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Chlorine in PDB 7bcx: The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.

Enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.

All present enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.:
3.2.1.17;

Protein crystallography data

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours., PDB code: 7bcx was solved by L.Chiniadis, P.Giastas, I.Bratsos, A.Papakyriakou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.07 / 1.06
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.211, 78.211, 37.507, 90, 90, 90
R / Rfree (%) 16.1 / 18.5

Other elements in 7bcx:

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. also contains other interesting chemical elements:

Ruthenium (Ru) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. (pdb code 7bcx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours., PDB code: 7bcx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 7bcx

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Chlorine binding site 1 out of 10 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:76.1
occ:1.00
 O A:HOH380 2.7 18.3 0.7
CL A:CL210 2.7 24.9 0.7
O A:DMS207 2.7 52.7 0.7
S A:DMS207 2.9 52.8 0.7
O A:HOH422 2.9 60.5 1.0
C2 A:DMS207 3.0 52.8 0.7
RU A:RU208 3.2 28.8 0.7
C1 A:DMS207 4.7 52.9 0.7
NZ A:LYS33 4.7 20.1 1.0
NE A:ARG5 4.7 25.5 1.0
N1 A:IMD206 4.8 28.1 0.7
CL A:CL209 4.9 31.2 0.7
CD A:ARG5 4.9 24.5 1.0
O A:HOH406 4.9 17.5 0.7

Chlorine binding site 2 out of 10 in 7bcx

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Chlorine binding site 2 out of 10 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:15.1
occ:0.82
 OH A:TYR23 3.0 13.0 1.0
O A:HOH414 3.1 34.1 1.0
O A:HOH348 3.2 17.1 1.0
CZ A:TYR23 3.7 12.8 1.0
CE2 A:TYR23 3.7 12.6 1.0
CA A:GLY104 4.2 14.0 1.0
O A:ARG21 4.6 16.2 1.0
O A:HOH439 4.6 47.6 1.0
N A:GLY104 4.7 14.8 1.0
CE1 A:TYR23 4.8 12.5 1.0
CD2 A:TYR23 4.9 12.4 1.0

Chlorine binding site 3 out of 10 in 7bcx

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Chlorine binding site 3 out of 10 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:16.6
occ:0.79
 O A:HOH366 3.1 14.0 1.0
O A:HOH344 3.1 48.0 1.0
O A:HOH420 3.2 40.6 1.0
O A:HOH402 3.2 54.6 1.0
N A:THR69 3.2 15.0 1.0
O A:THR69 3.3 17.6 1.0
N A:ARG68 3.6 14.4 1.0
OD1 A:ASN65 3.6 17.5 1.0
C A:THR69 3.6 16.4 1.0
C A:GLY67 3.6 15.2 1.0
CA A:GLY67 3.7 15.2 1.0
N A:GLY67 3.7 13.9 1.0
OG A:SER72 3.8 20.5 1.0
CA A:THR69 3.9 14.5 1.0
O A:HOH388 4.0 18.4 1.0
CB A:THR69 4.2 14.3 1.0
C A:ARG68 4.2 16.2 1.0
O A:GLY67 4.3 17.8 1.0
OD1 A:ASP66 4.3 13.2 1.0
CA A:ARG68 4.4 15.4 1.0
N A:PRO70 4.4 17.1 1.0
NA A:NA201 4.7 13.5 0.9
C A:ASP66 4.8 13.3 1.0
CG A:ASN65 4.8 16.8 1.0
CA A:PRO70 4.8 18.8 1.0
OG1 A:THR69 4.8 14.1 1.0
N A:ASP66 4.9 12.4 1.0
O A:HOH355 5.0 29.2 0.5

Chlorine binding site 4 out of 10 in 7bcx

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Chlorine binding site 4 out of 10 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:100.9
occ:0.80
 CG1 A:VAL109 1.7 22.1 1.0
OE2 A:GLU35 2.6 12.7 1.0
N A:VAL109 2.7 16.1 1.0
N A:ALA110 2.7 16.8 1.0
CB A:VAL109 2.8 20.6 1.0
O A:HOH313 2.9 19.1 1.0
O A:HOH365 2.9 27.9 1.0
CA A:VAL109 3.0 17.5 1.0
C A:VAL109 3.2 15.6 1.0
CD A:GLU35 3.4 11.9 1.0
OE1 A:GLU35 3.5 12.9 1.0
C A:TRP108 3.6 14.1 1.0
O A:HOH328 3.8 39.6 1.0
CA A:ALA110 3.8 16.0 1.0
CB A:ALA110 3.9 17.7 1.0
CG2 A:VAL109 4.0 21.3 1.0
CA A:TRP108 4.2 13.0 1.0
O A:VAL109 4.4 17.4 1.0
O A:TRP108 4.5 13.7 1.0
CB A:TRP108 4.8 12.6 1.0
CG A:GLU35 4.8 11.9 1.0
O A:HOH340 4.9 17.8 1.0

