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Cadmium 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:

Chlorine (Cl) 10 atoms
Sodium (Na) 1 atom

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 10 in 5myy

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd201

b:12.1
occ:0.40
CD A:CD202 1.7 17.6 0.1
OD2 A:ASP52 2.3 11.6 0.5
O A:HOH325 2.3 15.4 1.0
O A:HOH340 2.3 17.4 1.0
O A:HOH324 2.3 22.7 1.0
O A:HOH333 2.4 35.0 1.0
CD A:CD210 2.4 12.0 0.1
CL A:CL214 2.7 19.5 1.0
OD2 A:ASP52 2.8 18.5 0.5
CG A:ASP52 3.2 10.0 0.5
CG A:ASP52 3.4 12.9 0.5
OD1 A:ASP52 3.6 10.5 0.5
OD1 A:ASP52 3.6 13.3 0.5
O1 A:EDO222 3.7 18.7 1.0
O A:HOH330 3.7 46.3 1.0
O A:HOH304 3.8 13.3 1.0
O A:GLN57 3.9 9.9 1.0
O A:HOH331 4.2 16.1 1.0
OE1 A:GLU35 4.4 11.1 1.0
CB A:ASP52 4.5 10.4 0.5
CB A:ASP52 4.5 9.2 0.5
ND2 A:ASN46 4.6 17.1 1.0
O A:HOH401 4.6 25.9 1.0
CB A:GLN57 4.7 9.4 1.0
OE2 A:GLU35 4.9 11.3 1.0
C1 A:EDO222 5.0 15.8 1.0
C A:GLN57 5.0 8.9 1.0

Cadmium binding site 2 out of 10 in 5myy

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd202

b:17.6
occ:0.15
CD A:CD201 1.7 12.1 0.4
O A:HOH333 1.8 35.0 1.0
O A:HOH324 2.0 22.7 1.0
OD2 A:ASP52 2.2 11.6 0.5
OD2 A:ASP52 2.3 18.5 0.5
OD1 A:ASP52 2.5 13.3 0.5
OD1 A:ASP52 2.7 10.5 0.5
CG A:ASP52 2.7 10.0 0.5
CG A:ASP52 2.8 12.9 0.5
O A:HOH330 3.0 46.3 1.0
ND2 A:ASN46 3.3 17.1 1.0
O A:HOH340 3.5 17.4 1.0
CL A:CL214 3.6 19.5 1.0
O A:HOH325 3.7 15.4 1.0
OD1 A:ASN46 3.7 18.3 1.0
CG A:ASN46 3.8 16.0 1.0
OD1 A:ASN59 3.8 17.5 0.5
ND2 A:ASN59 4.0 10.5 0.2
CD A:CD210 4.1 12.0 0.1
CB A:ASP52 4.2 10.4 0.5
CB A:ASP52 4.2 9.2 0.5
CG A:ASN59 4.4 13.8 0.5
CB A:ASN59 4.4 12.7 0.5
O1 A:EDO222 4.4 18.7 1.0
O A:GLN57 4.5 9.9 1.0
CG A:ASN59 4.5 8.8 0.2
CB A:ASN59 4.6 11.8 0.2
CB A:ASN59 4.7 9.4 0.2
O A:HOH331 4.7 16.1 1.0

Cadmium binding site 3 out of 10 in 5myy

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd203

b:23.8
occ:0.25
O A:HOH391 2.4 25.7 1.0
OG1 A:THR47 4.0 25.5 1.0
CB A:ASN46 4.4 15.8 1.0
O A:HOH305 4.5 37.8 1.0
N A:THR47 4.5 18.4 1.0
O A:HOH333 4.6 35.0 1.0
ND2 A:ASN46 4.7 17.1 1.0
CG A:ASN46 4.7 16.0 1.0

Cadmium binding site 4 out of 10 in 5myy

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd204

b:19.4
occ:0.15
OD1 A:ASN65 2.0 14.5 1.0
O A:HOH380 2.2 15.4 1.0
CL A:CL212 2.4 16.3 1.0
O A:HOH353 2.6 33.1 1.0
O A:HOH361 3.1 13.1 1.0
O A:HOH392 3.2 25.5 1.0
CG A:ASN65 3.2 13.7 1.0
O A:HOH373 3.4 39.5 1.0
OG A:SER72 3.8 15.2 1.0
N A:GLY67 3.9 12.9 1.0
CB A:ASN65 4.0 12.1 1.0
NA A:NA221 4.0 12.4 1.0
CA A:ASN65 4.1 10.9 1.0
ND2 A:ASN65 4.2 16.1 1.0
CA A:GLY67 4.3 14.1 1.0
N A:ASP66 4.4 10.3 1.0
C A:ASN65 4.7 10.1 1.0
O A:HOH386 4.9 22.8 1.0
O A:THR69 5.0 14.6 1.0
C A:GLY67 5.0 13.2 1.0

