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Chlorine 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:

Ruthenium (Ru) 9 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 9 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4w94

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl202

b:25.4
occ:1.00
 OH A:TYR23 2.9 19.6 1.0
O A:HOH332 3.3 25.0 1.0
CZ A:TYR23 3.6 17.8 1.0
CE2 A:TYR23 3.6 15.4 1.0
CA A:GLY104 4.1 18.8 1.0
N A:GLY104 4.7 18.9 1.0
O A:ARG21 4.8 23.0 1.0
CE1 A:TYR23 4.8 15.9 1.0
CD2 A:TYR23 4.9 16.2 1.0
O A:HOH314 5.0 27.6 1.0

Chlorine binding site 2 out of 9 in 4w94

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl203

b:30.7
occ:1.00
 OG A:SER24 2.9 25.2 1.0
N A:GLY26 3.1 19.6 1.0
CB A:SER24 3.4 21.7 1.0
CA A:GLN121 3.5 24.5 1.0
CA A:GLY26 3.5 19.2 1.0
N A:GLN121 3.8 24.2 1.0
CB A:GLN121 3.9 26.1 1.0
C A:VAL120 4.1 23.1 1.0
CG2 A:VAL120 4.2 21.3 1.0
CG A:GLN121 4.2 36.5 1.0
O A:VAL120 4.2 23.2 1.0
CD1 A:ILE124 4.2 30.9 1.0
C A:LEU25 4.3 19.3 1.0
N A:LEU25 4.3 20.4 1.0
C A:SER24 4.4 20.5 1.0
CG1 A:ILE124 4.4 27.4 1.0
C A:GLY26 4.4 17.9 1.0
CA A:SER24 4.5 19.7 1.0
N A:ASN27 4.6 16.9 1.0
C A:GLN121 4.7 23.1 1.0
O A:SER24 4.8 20.4 1.0
CA A:LEU25 4.8 20.6 1.0
CL A:CL211 4.9 26.5 0.5
CB A:VAL120 5.0 20.9 1.0
O A:GLN121 5.0 25.8 1.0

Chlorine binding site 3 out of 9 in 4w94

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl204

b:27.4
occ:1.00
 N A:THR69 3.1 19.8 1.0
O A:HOH351 3.1 43.1 1.0
O A:HOH383 3.2 20.7 1.0
O A:HOH354 3.2 35.1 1.0
O A:THR69 3.3 22.7 1.0
O A:HOH396 3.4 44.0 1.0
N A:ARG68 3.5 20.3 1.0
OG A:SER72 3.6 26.6 1.0
OD1 A:ASN65 3.6 23.8 1.0
C A:GLY67 3.6 23.3 1.0
CA A:GLY67 3.6 22.3 1.0
N A:GLY67 3.6 19.2 1.0
C A:THR69 3.6 19.9 1.0
CA A:THR69 3.8 20.2 1.0
O A:HOH382 4.0 28.1 1.0
C A:ARG68 4.1 23.2 1.0
CB A:THR69 4.2 19.9 1.0
OD1 A:ASP66 4.2 17.8 1.0
CA A:ARG68 4.3 20.8 1.0
O A:GLY67 4.3 24.5 1.0
N A:PRO70 4.6 21.5 1.0
NA A:NA205 4.6 24.0 1.0
C A:ASP66 4.7 20.0 1.0
O A:HOH309 4.8 27.8 0.5
CG A:ASN65 4.8 20.1 1.0
CB A:SER72 4.8 26.1 1.0
OG1 A:THR69 4.9 18.7 1.0
N A:ASP66 4.9 16.3 1.0

Chlorine binding site 4 out of 9 in 4w94

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl207

b:50.8
occ:0.75
 RU A:RU1206 2.5 39.4 0.8
C2 A:RU1206 2.9 35.2 0.8
C1 A:RU1206 3.0 39.5 0.8
O A:HOH301 3.3 38.4 0.8
NE A:ARG14 3.7 52.7 1.0
O2 A:RU1206 3.7 35.1 0.8
O1 A:RU1206 3.7 40.1 0.8
NE2 A:HIS15 3.8 39.7 1.0
NH2 A:ARG14 3.9 58.1 1.0
CZ A:ARG14 4.3 56.1 1.0
CD2 A:HIS15 4.5 32.3 1.0
CE1 A:HIS15 4.5 38.6 1.0
CG A:ARG14 4.7 41.9 1.0
CD A:ARG14 4.7 46.6 1.0
CL A:CL208 4.7 46.3 0.8
CB A:ARG14 5.0 32.6 1.0

Chlorine binding site 5 out of 9 in 4w94

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl208

b:46.3
occ:0.75
 RU A:RU1206 2.3 39.4 0.8
NE2 A:HIS15 2.9 39.7 1.0
C1 A:RU1206 2.9 39.5 0.8
O A:HOH301 3.0 38.4 0.8
C2 A:RU1206 3.1 35.2 0.8
N A:ILE88 3.5 24.6 1.0
CE1 A:HIS15 3.6 38.6 1.0
OD2 A:ASP87 3.6 46.8 1.0
CG1 A:ILE88 3.8 24.2 1.0
O1 A:RU1206 3.8 40.1 0.8
O2 A:RU1206 3.9 35.1 0.8
CD2 A:HIS15 3.9 32.3 1.0
CA A:ASP87 4.0 29.5 1.0
CG A:ASP87 4.0 38.1 1.0
C A:ASP87 4.2 27.2 1.0
OD1 A:ASP87 4.5 37.5 1.0
CA A:ILE88 4.5 25.2 1.0
CB A:ILE88 4.5 23.7 1.0
CB A:ASP87 4.6 32.3 1.0
O A:SER86 4.6 30.1 1.0
ND1 A:HIS15 4.7 38.8 1.0
CG2 A:ILE88 4.7 25.4 1.0
CD1 A:ILE88 4.7 26.0 1.0
CL A:CL207 4.7 50.8 0.8
CB A:ALA11 4.8 25.8 1.0
N A:THR89 4.8 24.4 1.0
CG A:HIS15 4.9 35.8 1.0