Chlorine binding site 5 out of 10 in 7bcx

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Chlorine binding site 5 out of 10 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:31.2
occ:0.72
 RU A:RU208 2.3 28.8 0.7
O A:HOH301 2.5 50.7 1.0
S A:DMS207 3.2 52.8 0.7
N1 A:IMD206 3.3 28.1 0.7
O A:HOH406 3.3 17.5 0.7
C1 A:DMS207 3.4 52.9 0.7
C2 A:IMD206 3.4 27.6 0.7
CL A:CL210 3.4 24.9 0.7
N A:ARG5 3.5 21.2 1.0
C4 A:IMD211 3.6 18.0 0.3
N3 A:IMD211 3.8 18.0 0.3
O A:DMS207 4.0 52.7 0.7
CA A:GLY4 4.0 20.7 1.0
C5 A:IMD216 4.0 20.6 0.5
CB A:ARG5 4.1 23.2 1.0
O A:HOH397 4.1 18.0 0.5
C A:GLY4 4.2 20.6 1.0
CE2 A:PHE38 4.2 16.6 1.0
CD2 A:PHE38 4.2 16.3 1.0
C5 A:IMD206 4.2 27.9 0.7
CA A:ARG5 4.3 22.2 1.0
O A:PHE3 4.4 18.6 1.0
N3 A:IMD206 4.4 25.8 0.7
O A:HOH380 4.4 18.3 0.7
C4 A:IMD216 4.5 21.0 0.5
C2 A:DMS207 4.8 52.8 0.7
N1 A:IMD216 4.8 20.4 0.5
C5 A:IMD211 4.9 18.2 0.3
C4 A:IMD206 4.9 27.2 0.7
CL A:CL202 4.9 76.1 1.0

Chlorine binding site 6 out of 10 in 7bcx

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Chlorine binding site 6 out of 10 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:24.9
occ:0.72
 RU A:RU208 2.5 28.8 0.7
CL A:CL202 2.7 76.1 1.0
O A:HOH380 3.3 18.3 0.7
NZ A:LYS33 3.4 20.1 1.0
N1 A:IMD206 3.4 28.1 0.7
CL A:CL209 3.4 31.2 0.7
CE2 A:PHE38 3.5 16.6 1.0
C2 A:IMD206 3.6 27.6 0.7
S A:DMS207 3.6 52.8 0.7
O A:DMS207 3.6 52.7 0.7
O A:HOH422 3.8 60.5 1.0
CE A:LYS33 3.9 18.9 1.0
CD A:LYS33 4.0 16.3 1.0
CZ A:PHE38 4.2 15.6 1.0
CB A:ARG5 4.2 23.2 1.0
CD A:ARG5 4.2 24.5 1.0
CZ3 A:TRP123 4.3 19.1 1.0
CD2 A:PHE38 4.3 16.3 1.0
CG A:ARG5 4.6 23.5 1.0
C5 A:IMD206 4.7 27.9 0.7
NE A:ARG5 4.7 25.5 1.0
C2 A:DMS207 4.8 52.8 0.7
O A:HOH301 4.9 50.7 1.0
N3 A:IMD206 4.9 25.8 0.7
O A:HOH406 4.9 17.5 0.7
CE3 A:TRP123 5.0 17.9 1.0

Chlorine binding site 7 out of 10 in 7bcx

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Chlorine binding site 7 out of 10 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:18.2
occ:0.34
 RU A:RU215 2.4 14.2 0.3
N1 A:IMD211 3.2 17.1 0.3
S A:DMS212 3.3 16.5 0.3
O A:HOH398 3.4 9.2 0.3
C2 A:DMS212 3.4 17.2 0.3
CL A:CL214 3.4 16.0 0.3
O A:HOH374 3.5 29.0 1.0
C2 A:IMD211 3.5 17.5 0.3
CB A:VAL2 3.7 16.5 1.0
O A:DMS212 4.1 17.0 0.3
CG2 A:VAL2 4.2 16.6 1.0
O A:VAL2 4.2 17.4 1.0
CG1 A:VAL2 4.4 18.8 1.0
C5 A:IMD211 4.4 18.2 0.3
CA A:VAL2 4.7 15.8 1.0
O A:HOH395 4.7 7.8 0.3
N3 A:IMD211 4.8 18.0 0.3
N A:VAL2 4.8 15.8 1.0
C1 A:DMS212 4.9 16.7 0.3
C A:VAL2 4.9 16.4 1.0

