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Chlorine in PDB 5myy: Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate

Enzymatic activity of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate

All present enzymatic activity of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate, PDB code: 5myy was solved by S.Panneerselvam, A.Burkhardt, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.68 / 1.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.740, 78.740, 37.010, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 14.3

Other elements in 5myy:

The structure of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate also contains other interesting chemical elements:

Cadmium (Cd) 10 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate (pdb code 5myy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate, PDB code: 5myy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 5myy

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Chlorine binding site 1 out of 10 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:13.1
occ:1.00
 OH A:TYR23 3.0 10.7 1.0
O A:HOH351 3.3 13.1 1.0
CZ A:TYR23 3.7 9.4 1.0
CE2 A:TYR23 3.7 9.5 1.0
CA A:GLY104 4.1 10.1 1.0
O A:ARG21 4.6 12.6 1.0
N A:GLY104 4.7 10.4 1.0
CE1 A:TYR23 4.9 9.5 1.0
CD2 A:TYR23 4.9 9.3 1.0

Chlorine binding site 2 out of 10 in 5myy

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Chlorine binding site 2 out of 10 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:16.3
occ:1.00
 CD A:CD204 2.4 19.4 0.1
O A:HOH361 3.1 13.1 1.0
O A:HOH392 3.2 25.5 1.0
O A:HOH402 3.2 26.1 1.0
N A:THR69 3.2 12.6 1.0
O A:THR69 3.3 14.6 1.0
N A:ARG68 3.5 14.7 0.5
N A:ARG68 3.5 10.6 0.5
C A:GLY67 3.6 13.2 1.0
O A:HOH353 3.6 33.1 1.0
C A:THR69 3.6 12.5 1.0
CA A:GLY67 3.6 14.1 1.0
OG A:SER72 3.7 15.2 1.0
N A:GLY67 3.7 12.9 1.0
OD1 A:ASN65 3.8 14.5 1.0
CA A:THR69 3.8 12.7 1.0
O A:HOH380 4.0 15.4 1.0
O A:GLY67 4.2 16.5 1.0
C A:ARG68 4.2 11.8 0.5
CB A:THR69 4.2 11.9 1.0
C A:ARG68 4.3 14.6 0.5
OD1 A:ASP66 4.3 11.1 1.0
CA A:ARG68 4.3 9.9 0.5
CA A:ARG68 4.5 16.8 0.5
N A:PRO70 4.5 13.4 1.0
NA A:NA221 4.7 12.4 1.0
C A:ASP66 4.8 11.2 1.0
OG1 A:THR69 4.8 11.9 1.0
CB A:SER72 4.9 15.0 1.0
N A:ASP66 4.9 10.3 1.0
O A:HOH352 4.9 29.5 0.5

Chlorine binding site 3 out of 10 in 5myy

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Chlorine binding site 3 out of 10 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:17.7
occ:1.00
 OG A:SER24 3.0 15.8 1.0
N A:GLY26 3.2 10.6 1.0
CB A:SER24 3.5 13.5 1.0
CA A:GLY26 3.5 10.7 1.0
CA A:GLN121 3.7 16.7 1.0
CD1 A:ILE124 3.7 24.3 1.0
N A:GLN121 4.0 14.9 1.0
CB A:GLN121 4.0 21.1 1.0
CG1 A:ILE124 4.1 19.5 1.0
N A:LEU25 4.2 11.4 1.0
CG A:GLN121 4.2 24.6 1.0
CG2 A:VAL120 4.2 15.1 1.0
O A:VAL120 4.3 13.6 1.0
C A:VAL120 4.3 13.6 1.0
C A:LEU25 4.3 10.7 1.0
C A:SER24 4.3 11.3 1.0
CA A:SER24 4.5 11.6 1.0
C A:GLY26 4.6 9.5 1.0
N A:ASN27 4.7 9.6 1.0
CA A:LEU25 4.7 11.7 1.0
O A:HOH394 4.8 23.3 1.0
O A:SER24 4.8 11.7 1.0
C A:GLN121 4.9 14.7 1.0

