101 3.3 36.8 1.0
OD2 A:ASP101 3.7 39.2 1.0
RU A:RU216 4.1 26.9 0.1
O A:HOH403 4.4 40.2 1.0
O A:ASP101 4.5 33.9 1.0
CB A:ASP101 4.6 31.9 1.0
CA A:ASP101 4.8 31.4 1.0

Ruthenium binding site 6 out of 9 in 4w94

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru216

b:26.9
occ:0.10
 OD2 A:ASP101 2.3 39.2 1.0
CG A:ASP101 3.4 36.8 1.0
OD1 A:ASP101 3.9 43.1 1.0
RU A:RU215 4.1 33.7 0.1
CB A:ASP101 4.6 31.9 1.0
CH2 A:TRP63 4.6 20.7 1.0
CZ2 A:TRP63 4.7 20.7 1.0

Ruthenium binding site 7 out of 9 in 4w94

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru217

b:42.4
occ:0.50
 OD2 A:ASP119 2.4 40.8 1.0
CL A:CL218 2.4 33.9 0.3
CG A:ASP119 3.1 35.9 1.0
OD1 A:ASP119 3.2 37.6 1.0
OE1 A:GLN121 4.1 54.8 1.0
CB A:ASP119 4.5 27.1 1.0

Ruthenium binding site 8 out of 9 in 4w94

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru219

b:43.7
occ:0.50
 O A:HOH364 2.1 37.3 0.5
O A:LEU129 2.6 48.0 1.0
NZ A:LYS13 3.4 51.7 1.0
C A:LEU129 3.4 45.2 1.0
CD A:LYS13 3.8 39.2 1.0
CE A:LYS13 3.8 45.9 1.0
CA A:LEU129 4.0 43.1 1.0
OXT A:LEU129 4.3 46.7 1.0
RU A:RU220 4.4 29.3 0.3
CG A:LYS13 4.8 34.6 1.0
CB A:LEU129 4.8 41.6 1.0

Ruthenium binding site 9 out of 9 in 4w94

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru220

b:29.3
occ:0.30
 NZ A:LYS13 1.8 51.7 1.0
O A:HOH330 2.7 31.4 1.0
O A:LEU129 3.0 48.0 1.0
CE A:LYS13 3.2 45.9 1.0
CL A:CL213 3.9 43.3 0.5
C A:LEU129 4.0 45.2 1.0
OXT A:LEU129 4.1 46.7 1.0
CD A:LYS13 4.4 39.2 1.0
RU A:RU219 4.4 43.7 0.5
RU A:RU1212 4.5 27.9 0.5
C1 A:RU1212 4.7 27.8 0.5

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 12:56:06 2024

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