Chlorine binding site 8 out of 10 in 7bcx

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Chlorine binding site 8 out of 10 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl214

b:16.0
occ:0.34
 RU A:RU215 2.4 14.2 0.3
N1 A:IMD211 3.2 17.1 0.3
S A:DMS212 3.3 16.5 0.3
O A:HOH395 3.4 7.8 0.3
CL A:CL213 3.4 18.2 0.3
C1 A:DMS212 3.5 16.7 0.3
C2 A:IMD211 3.5 17.5 0.3
N3 A:IMD216 3.7 21.5 0.5
C2 A:DMS212 3.7 17.2 0.3
C4 A:IMD216 3.8 21.0 0.5
O A:HOH321 3.8 35.4 1.0
O A:VAL2 4.3 17.4 1.0
C5 A:IMD211 4.3 18.2 0.3
N3 A:IMD211 4.7 18.0 0.3
O A:DMS212 4.8 17.0 0.3
O A:HOH398 4.8 9.2 0.3
O A:HOH374 4.9 29.0 1.0
C2 A:IMD216 5.0 21.4 0.5

Chlorine binding site 9 out of 10 in 7bcx

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Chlorine binding site 9 out of 10 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:36.3
occ:0.54
 RU A:RU220 2.5 22.7 0.5
N1 A:IMD216 3.3 20.4 0.5
C2 A:IMD216 3.3 21.4 0.5
CL A:CL219 3.4 26.0 0.5
S A:DMS217 3.5 31.6 0.5
C1 A:DMS217 3.5 31.8 0.5
O A:HOH396 3.5 15.9 0.5
O A:DMS217 4.1 31.5 0.5
C5 A:IMD216 4.5 20.6 0.5
N3 A:IMD216 4.5 21.5 0.5
O A:HOH397 4.8 18.0 0.5

Chlorine binding site 10 out of 10 in 7bcx

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Chlorine binding site 10 out of 10 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl219

b:26.0
occ:0.54
 RU A:RU220 2.5 22.7 0.5
N1 A:IMD216 3.2 20.4 0.5
C2 A:IMD216 3.2 21.4 0.5
N A:GLU7 3.2 20.5 1.0
O A:HOH397 3.3 18.0 0.5
CL A:CL218 3.4 36.3 0.5
O A:DMS217 3.6 31.5 0.5
S A:DMS217 3.6 31.6 0.5
N A:CYS6 3.7 22.2 1.0
CB A:CYS6 3.8 23.5 1.0
CB A:GLU7 3.8 21.3 1.0
CA A:GLY4 3.9 20.7 1.0
C A:CYS6 4.0 20.9 1.0
CA A:CYS6 4.0 22.5 1.0
C A:GLY4 4.1 20.6 1.0
CA A:GLU7 4.1 20.5 1.0
N A:ARG5 4.2 21.2 1.0
C5 A:IMD216 4.4 20.6 0.5
N3 A:IMD216 4.4 21.5 0.5
O A:GLY4 4.5 20.5 1.0
C A:ARG5 4.7 21.6 1.0
N A:GLY4 4.8 19.6 1.0
O A:HOH396 4.8 15.9 0.5
C2 A:DMS217 4.9 31.1 0.5
SG A:CYS6 5.0 25.4 1.0

Reference:

L.Chiniadis, P.Giastas, I.Bratsos, A.Papakyriakou. Insights Into the Protein Ruthenation Mechanism By Antimetastatic Metallodrugs: High-Resolution X-Ray Structures of the Adduct Formed Between Hen Egg-White Lysozyme and Nami-A at Various Time Points. Inorg.Chem. V. 60 10729 2021.
ISSN: ISSN 0020-1669
PubMed: 34197115
DOI: 10.1021/ACS.INORGCHEM.1C01441
Page generated: Mon Jul 29 19:04:22 2024

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