Chlorine binding site 4 out of 10 in 5myy

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Chlorine binding site 4 out of 10 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl214

b:19.5
occ:1.00
 CD A:CD201 2.7 12.1 0.4
O A:HOH304 2.9 13.3 1.0
CD A:CD210 2.9 12.0 0.1
O1 A:EDO222 3.1 18.7 1.0
O A:HOH325 3.3 15.4 1.0
N A:VAL109 3.4 10.3 1.0
O A:HOH324 3.6 22.7 1.0
CD A:CD202 3.6 17.6 0.1
CG2 A:VAL109 3.7 14.5 1.0
O A:ALA107 3.7 11.5 1.0
CB A:VAL109 3.8 13.1 1.0
O A:HOH330 3.8 46.3 1.0
O A:HOH340 3.8 17.4 1.0
O A:HOH333 3.9 35.0 1.0
CA A:TRP108 4.2 9.2 1.0
CA A:VAL109 4.2 11.0 1.0
C A:TRP108 4.3 9.2 1.0
C1 A:EDO222 4.5 15.8 1.0
OE2 A:GLU35 4.6 11.3 1.0
O A:HOH401 4.7 25.9 1.0
C A:ALA107 4.7 9.9 1.0
OD2 A:ASP52 4.9 11.6 0.5
N A:ALA110 4.9 10.3 1.0
N A:TRP108 5.0 8.9 1.0

Chlorine binding site 5 out of 10 in 5myy

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Chlorine binding site 5 out of 10 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl215

b:31.4
occ:1.00
 N A:ASN74 3.2 14.2 1.0
NE A:ARG73 3.3 19.7 1.0
O A:ASN74 3.8 14.8 1.0
C A:ASN74 3.8 13.8 1.0
CB A:ARG73 3.8 15.5 1.0
CA A:ASN74 3.9 13.4 1.0
CD A:ARG73 3.9 19.1 1.0
CA A:ARG73 3.9 14.8 1.0
C A:ARG73 4.0 14.0 1.0
CD2 A:LEU75 4.2 20.3 1.0
CZ A:ARG73 4.2 18.7 1.0
N A:LEU75 4.3 13.4 1.0
NH2 A:ARG73 4.3 21.7 1.0
CB A:ASN74 4.3 14.1 1.0
CG A:ARG73 4.5 17.6 1.0
CA A:LEU75 4.7 14.6 1.0
CG A:LEU75 4.9 16.4 1.0

Chlorine binding site 6 out of 10 in 5myy

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Chlorine binding site 6 out of 10 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl216

b:25.0
occ:1.00
 CD A:CD206 2.7 75.4 0.1
O A:HOH416 2.7 82.8 1.0
O A:HOH303 2.8 42.0 1.0
N A:ILE88 3.3 13.8 1.0
O A:HOH341 3.4 24.0 1.0
O A:HOH389 3.6 26.6 1.0
CG1 A:ILE88 3.7 14.6 1.0
CA A:ASP87 3.8 15.4 1.0
NE2 A:HIS15 4.0 24.5 1.0
O A:SER86 4.0 17.2 1.0
C A:ASP87 4.1 13.9 1.0
CZ A:PHE3 4.2 14.6 1.0
CG2 A:ILE88 4.2 16.2 1.0
OD1 A:ASP87 4.3 22.9 1.0
CB A:ILE88 4.3 13.9 1.0
CB A:ALA11 4.3 15.9 1.0
CA A:ILE88 4.3 12.6 1.0
CG A:ASP87 4.6 21.4 1.0
CD1 A:ILE88 4.6 16.0 1.0
CD2 A:HIS15 4.6 21.3 1.0
CB A:ASP87 4.7 17.8 1.0
CE2 A:PHE3 4.7 14.9 1.0
N A:ASP87 4.8 14.6 1.0
C A:SER86 4.8 14.6 1.0

