Atomistry » Sodium » PDB 1w5n-1x7d » 1wx5
Atomistry »
  Sodium »
    PDB 1w5n-1x7d »
      1wx5 »

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

Go back to Sodium Binding Sites List in 1wx5
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

Go back to Sodium Binding Sites List in 1wx5
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

Go back to Sodium Binding Sites List in 1wx5
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: Tue Dec 15 05:41:24 2020

Last articles

Zn in 8PFC
Zn in 8SF0
Zn in 8SOJ
Zn in 8SOK
Zn in 8SYI
Zn in 8SLG
Zn in 8SEX
Zn in 8SEZ
Zn in 8SJG
Zn in 8SEY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy