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Chlorine 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:

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 Followed By the Reaction in Deoxy- Myoglobin Solution (pdb code 4w96). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 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 Followed By the Reaction in Deoxy- Myoglobin Solution, PDB code: 4w96:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4w96

Go back to Chlorine Binding Sites List in 4w96
Chlorine binding site 1 out of 8 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 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 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:24.8
occ:1.00
 OH A:TYR23 2.9 18.7 1.0
O A:HOH324 3.3 25.5 1.0
CZ A:TYR23 3.6 18.4 1.0
CE2 A:TYR23 3.6 14.8 1.0
CA A:GLY104 4.1 18.2 1.0
N A:GLY104 4.7 18.8 1.0
O A:ARG21 4.7 23.4 1.0
CE1 A:TYR23 4.9 15.8 1.0
CD2 A:TYR23 4.9 15.9 1.0
O A:HOH310 5.0 25.5 1.0

Chlorine binding site 2 out of 8 in 4w96

Go back to Chlorine Binding Sites List in 4w96
Chlorine binding site 2 out of 8 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 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 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:29.6
occ:1.00
 OG A:SER24 3.0 24.8 1.0
N A:GLY26 3.1 19.7 1.0
CA A:GLY26 3.5 17.1 1.0
CB A:SER24 3.5 22.0 1.0
CA A:GLN121 3.5 23.7 1.0
N A:GLN121 3.8 23.2 1.0
CB A:GLN121 3.9 26.5 1.0
CD1 A:ILE124 4.1 31.6 1.0
CG2 A:VAL120 4.1 21.9 1.0
O A:VAL120 4.1 21.1 1.0
C A:VAL120 4.1 22.0 1.0
CG A:GLN121 4.2 34.6 1.0
CG1 A:ILE124 4.2 27.7 1.0
C A:LEU25 4.3 19.3 1.0
N A:LEU25 4.3 19.8 1.0
C A:SER24 4.4 20.8 1.0
C A:GLY26 4.5 17.3 1.0
CA A:SER24 4.6 20.9 1.0
N A:ASN27 4.6 16.1 1.0
CA A:LEU25 4.7 20.7 1.0
C A:GLN121 4.8 21.7 1.0
CL A:CL212 4.8 21.0 0.3
O A:SER24 4.8 20.1 1.0
CB A:VAL120 5.0 22.1 1.0

Chlorine binding site 3 out of 8 in 4w96

Go back to Chlorine Binding Sites List in 4w96
Chlorine binding site 3 out of 8 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 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 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:35.5
occ:1.00
 O A:HOH387 3.0 26.1 1.0
ND2 A:ASN65 3.3 23.0 1.0
CB A:PRO79 3.6 19.6 1.0
CA A:PRO79 3.6 20.3 1.0
CB A:ASN65 3.8 18.3 1.0
N A:PRO79 3.9 22.3 1.0
CG A:ASN65 4.0 20.6 1.0
CD A:PRO79 4.2 21.6 1.0
O A:ASN65 4.2 17.6 1.0
CG A:PRO79 4.3 24.9 1.0
C A:ILE78 4.5 21.6 1.0
O A:ILE78 4.7 21.0 1.0
C A:ASN65 4.8 15.7 1.0
ND2 A:ASN74 4.9 22.1 1.0
CA A:ASN65 4.9 17.4 1.0

Chlorine binding site 4 out of 8 in 4w96

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Chlorine binding site 4 out of 8 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 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 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:24.4
occ:1.00
 O A:HOH375 3.2 18.7 1.0
N A:THR69 3.2 18.0 1.0
O A:HOH354 3.2 28.6 1.0
O A:HOH344 3.3 34.9 1.0
O A:THR69 3.3 21.8 1.0
OG A:SER72 3.5 24.4 1.0
N A:ARG68 3.5 20.2 1.0
O A:HOH393 3.6 37.0 1.0
C A:GLY67 3.6 20.7 1.0
CA A:GLY67 3.6 20.7 1.0
N A:GLY67 3.6 19.2 1.0
OD1 A:ASN65 3.7 21.7 1.0
C A:THR69 3.7 19.0 1.0
CA A:THR69 3.9 20.2 1.0
O A:HOH376 4.0 25.4 1.0
CB A:THR69 4.2 19.0 1.0
C A:ARG68 4.2 22.1 1.0
O A:GLY67 4.2 23.7 1.0
OD1 A:ASP66 4.3 16.9 1.0
CA A:ARG68 4.3 20.1 1.0
N A:PRO70 4.6 19.8 1.0
NA A:NA206 4.7 21.9 1.0
CB A:SER72 4.7 24.5 1.0
C A:ASP66 4.7 18.7 1.0
CG A:ASN65 4.9 20.6 1.0
OG1 A:THR69 4.9 18.7 1.0
N A:ASP66 4.9 16.1 1.0
O A:HOH313 4.9 26.4 0.5