Cadmium binding site 5 out of 10 in 5myy

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd205

b:24.6
occ:0.25
O A:LEU129 2.4 35.5 1.0
O A:HOH390 2.6 37.4 1.0
OXT A:LEU129 3.0 42.2 1.0
O A:HOH301 3.0 25.4 1.0
C A:LEU129 3.1 35.0 1.0
CA A:LEU129 4.6 28.9 1.0
CE A:LYS13 4.9 28.5 1.0

Cadmium binding site 6 out of 10 in 5myy

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd206

b:75.4
occ:0.15
O A:HOH416 1.5 82.8 1.0
O A:HOH341 2.1 24.0 1.0
CL A:CL216 2.7 25.0 1.0
O A:HOH389 3.9 26.6 1.0
NZ A:LYS1 3.9 21.3 1.0
O A:HOH303 4.2 42.0 1.0
CZ A:PHE3 4.3 14.6 1.0
CE2 A:PHE3 4.4 14.9 1.0
O A:SER86 4.5 17.2 1.0

Cadmium binding site 7 out of 10 in 5myy

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd207

b:25.7
occ:0.20
O A:HOH384 2.3 27.6 1.0
O A:CYS76 2.3 16.0 1.0
O A:HOH378 2.3 31.6 1.0
C A:CYS76 3.3 14.6 1.0
O A:HOH360 3.9 21.3 1.0
CA A:CYS76 4.1 14.3 1.0
CB A:ASN77 4.3 17.7 1.0
O A:HOH403 4.3 33.1 1.0
CG2 A:ILE78 4.3 18.3 1.0
N A:ASN77 4.4 14.5 1.0
O A:ASN77 4.4 17.2 1.0
CB A:CYS76 4.5 12.8 1.0
C A:ASN77 4.6 14.9 1.0
CA A:ASN77 4.6 15.6 1.0
OD1 A:ASN77 4.6 31.8 1.0
CG A:ASN77 5.0 24.6 1.0

Cadmium binding site 8 out of 10 in 5myy

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd208

b:27.4
occ:0.20
CL A:CL218 2.3 24.3 1.0
O A:HOH388 2.8 34.2 1.0
O A:HOH379 4.0 33.8 1.0
CB A:ARG5 4.6 16.9 1.0
NZ A:LYS33 4.7 20.0 1.0
CE2 A:PHE38 5.0 13.5 1.0
CD A:ARG5 5.0 18.7 1.0
NE A:ARG5 5.0 19.8 1.0

Cadmium binding site 9 out of 10 in 5myy

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd209

b:21.4
occ:0.20
NH1 A:ARG68 2.9 9.9 0.5
NH1 A:ARG68 3.2 15.0 0.5
CD A:ARG68 3.8 11.1 0.5
CD A:ARG68 4.0 15.4 0.5
CZ A:ARG68 4.0 9.2 0.5
CG A:ARG68 4.1 20.2 0.5
CZ A:ARG68 4.3 12.7 0.5
NE A:ARG68 4.4 10.3 0.5
NE A:ARG68 4.6 13.9 0.5
NH2 A:ARG45 4.8 38.6 1.0

Cadmium binding site 10 out of 10 in 5myy

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd210

b:12.0
occ:0.10
O A:HOH340 1.7 17.4 1.0
O A:HOH304 1.8 13.3 1.0
O A:HOH325 2.2 15.4 1.0
CD A:CD201 2.4 12.1 0.4
OE1 A:GLU35 2.5 11.1 1.0
OE2 A:GLU35 2.6 11.3 1.0
CD A:GLU35 2.9 9.8 1.0
CL A:CL214 2.9 19.5 1.0
O A:HOH401 3.1 25.9 1.0
OD2 A:ASP52 3.9 11.6 0.5
CD A:CD202 4.1 17.6 0.1
O1 A:EDO222 4.2 18.7 1.0
O A:HOH333 4.2 35.0 1.0
O A:HOH331 4.3 16.1 1.0
CG A:GLU35 4.3 9.8 1.0
CB A:GLN57 4.4 9.4 1.0
O A:HOH324 4.4 22.7 1.0
OD2 A:ASP52 4.5 18.5 0.5
N A:VAL109 4.6 10.3 1.0
O A:GLN57 4.7 9.9 1.0
CD1 A:TRP108 4.7 9.6 1.0
N A:ALA110 4.7 10.3 1.0
CB A:ALA110 4.8 12.4 1.0
CA A:TRP108 4.9 9.2 1.0
O A:HOH344 5.0 17.0 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: Sat Dec 12 08:27:10 2020

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