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Cadmium in PDB 6bre: Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.

Enzymatic activity of Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.

All present enzymatic activity of Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source., PDB code: 6bre was solved by J.Sakon, P.Caviness, T.Jack, J.B.Pickens, P.Reed, C.Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.74 / 1.86
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.410, 81.410, 36.390, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 24.8

Other elements in 6bre:

The structure of Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source. also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Sodium (Na) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source. (pdb code 6bre). 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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source., PDB code: 6bre:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 6bre

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Cadmium binding site 1 out of 10 in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.


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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:20.9
occ:0.50
 O A:HOH409 2.3 22.8 1.0
CL A:CL213 2.5 32.7 1.0
O A:HOH494 2.5 30.4 1.0
O A:HOH420 2.6 23.3 1.0
CB A:ARG5 4.3 24.6 1.0
NZ A:LYS33 4.6 23.6 1.0
CD A:ARG5 4.8 26.5 1.0
N A:ARG5 4.8 23.6 1.0
CE2 A:PHE38 4.8 19.3 1.0
NE A:ARG5 4.9 25.8 1.0

Cadmium binding site 2 out of 10 in 6bre

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Cadmium binding site 2 out of 10 in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.


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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:24.9
occ:0.50
 O A:HOH313 2.3 17.5 1.0
CD A:CD211 2.3 39.8 0.5
OD2 A:ASP52 2.4 23.9 1.0
O A:HOH305 2.7 27.9 1.0
CL A:CL215 2.7 29.7 1.0
O A:HOH355 2.8 23.6 1.0
CG A:ASP52 3.3 24.2 1.0
OD1 A:ASP52 3.7 20.0 1.0
O1 A:EDO218 3.8 23.1 1.0
O A:GLN57 3.8 12.8 1.0
O A:HOH328 4.2 17.3 1.0
OE1 A:GLU35 4.3 14.0 1.0
O A:HOH502 4.4 35.1 1.0
CB A:GLN57 4.4 14.7 1.0
CB A:ASP52 4.6 14.1 1.0
O A:HOH449 4.7 29.8 1.0
OD1 A:ASN46 4.8 21.6 1.0
OE2 A:GLU35 4.8 15.2 1.0
O A:HOH439 4.8 29.1 1.0
C A:GLN57 4.9 13.7 1.0
CD A:GLU35 4.9 17.3 1.0
O2 A:EDO218 5.0 19.3 1.0

Cadmium binding site 3 out of 10 in 6bre

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Cadmium binding site 3 out of 10 in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.


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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:32.3
occ:0.50
 OD1 A:ASN65 2.2 26.9 1.0
O A:HOH430 2.2 25.9 1.0
CL A:CL217 2.4 35.7 1.0
O A:HOH351 2.5 39.4 1.0
O A:HOH422 2.6 28.9 1.0
O A:HOH397 2.7 17.9 1.0
CG A:ASN65 3.3 23.6 1.0
CB A:ASN65 3.9 19.6 1.0
OG A:SER72 4.0 25.0 1.0
NA A:NA201 4.0 24.1 1.0
CA A:ASN65 4.1 19.3 1.0
N A:GLY67 4.2 19.3 1.0
ND2 A:ASN65 4.4 26.2 1.0
CA A:GLY67 4.4 21.4 1.0
O A:HOH466 4.5 31.2 0.5
O A:HOH411 4.5 41.3 1.0
O A:THR69 4.5 24.0 1.0
N A:ASP66 4.5 16.4 1.0
C A:ASN65 4.8 16.8 1.0
O A:HOH377 4.9 30.1 1.0
O A:HOH481 5.0 33.8 1.0

Cadmium binding site 4 out of 10 in 6bre

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Cadmium binding site 4 out of 10 in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.


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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:29.5
occ:0.50
 O A:HOH439 2.4 29.1 1.0
O A:HOH507 2.4 38.9 1.0
O A:HOH436 2.5 33.9 1.0
O A:HOH438 2.6 22.4 1.0
CB A:ASN46 4.3 21.9 1.0
O A:HOH305 4.3 27.9 1.0
O A:HOH340 4.3 32.5 1.0
OD1 A:ASN46 4.4 21.6 1.0
CG A:ASN46 4.5 22.1 1.0
OG1 A:THR47 4.6 33.5 1.0
O A:HOH447 4.7 43.0 1.0
N A:THR47 4.7 25.8 1.0
O A:HOH502 4.8 35.1 1.0
CA A:ASN46 4.9 23.0 1.0

Cadmium binding site 5 out of 10 in 6bre

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Cadmium binding site 5 out of 10 in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.


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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:36.0
occ:0.50
 O A:HOH433 2.4 19.3 1.0
O A:HOH416 2.5 46.2 1.0
O A:HOH426 2.5 16.5 1.0
CG2 A:VAL120 4.2 23.9 1.0
O A:HOH364 4.2 24.5 1.0
OG A:SER24 4.6 20.6 1.0

Cadmium binding site 6 out of 10 in 6bre

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Cadmium binding site 6 out of 10 in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.


