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Rhodium in PDB 3a93: Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3

Enzymatic activity of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3

All present enzymatic activity of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3, PDB code: 3a93 was solved by S.Abe, T.Koshiyama, T.Ohki, T.Hikage, Y.Watanabe, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.80 / 1.55
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.994, 77.994, 37.259, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 20.7

Other elements in 3a93:

The structure of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3 also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Rhodium Binding Sites:

The binding sites of Rhodium atom in the Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3 (pdb code 3a93). This binding sites where shown within 5.0 Angstroms radius around Rhodium atom.
In total 7 binding sites of Rhodium where determined in the Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3, PDB code: 3a93:
Jump to Rhodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Rhodium binding site 1 out of 7 in 3a93

Go back to Rhodium Binding Sites List in 3a93
Rhodium binding site 1 out of 7 in the Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 1 of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh136

b:36.4
occ:0.30
 O A:HOH172 2.4 21.5 1.0
O A:HOH207 2.5 25.8 1.0
NH2 A:ARG61 3.7 25.6 0.5
OG1 A:THR47 4.0 24.5 1.0
CB A:ASN46 4.5 17.7 1.0
CZ A:ARG61 4.6 24.7 0.5
N A:THR47 4.6 20.1 1.0
NH1 A:ARG61 4.7 26.2 0.5
CG A:ASN46 4.9 18.6 1.0
OD1 A:ASN46 4.9 20.0 1.0

Rhodium binding site 2 out of 7 in 3a93

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Rhodium binding site 2 out of 7 in the Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 2 of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh137

b:31.6
occ:0.50
 RH A:RH3142 1.5 34.4 0.5
O A:HOH143 2.2 25.7 1.0
O A:HOH213 2.4 28.4 1.0
RH A:RH3138 3.0 33.5 0.5
NH1 A:ARG14 3.0 29.2 1.0
NE2 A:HIS15 3.4 25.9 1.0
NH2 A:ARG14 3.5 29.7 1.0
OD2 A:ASP87 3.6 30.0 1.0
CZ A:ARG14 3.7 28.3 1.0
CG A:ASP87 3.8 26.1 1.0
OD1 A:ASP87 3.9 27.7 1.0
CE1 A:HIS15 4.2 25.6 1.0
CD2 A:HIS15 4.5 24.5 1.0
N A:ILE88 4.6 18.7 1.0
CA A:ASP87 4.6 21.0 1.0
OG1 A:THR89 4.6 21.3 1.0
CB A:ASP87 4.7 21.7 1.0
O A:HOH228 4.7 32.5 1.0

Rhodium binding site 3 out of 7 in 3a93

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Rhodium binding site 3 out of 7 in the Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 3 of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh138

b:33.5
occ:0.50
 OD2 A:ASP87 2.2 30.0 1.0
O A:HOH228 2.2 32.5 1.0
RH A:RH3137 3.0 31.6 0.5
CG A:ASP87 3.1 26.1 1.0
RH A:RH3142 3.3 34.4 0.5
OD1 A:ASP87 3.5 27.7 1.0
OG1 A:THR89 4.0 21.3 1.0
CB A:ASP87 4.4 21.7 1.0
NH2 A:ARG14 4.6 29.7 1.0
NE2 A:HIS15 4.9 25.9 1.0
CE1 A:HIS15 4.9 25.6 1.0
O A:HOH143 4.9 25.7 1.0
O A:HOH213 5.0 28.4 1.0

Rhodium binding site 4 out of 7 in 3a93

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Rhodium binding site 4 out of 7 in the Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 4 of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh139

b:39.4
occ:0.40
 OD2 A:ASP18 2.2 27.2 1.0
O A:HOH234 2.5 35.9 1.0
RH A:RH3141 2.6 31.5 0.1
CG A:ASP18 3.0 23.6 1.0
OD1 A:ASP18 3.1 23.4 1.0
CB A:ASP18 4.4 21.0 1.0
OD1 A:ASN19 4.7 31.3 1.0
NZ A:LYS13 4.8 31.4 1.0
CB A:LEU25 5.0 14.2 1.0

Rhodium binding site 5 out of 7 in 3a93

Go back to Rhodium Binding Sites List in 3a93
Rhodium binding site 5 out of 7 in the Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 5 of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh140

b:28.6
occ:0.10
 OD2 A:ASP119 2.1 28.1 1.0
CG A:ASP119 2.9 23.4 1.0
OD1 A:ASP119 3.2 27.0 1.0
CB A:ASP119 4.3 20.3 1.0
N A:ALA122 4.8 16.5 1.0
CB A:ALA122 5.0 17.5 1.0

Rhodium binding site 6 out of 7 in 3a93

Go back to Rhodium Binding Sites List in 3a93
Rhodium binding site 6 out of 7 in the Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 6 of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh141

b:31.5
occ:0.10
 OD1 A:ASN19 2.6 31.3 1.0
RH A:RH3139 2.6 39.4 0.4
OD2 A:ASP18 2.8 27.2 1.0
CG A:ASP18 3.3 23.6 1.0
OD1 A:ASP18 3.3 23.4 1.0
CG A:ASN19 3.8 25.0 1.0
CB A:ASN19 4.5 21.0 1.0
CB A:ASP18 4.6 21.0 1.0
O A:HOH234 4.8 35.9 1.0
ND2 A:ASN19 4.8 29.7 1.0
C A:ASP18 5.0 20.6 1.0

Rhodium binding site 7 out of 7 in 3a93

Go back to Rhodium Binding Sites List in 3a93
Rhodium binding site 7 out of 7 in the Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 7 of Crystal Structure of Hen Egg White Lysozyme Soaked with 30MM RHCL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh142

b:34.4
occ:0.50
 RH A:RH3137 1.5 31.6 0.5
NH2 A:ARG14 2.2 29.7 1.0
NE2 A:HIS15 2.4 25.9 1.0
NH1 A:ARG14 2.4 29.2 1.0
CZ A:ARG14 2.6 28.3 1.0
O A:HOH143 3.1 25.7 1.0
CE1 A:HIS15 3.2 25.6 1.0
RH A:RH3138 3.3 33.5 0.5
O A:HOH213 3.4 28.4 1.0
CD2 A:HIS15 3.4 24.5 1.0
NE A:ARG14 3.9 28.0 1.0
ND1 A:HIS15 4.3 26.1 1.0
OG1 A:THR89 4.4 21.3 1.0
CG A:HIS15 4.5 22.2 1.0
OD2 A:ASP87 4.5 30.0 1.0
OD1 A:ASP87 4.6 27.7 1.0
O A:HOH228 4.7 32.5 1.0
CG A:ASP87 4.8 26.1 1.0
CD A:ARG14 4.8 26.0 1.0

Reference:

T.Ueno, S.Abe, T.Koshiyama, T.Ohki, T.Hikage, Y.Watanabe. Elucidation of Metal-Ion Accumulation Induced By Hydrogen Bonds on Protein Surfaces By Using Porous Lysozyme Crystals Containing Rh(III) Ions As the Model Surfaces Chemistry V. 16 2730 2010.
ISSN: ISSN 0947-6539
PubMed: 20146274
DOI: 10.1002/CHEM.200903269
Page generated: Thu Oct 10 12:33:44 2024

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