Chlorine binding site 7 out of 10 in 5myy

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Chlorine binding site 7 out of 10 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:24.0
occ:1.00
 O A:HOH385 3.1 21.6 1.0
ND2 A:ASN65 3.2 16.1 1.0
CB A:PRO79 3.7 12.6 1.0
CA A:PRO79 3.7 11.8 1.0
CB A:ASN65 3.8 12.1 1.0
N A:PRO79 3.9 12.3 1.0
CG A:ASN65 3.9 13.7 1.0
CD A:PRO79 4.2 14.6 1.0
O A:ASN65 4.3 10.7 1.0
CG A:PRO79 4.4 15.6 1.0
C A:ILE78 4.5 12.4 1.0
O A:ILE78 4.6 12.4 1.0
ND2 A:ASN74 4.8 15.5 1.0
CA A:ASN65 4.9 10.9 1.0
C A:ASN65 4.9 10.1 1.0

Chlorine binding site 8 out of 10 in 5myy

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Chlorine binding site 8 out of 10 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:24.3
occ:1.00
 CD A:CD208 2.3 27.4 0.2
NZ A:LYS33 3.4 20.0 1.0
CE2 A:PHE38 3.7 13.5 1.0
CZ3 A:TRP123 3.9 17.7 1.0
CE A:LYS33 3.9 17.5 1.0
O A:HOH388 4.0 34.2 1.0
CD A:LYS33 4.1 14.9 1.0
CD A:ARG5 4.2 18.7 1.0
CB A:ARG5 4.3 16.9 1.0
O A:HOH379 4.3 33.8 1.0
CZ A:PHE38 4.4 12.0 1.0
CG A:ARG5 4.6 17.5 1.0
CE3 A:TRP123 4.7 15.2 1.0
CD2 A:PHE38 4.7 12.2 1.0
NE A:ARG5 4.8 19.8 1.0
CH2 A:TRP123 4.8 18.1 1.0

Chlorine binding site 9 out of 10 in 5myy

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Chlorine binding site 9 out of 10 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl219

b:23.6
occ:1.00
 O A:HOH336 2.9 12.4 1.0
O A:HOH398 3.3 41.8 1.0
O A:HOH377 3.4 25.9 1.0
CG2 A:VAL2 3.8 13.6 1.0
N A:VAL2 4.1 12.6 1.0
CA A:LYS1 4.5 13.3 1.0
C A:LYS1 4.5 12.0 1.0
CB A:VAL2 4.6 13.4 1.0
N A:LYS1 4.6 13.9 1.0
NE2 A:GLN41 4.7 11.7 1.0
CA A:VAL2 5.0 12.1 1.0

Chlorine binding site 10 out of 10 in 5myy

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Chlorine binding site 10 out of 10 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl220

b:34.0
occ:1.00
 O A:HOH393 3.0 24.6 1.0
N A:GLU7 3.1 15.8 1.0
N A:CYS6 3.5 16.7 1.0
CA A:GLY4 3.6 16.9 1.0
CB A:GLU7 3.6 16.7 1.0
C A:GLY4 3.6 15.3 1.0
CB A:CYS6 3.8 18.8 1.0
N A:ARG5 3.9 16.8 1.0
CA A:GLU7 3.9 15.2 1.0
C A:CYS6 3.9 15.4 1.0
CA A:CYS6 3.9 16.6 1.0
O A:GLY4 4.1 15.0 1.0
C A:ARG5 4.4 15.6 1.0
N A:GLY4 4.5 16.5 1.0
CA A:ARG5 4.7 15.7 1.0
CG A:GLU7 5.0 18.1 1.0

Reference:

S.Panneerselvam, E.P.Kumpula, I.Kursula, A.Burkhardt, A.Meents. Rapid Cadmium Sad Phasing at the Standard Wavelength (1 Angstrom ). Acta Crystallogr D Struct V. 73 581 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28695858
DOI: 10.1107/S2059798317006970
Page generated: Fri Jul 26 13:03:19 2024

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