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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:36.3
occ:0.50
 O A:HOH410 2.5 27.4 1.0
O A:HOH392 2.6 42.5 1.0
O A:HOH489 3.7 15.8 1.0
ND2 A:ASN44 4.2 22.5 1.0
O A:HOH378 4.3 23.3 1.0
O A:GLU35 4.4 15.2 1.0
O A:HOH427 4.5 36.7 1.0
O A:HOH363 4.5 37.5 1.0
OD1 A:ASN44 4.8 25.9 1.0
CG A:ASN44 5.0 21.9 1.0

Cadmium binding site 7 out of 10 in 6bre

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Cadmium binding site 7 out of 10 in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.


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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:40.7
occ:0.50
 NH1 A:ARG68 3.2 27.0 1.0
CD A:ARG68 3.8 24.4 1.0
CZ A:ARG68 4.3 27.8 1.0
NE A:ARG68 4.5 27.4 1.0
CG A:ARG68 4.7 20.6 1.0
CB A:ARG68 4.8 20.4 1.0

Cadmium binding site 8 out of 10 in 6bre

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Cadmium binding site 8 out of 10 in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.


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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:49.7
occ:0.50
 CL A:CL216 1.8 50.1 0.5
OXT A:LEU129 2.2 37.6 1.0
O A:HOH431 2.6 32.5 1.0
O A:LEU129 2.6 42.2 1.0
O A:HOH401 2.6 49.2 1.0
C A:LEU129 2.8 40.2 1.0
O A:HOH319 3.0 34.4 1.0
NH1 A:ARG128 3.5 62.1 1.0
NZ A:LYS13 4.2 34.8 1.0
CA A:LEU129 4.4 39.6 1.0
O A:HOH339 4.4 47.8 1.0
CZ A:ARG128 4.8 60.9 1.0
O A:HOH463 4.9 46.4 1.0
O A:HOH393 4.9 41.5 1.0

Cadmium binding site 9 out of 10 in 6bre

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Cadmium binding site 9 out of 10 in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.


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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:43.1
occ:0.50
 O A:HOH303 2.1 17.4 0.5
O A:HOH302 2.2 22.1 1.0
CL A:CL214 2.5 32.5 1.0
O A:HOH322 2.5 25.1 1.0
O A:HOH465 3.1 31.5 1.0
O A:HOH446 3.2 28.9 1.0
NH2 A:ARG14 3.2 57.8 1.0
CZ A:ARG14 3.5 55.5 1.0
NH1 A:ARG14 3.8 56.4 1.0
O A:HOH338 3.9 24.1 1.0
O A:HOH381 4.1 34.9 1.0
NE A:ARG14 4.1 52.5 1.0
NE2 A:HIS15 4.3 28.1 1.0
O A:HOH464 4.5 42.7 1.0
CB A:ALA11 4.8 23.7 1.0

Cadmium binding site 10 out of 10 in 6bre

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Cadmium binding site 10 out of 10 in the Hen Egg-White Lysozyme Cocrystallized with Cadmium Sulphate Using Cukalpha Source.


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 Cocrystallized with Cadmium Sulphate Using Cukalpha Source. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd211

b:39.8
occ:0.50
 O A:HOH313 2.3 17.5 1.0
CD A:CD203 2.3 24.9 0.5
O A:HOH355 2.4 23.6 1.0
OE1 A:GLU35 2.5 14.0 1.0
OE2 A:GLU35 2.5 15.2 1.0
CL A:CL215 2.6 29.7 1.0
CD A:GLU35 2.8 17.3 1.0
O A:HOH449 3.3 29.8 1.0
O1 A:EDO218 4.0 23.1 1.0
OD2 A:ASP52 4.2 23.9 1.0
CB A:GLN57 4.3 14.7 1.0
CG A:GLU35 4.3 13.9 1.0
N A:VAL109 4.3 16.8 1.0
O A:GLN57 4.5 12.8 1.0
O A:HOH328 4.5 17.3 1.0
N A:ALA110 4.6 15.5 1.0
CD1 A:TRP108 4.6 13.8 1.0
O A:HOH305 4.6 27.9 1.0
O A:HOH502 4.7 35.1 1.0
CA A:TRP108 4.8 14.1 1.0
CB A:ALA110 4.9 17.8 1.0
O A:HOH508 5.0 39.8 1.0
C A:TRP108 5.0 14.5 1.0

Reference:

J.Sakon, P.Caviness, T.Jack, J.B.Pickens, P.Reed, C.Ruth. Hen Egg-White Lysozyme (Hewl) Cocrystallized with Cadmium Sulphate. To Be Published.
Page generated: Sat Dec 12 08:28:06 2020

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