Chlorine binding site 5 out of 8 in 4w96

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Chlorine binding site 5 out of 8 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 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 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:49.7
occ:0.70
 RU A:RU1207 2.3 38.2 0.7
C2 A:RU1207 2.7 38.8 0.7
O A:HOH339 2.8 35.3 0.7
C1 A:RU1207 3.0 33.5 0.7
NH1 A:ARG14 3.4 59.6 1.0
O2 A:RU1207 3.6 42.2 0.7
NE2 A:HIS15 3.6 39.0 1.0
O1 A:RU1207 3.9 33.6 0.7
CZ A:ARG14 4.2 56.5 1.0
CE1 A:HIS15 4.2 40.4 1.0
CD A:ARG14 4.2 48.4 1.0
NE A:ARG14 4.5 54.0 1.0
CD2 A:HIS15 4.5 33.8 1.0
CL A:CL209 4.7 40.7 0.7

Chlorine binding site 6 out of 8 in 4w96

Go back to Chlorine Binding Sites List in 4w96
Chlorine binding site 6 out of 8 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 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 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:40.7
occ:0.70
 RU A:RU1207 2.4 38.2 0.7
NE2 A:HIS15 2.9 39.0 1.0
O A:HOH339 3.1 35.3 0.7
C2 A:RU1207 3.2 38.8 0.7
C1 A:RU1207 3.2 33.5 0.7
OD1 A:ASP87 3.4 37.6 1.0
CE1 A:HIS15 3.4 40.4 1.0
N A:ILE88 3.5 23.9 1.0
CD2 A:HIS15 3.8 33.8 1.0
CG1 A:ILE88 3.8 22.2 1.0
CA A:ASP87 4.0 28.1 1.0
O2 A:RU1207 4.1 42.2 0.7
O1 A:RU1207 4.2 33.6 0.7
C A:ASP87 4.2 26.9 1.0
CG A:ASP87 4.3 33.2 1.0
ND1 A:HIS15 4.4 40.0 1.0
CA A:ILE88 4.5 23.4 1.0
CB A:ILE88 4.5 22.7 1.0
CB A:ASP87 4.6 30.4 1.0
CG A:HIS15 4.6 34.4 1.0
N A:THR89 4.7 24.0 1.0
CL A:CL208 4.7 49.7 0.7
CG2 A:ILE88 4.7 23.7 1.0
CD1 A:ILE88 4.7 24.2 1.0
O A:SER86 4.8 29.1 1.0
CB A:ALA11 4.9 28.4 1.0
C A:ILE88 4.9 21.4 1.0

Chlorine binding site 7 out of 8 in 4w96

Go back to Chlorine Binding Sites List in 4w96
Chlorine binding site 7 out of 8 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 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 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:21.0
occ:0.30
 RU A:RU211 2.4 28.1 0.5
OD1 A:ASP18 2.8 36.7 1.0
N A:LEU25 3.4 19.8 1.0
CB A:SER24 3.5 22.0 1.0
CA A:SER24 3.5 20.9 1.0
C A:SER24 3.9 20.8 1.0
CG A:ASP18 4.1 38.0 1.0
CB A:LEU25 4.2 20.8 1.0
N A:ASN19 4.3 29.4 1.0
CA A:LEU25 4.4 20.7 1.0
CB A:ASN19 4.5 29.2 1.0
OD1 A:ASN19 4.6 34.1 1.0
OG A:SER24 4.7 24.8 1.0
C A:ASP18 4.8 32.5 1.0
CL A:CL203 4.8 29.6 1.0
CG A:ASN19 4.8 31.7 1.0
CA A:ASN19 4.8 28.1 1.0
CA A:ASP18 4.8 32.9 1.0
OD2 A:ASP18 4.8 40.4 1.0
N A:SER24 4.9 19.7 1.0
RU A:RU210 4.9 29.5 0.5

Chlorine binding site 8 out of 8 in 4w96

Go back to Chlorine Binding Sites List in 4w96
Chlorine binding site 8 out of 8 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 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 Followed By the Reaction in Deoxy- Myoglobin Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:37.8
occ:0.30
 RU A:RU216 2.1 31.8 0.3
OD2 A:ASP119 2.8 38.9 1.0
OE1 A:GLN121 2.9 48.9 1.0
OD1 A:ASP119 3.4 32.7 1.0
CG A:ASP119 3.4 32.6 1.0
N A:ALA122 3.6 22.0 1.0
CA A:ALA122 3.8 22.2 1.0
CB A:ALA122 4.0 23.6 1.0
C A:GLN121 4.1 21.7 1.0
CD A:GLN121 4.1 45.3 1.0
CB A:GLN121 4.3 26.5 1.0
O A:GLN121 4.6 23.6 1.0
CA A:GLN121 4.7 23.7 1.0
CG A:GLN121 4.8 34.6 1.0
CB A:ASP119 4.9 25.6 1.0
O A:ASP119 5.0 25.1 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 26 02:43:28 2024

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