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Sodium in PDB 1wx5: Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal

Enzymatic activity of Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal

All present enzymatic activity of Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal:
1.14.18.1;

Protein crystallography data

The structure of Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal, PDB code: 1wx5 was solved by Y.Matoba, T.Kumagai, A.Yamamoto, H.Yoshitsu, M.Sugiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.850, 93.200, 65.590, 90.00, 93.80, 90.00
R / Rfree (%) 20.1 / 29.1

Other elements in 1wx5:

The structure of Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal (pdb code 1wx5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal, PDB code: 1wx5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1wx5

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Sodium binding site 1 out of 3 in the Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na282

b:2.0
occ:1.00
 O A:THR241 2.3 11.1 1.0
OD1 A:ASP246 2.3 4.9 1.0
O A:HOH322 2.3 14.7 1.0
OE1 A:GLU249 2.5 12.5 1.0
O A:VAL244 2.5 14.6 1.0
OE2 A:GLU249 2.6 18.1 1.0
O A:HOH423 2.7 31.1 1.0
CD A:GLU249 2.8 18.5 1.0
C A:THR241 3.4 11.3 1.0
CG A:ASP246 3.5 5.5 1.0
C A:VAL244 3.7 12.9 1.0
N A:THR241 4.0 10.0 1.0
N A:ASP246 4.1 8.5 1.0
CA A:THR241 4.1 3.5 1.0
CG A:GLU249 4.2 15.2 1.0
CB A:ASP246 4.2 13.6 1.0
N A:PRO242 4.4 10.1 1.0
O A:HOH387 4.4 26.7 1.0
N A:VAL244 4.4 13.7 1.0
C A:GLY240 4.4 12.6 1.0
CB A:THR241 4.4 6.8 1.0
OD2 A:ASP246 4.5 10.0 1.0
O A:HOH330 4.5 16.7 1.0
CA A:PRO242 4.6 13.9 1.0
CA A:VAL244 4.6 10.7 1.0
CA A:VAL245 4.6 7.2 1.0
N A:VAL245 4.6 7.9 1.0
C A:VAL245 4.8 5.4 1.0
N A:GLY240 4.8 17.2 1.0
CA A:ASP246 4.8 9.9 1.0
O A:GLY240 4.8 13.8 1.0
N A:ASP243 4.9 11.6 1.0
C A:PRO242 4.9 13.6 1.0
CA A:GLY240 5.0 12.0 1.0

Sodium binding site 2 out of 3 in 1wx5

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Sodium binding site 2 out of 3 in the Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na282

b:11.4
occ:1.00
 O C:THR241 2.2 21.2 1.0
OE1 C:GLU249 2.4 26.9 1.0
O C:VAL244 2.4 23.0 1.0
OD1 C:ASP246 2.4 18.0 1.0
OE2 C:GLU249 2.6 22.4 1.0
CD C:GLU249 2.8 18.7 1.0
O C:HOH463 3.0 35.5 1.0
C C:THR241 3.4 18.3 1.0
C C:VAL244 3.5 15.7 1.0
CG C:ASP246 3.6 13.8 1.0
N C:VAL244 3.9 16.1 1.0
CA C:PRO242 4.2 20.1 1.0
N C:ASP246 4.2 17.9 1.0
N C:PRO242 4.2 21.8 1.0
N C:THR241 4.3 16.8 1.0
CA C:THR241 4.3 16.0 1.0
CG C:GLU249 4.3 16.8 1.0
CA C:VAL244 4.3 16.7 1.0
N C:ASP243 4.3 21.6 1.0
N C:VAL245 4.4 16.2 1.0
C C:PRO242 4.4 23.4 1.0
OD2 C:ASP246 4.4 9.0 1.0
CA C:VAL245 4.5 17.6 1.0
CB C:ASP246 4.6 9.3 1.0
CB C:THR241 4.6 7.7 1.0
C C:VAL245 4.7 14.7 1.0
O C:HOH391 4.7 21.5 1.0
C C:GLY240 4.7 21.6 1.0
C C:ASP243 4.9 16.6 1.0
O C:HOH361 5.0 26.7 1.0

Sodium binding site 3 out of 3 in 1wx5

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Sodium binding site 3 out of 3 in the Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed with A Caddie Protein in the Monoclinic Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na283

b:14.2
occ:1.00
 O C:ASP243 2.8 13.9 1.0
O C:ARG51 2.9 17.5 1.0
C C:ASP243 3.3 16.6 1.0
CG C:GLU50 3.3 33.4 1.0
C C:ARG51 3.5 19.5 1.0
OG1 C:THR52 3.7 19.7 1.0
N C:VAL244 3.7 16.1 1.0
N C:ARG51 3.7 25.0 1.0
CA C:VAL244 3.7 16.7 1.0
N C:VAL245 3.8 16.2 1.0
O C:HOH463 3.8 35.5 1.0
CG2 C:VAL245 3.9 16.6 1.0
C C:VAL244 3.9 15.7 1.0
O C:HOH449 4.0 37.2 1.0
CD C:GLU50 4.1 36.6 1.0
CA C:ASP243 4.1 18.1 1.0
O C:HOH471 4.2 37.4 1.0
N C:THR52 4.3 16.7 1.0
CA C:ARG51 4.3 20.6 1.0
CA C:THR52 4.4 17.1 1.0
CB C:THR52 4.4 19.0 1.0
OE1 C:GLU50 4.5 38.6 1.0
C C:GLU50 4.5 25.2 1.0
CG2 C:THR52 4.6 16.6 1.0
CB C:GLU50 4.6 29.1 1.0
CA C:VAL245 4.6 17.6 1.0
CA C:GLU50 4.7 27.3 1.0
O C:VAL244 4.7 23.0 1.0
OE2 C:GLU50 4.9 36.9 1.0
CB C:VAL245 4.9 19.4 1.0

Reference:

Y.Matoba, T.Kumagai, A.Yamamoto, H.Yoshitsu, M.Sugiyama. Crystallographic Evidence That the Dinuclear Copper Center of Tyrosinase Is Flexible During Catalysis J.Biol.Chem. V. 281 8981 2006.
ISSN: ISSN 0021-9258
PubMed: 16436386
DOI: 10.1074/JBC.M509785200
Page generated: Mon Oct 7 00:29:09 2024

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