Chlorine binding site 6 out of 9 in 4w94

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl210

b:41.0
occ:0.50
 RU A:RU1209 2.5 25.7 0.5
CL A:CL213 3.0 43.3 0.5
C2 A:RU1209 3.3 25.3 0.5
OD1 A:ASP18 3.4 32.1 1.0
CD1 A:ILE124 3.4 30.9 1.0
RU A:RU1212 3.7 27.9 0.5
CD2 A:LEU25 3.7 25.5 1.0
CL A:CL211 3.7 26.5 0.5
CB A:LEU25 4.0 21.1 1.0
CG A:ASP18 4.1 36.6 1.0
O2 A:RU1209 4.1 28.9 0.5
CD2 A:LEU129 4.2 36.3 1.0
OD2 A:ASP18 4.2 37.6 1.0
C1 A:RU1212 4.2 27.8 0.5
C1 A:RU1209 4.3 24.2 0.5
CG A:LEU25 4.6 20.6 1.0
CG1 A:ILE124 4.9 27.4 1.0
C2 A:RU1212 4.9 28.2 0.5
CG A:LEU129 4.9 41.1 1.0
O1 A:RU1212 5.0 27.8 0.5

Chlorine binding site 7 out of 9 in 4w94

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl211

b:26.5
occ:0.50
 RU A:RU1209 2.4 25.7 0.5
C1 A:RU1209 2.7 24.2 0.5
OD1 A:ASP18 2.8 32.1 1.0
C2 A:RU1209 3.3 25.3 0.5
O1 A:RU1209 3.3 33.9 0.5
N A:LEU25 3.4 20.4 1.0
CB A:SER24 3.5 21.7 1.0
CA A:SER24 3.5 19.7 1.0
CL A:CL210 3.7 41.0 0.5
C A:SER24 3.9 20.5 1.0
CG A:ASP18 4.1 36.6 1.0
N A:ASN19 4.2 27.9 1.0
O2 A:RU1209 4.2 28.9 0.5
CB A:ASN19 4.2 29.7 1.0
CB A:LEU25 4.3 21.1 1.0
OD1 A:ASN19 4.5 36.1 1.0
CA A:LEU25 4.5 20.6 1.0
CG A:ASN19 4.6 33.0 1.0
CA A:ASN19 4.7 27.7 1.0
C A:ASP18 4.7 30.9 1.0
OG A:SER24 4.7 25.2 1.0
C2 A:RU1212 4.7 28.2 0.5
CA A:ASP18 4.8 30.2 1.0
N A:SER24 4.8 19.3 1.0
OD2 A:ASP18 4.9 37.6 1.0
O2 A:RU1212 4.9 34.5 0.5
CL A:CL203 4.9 30.7 1.0
RU A:RU1212 4.9 27.9 0.5
O A:HOH303 4.9 37.6 1.0

Chlorine binding site 8 out of 9 in 4w94

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl213

b:43.3
occ:0.50
 RU A:RU1212 1.9 27.9 0.5
C1 A:RU1212 2.7 27.8 0.5
CL A:CL210 3.0 41.0 0.5
OD2 A:ASP18 3.0 37.6 1.0
NZ A:LYS13 3.2 51.7 1.0
O A:HOH330 3.3 31.4 1.0
CE A:LYS13 3.4 45.9 1.0
RU A:RU1209 3.4 25.7 0.5
CD A:LYS13 3.6 39.2 1.0
O1 A:RU1212 3.6 27.8 0.5
C2 A:RU1212 3.8 28.2 0.5
RU A:RU220 3.9 29.3 0.3
CG A:ASP18 3.9 36.6 1.0
OD1 A:ASP18 4.1 32.1 1.0
C2 A:RU1209 4.1 25.3 0.5
CB A:LEU129 4.2 41.6 1.0
O A:LEU129 4.4 48.0 1.0
CG A:LYS13 4.7 34.6 1.0
CG A:LEU129 4.7 41.1 1.0
C1 A:RU1209 4.8 24.2 0.5
O2 A:RU1209 4.8 28.9 0.5
CD2 A:LEU129 4.8 36.3 1.0
C A:LEU129 4.9 45.2 1.0
O2 A:RU1212 4.9 34.5 0.5

Chlorine binding site 9 out of 9 in 4w94

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl218

b:33.9
occ:0.30
 RU A:RU217 2.4 42.4 0.5
OE1 A:GLN121 2.6 54.8 1.0
OD2 A:ASP119 3.2 40.8 1.0
N A:ALA122 3.5 22.4 1.0
CA A:ALA122 3.7 22.3 1.0
OD1 A:ASP119 3.8 37.6 1.0
CG A:ASP119 3.8 35.9 1.0
CD A:GLN121 3.9 48.2 1.0
CB A:ALA122 3.9 24.9 1.0
C A:GLN121 4.0 23.1 1.0
CB A:GLN121 4.4 26.1 1.0
O A:GLN121 4.4 25.8 1.0
CG A:GLN121 4.7 36.5 1.0
CA A:GLN121 4.7 24.5 1.0
CB A:ARG125 4.8 28.4 1.0
NE2 A:GLN121 4.8 49.9 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: Fri Jul 11 22:23:34 2025

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