Atomistry » Ruthenium » PDB 4l55-5ira » 4w94
Atomistry »
  Ruthenium »
    PDB 4l55-5ira »
      4w94 »

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

Go back to Ruthenium Binding Sites List in 4w94
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

Go back to Ruthenium Binding Sites List in 4w94
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

Go back to Ruthenium Binding Sites List in 4w94
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

Go back to Ruthenium Binding Sites List in 4w94
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

Go back to Ruthenium Binding Sites List in 4w94
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

Go back to Ruthenium Binding Sites List in 4w94
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

Go back to Ruthenium Binding Sites List in 4w94
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

Go back to Ruthenium Binding Sites List in 4w94
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

Go back to Ruthenium Binding Sites List in 4w94
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: Wed Dec 16 02:08:23 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy