Chlorine in PDB 4j7v: Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2

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

All present enzymatic activity of Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2, PDB code: 4j7v was solved by H.Tabe, S.Abe, T.Hikage, S.Kitagawa, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.94 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 30.194, 55.572, 72.418, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.5

Other elements in 4j7v:

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

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2 (pdb code 4j7v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2, PDB code: 4j7v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 4j7v

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Chlorine binding site 1 out of 7 in the Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]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 Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:24.5
occ:1.00
 N A:SER81 3.3 18.2 1.0
O A:ASN65 3.5 22.1 1.0
CB A:SER81 3.6 20.3 1.0
CA A:ASP66 3.7 22.1 1.0
N A:CYS80 3.7 19.7 1.0
CA A:SER81 4.0 19.7 1.0
OG A:SER81 4.0 28.7 1.0
CB A:PRO79 4.1 23.1 1.0
CB A:ASP66 4.1 22.2 1.0
CA A:CYS80 4.1 17.6 1.0
CB A:CYS80 4.1 18.6 1.0
C A:CYS80 4.2 17.5 1.0
C A:PRO79 4.3 19.4 1.0
C A:ASP66 4.3 23.4 1.0
O A:ASP66 4.3 23.4 1.0
C A:ASN65 4.4 21.8 1.0
CA A:PRO79 4.5 21.3 1.0
N A:ASP66 4.5 23.0 1.0

Chlorine binding site 2 out of 7 in 4j7v

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Chlorine binding site 2 out of 7 in the Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]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 Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:31.6
occ:1.00
 O A:HOH329 3.1 22.7 1.0
ND2 A:ASN93 3.2 24.2 1.0
CB A:ASN93 3.8 20.0 1.0
CA A:ALA90 3.8 16.2 1.0
CG A:ASN93 4.0 23.6 1.0
CB A:ALA90 4.2 20.0 1.0
O A:THR89 4.5 19.3 1.0
N A:ALA90 4.5 19.1 1.0
CG2 A:THR89 4.6 27.2 1.0
O A:HOH330 4.6 27.6 1.0
O A:ALA90 4.7 15.8 1.0
C A:THR89 4.7 18.3 1.0
C A:ALA90 4.8 16.3 1.0
CG2 A:ILE78 5.0 30.8 1.0

Chlorine binding site 3 out of 7 in 4j7v

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Chlorine binding site 3 out of 7 in the Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]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 Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:32.3
occ:1.00
 OG A:SER24 3.0 25.9 1.0
N A:GLY26 3.1 18.4 1.0
CB A:SER24 3.4 21.4 1.0
CA A:GLN121 3.5 26.1 1.0
CA A:GLY26 3.6 18.7 1.0
CB A:GLN121 3.7 28.9 1.0
N A:GLN121 3.9 24.2 1.0
N A:LEU25 4.0 18.8 1.0
CD1 A:ILE124 4.1 32.7 1.0
C A:SER24 4.2 18.3 1.0
C A:LEU25 4.2 18.4 1.0
CG A:GLN121 4.2 37.3 1.0
CG1 A:ILE124 4.3 28.5 1.0
O A:VAL120 4.3 23.1 1.0
C A:VAL120 4.3 23.5 1.0
CA A:SER24 4.4 19.9 1.0
CG2 A:VAL120 4.6 24.8 1.0
C A:GLY26 4.6 17.0 1.0
CA A:LEU25 4.6 17.6 1.0
O A:SER24 4.6 20.2 1.0
C A:GLN121 4.6 23.0 1.0
N A:ASN27 4.7 16.3 1.0
O A:GLN121 4.8 22.6 1.0
CB A:LEU25 4.8 19.8 1.0

Chlorine binding site 4 out of 7 in 4j7v

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Chlorine binding site 4 out of 7 in the Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]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 Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:36.5
occ:1.00
 OG1 A:THR51 2.6 21.3 1.0
O A:GLY49 2.7 30.2 1.0
OD2 A:ASP66 2.8 20.0 1.0
NE A:ARG68 3.2 45.8 1.0
OG1 A:THR69 3.3 23.4 1.0
N A:THR51 3.4 19.5 1.0
NH1 A:ARG45 3.4 57.8 1.0
CG A:ARG68 3.5 34.0 1.0
CB A:THR51 3.5 18.8 1.0
C A:SER50 3.5 23.3 1.0
CG A:ASP66 3.7 22.1 1.0
CA A:SER50 3.7 23.5 1.0
C A:GLY49 3.8 27.5 1.0
O A:ARG68 3.9 32.2 1.0
CD A:ARG68 3.9 40.2 1.0
OD1 A:ASP66 3.9 22.5 1.0
O A:HOH323 3.9 40.1 1.0
OG A:SER60 4.0 20.2 1.0
O A:SER50 4.0 22.9 1.0
CA A:THR51 4.0 18.6 1.0
NH2 A:ARG68 4.1 43.0 1.0
CZ A:ARG68 4.1 47.5 1.0
CZ A:ARG45 4.1 56.7 1.0
C A:ARG68 4.3 32.4 1.0
N A:SER50 4.3 24.2 1.0
OH A:TYR53 4.3 21.3 1.0
CD A:ARG45 4.5 44.4 1.0
CB A:THR69 4.6 29.4 1.0
CB A:ARG68 4.6 33.1 1.0
NE A:ARG45 4.6 54.8 1.0
N A:THR69 4.7 30.4 1.0
CG2 A:THR51 4.7 20.2 1.0
CA A:THR69 4.8 30.6 1.0
NH2 A:ARG45 4.9 53.5 1.0
CA A:ARG68 5.0 31.6 1.0
CB A:SER60 5.0 19.3 1.0

Chlorine binding site 5 out of 7 in 4j7v

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Chlorine binding site 5 out of 7 in the Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]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 Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:41.1
occ:1.00
 O A:HOH327 3.1 26.6 1.0
O A:THR69 3.2 31.2 1.0
N A:THR69 3.3 30.4 1.0
N A:ARG68 3.4 31.1 1.0
OD1 A:ASN65 3.5 34.6 1.0
CA A:GLY67 3.5 29.8 1.0
N A:GLY67 3.5 26.3 1.0
C A:GLY67 3.6 31.9 1.0
OG A:SER72 3.6 32.9 1.0
C A:THR69 3.8 32.5 1.0
O A:HOH328 3.9 31.5 1.0
CA A:THR69 3.9 30.6 1.0
OD1 A:ASP66 4.2 22.5 1.0
CB A:THR69 4.2 29.4 1.0
C A:ARG68 4.3 32.4 1.0
CA A:ARG68 4.4 31.6 1.0
O A:GLY67 4.4 32.7 1.0
N A:ASP66 4.6 23.0 1.0
NA A:NA206 4.6 27.4 1.0
CG A:ASN65 4.6 31.4 1.0
C A:ASP66 4.7 23.4 1.0
OG1 A:THR69 4.7 23.4 1.0
N A:PRO70 4.9 37.9 1.0
CB A:SER72 4.9 37.0 1.0

Chlorine binding site 6 out of 7 in 4j7v

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Chlorine binding site 6 out of 7 in the Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]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 Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:42.7
occ:0.65
 CL1 A:RBN207 0.0 42.7 0.7
RU1 A:RBN207 2.4 30.4 0.7
C6 A:RBN207 3.1 33.6 0.7
NE2 A:HIS15 3.1 28.7 1.0
C5 A:RBN207 3.3 31.5 0.7
CL2 A:RBN207 3.4 31.4 0.7
CD2 A:HIS15 3.5 32.2 1.0
C1 A:RBN207 3.7 30.9 0.7
CE1 A:HIS15 3.8 33.4 1.0
C4 A:RBN207 4.1 33.5 0.7
CB A:ARG14 4.1 29.5 1.0
CG A:HIS15 4.4 30.5 1.0
C2 A:RBN207 4.4 34.1 0.7
NE A:ARG14 4.5 37.8 1.0
ND1 A:HIS15 4.6 31.9 1.0
C3 A:RBN207 4.6 35.5 0.7
O A:ARG14 4.6 30.5 1.0
C A:ARG14 4.7 28.0 1.0
CD A:ARG14 4.7 33.5 1.0
O A:HOH346 4.9 44.5 1.0
O A:HOH345 5.0 46.1 1.0

Chlorine binding site 7 out of 7 in 4j7v

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Chlorine binding site 7 out of 7 in the Crystal Structure of Cross-Linked Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]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 Hen Egg White Lysozyme Soaked with 5MM [Ru(Benzene)CL2]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:31.4
occ:0.65
 CL2 A:RBN207 0.0 31.4 0.7
RU1 A:RBN207 2.4 30.4 0.7
NH2 A:ARG14 3.1 36.2 1.0
C4 A:RBN207 3.1 33.5 0.7
NE A:ARG14 3.2 37.8 1.0
C3 A:RBN207 3.3 35.5 0.7
NE2 A:HIS15 3.3 28.7 1.0
CD2 A:HIS15 3.4 32.2 1.0
CL1 A:RBN207 3.4 42.7 0.7
CZ A:ARG14 3.6 34.7 1.0
CB A:ALA11 3.6 24.2 1.0
CA A:ALA11 3.6 23.1 1.0
C5 A:RBN207 3.8 31.5 0.7
O A:ALA11 4.0 23.8 1.0
C2 A:RBN207 4.0 34.1 0.7
CB A:ARG14 4.1 29.5 1.0
O A:HOH303 4.3 44.9 1.0
C A:ALA11 4.3 22.4 1.0
CD A:ARG14 4.3 33.5 1.0
C6 A:RBN207 4.5 33.6 0.7
C1 A:RBN207 4.6 30.9 0.7
CE1 A:HIS15 4.6 33.4 1.0
O A:HOH305 4.6 30.2 1.0
CG A:HIS15 4.7 30.5 1.0
CG A:ARG14 4.8 32.2 1.0
N A:ALA11 4.8 23.9 1.0
NH1 A:ARG14 4.9 39.5 1.0

Reference:

T.Ueno, H.Tabe, S.Abe, T.Hikage, S.Kitagawa. Solid Artificial Metalloenzymes: Post-Engineering of Porous Protein Crystals By Organometallic Complexes To Be Published.
Page generated: Sat Dec 12 10:47:44 2020

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