Atomistry » Copper » PDB 5ce9-5i0y » 5ce9
Atomistry »
  Copper »
    PDB 5ce9-5i0y »
      5ce9 »

Copper in PDB 5ce9: Structure of Tyrosinase From Walnut (Juglans Regia)

Protein crystallography data

The structure of Structure of Tyrosinase From Walnut (Juglans Regia), PDB code: 5ce9 was solved by A.Bijelic, M.Pretzler, F.Zekiri, A.Rompel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.10 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.430, 90.940, 86.580, 90.00, 130.18, 90.00
R / Rfree (%) 17 / 18.8

Other elements in 5ce9:

The structure of Structure of Tyrosinase From Walnut (Juglans Regia) also contains other interesting chemical elements:

Sodium (Na) 7 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Tyrosinase From Walnut (Juglans Regia) (pdb code 5ce9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Structure of Tyrosinase From Walnut (Juglans Regia), PDB code: 5ce9:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 5ce9

Go back to Copper Binding Sites List in 5ce9
Copper binding site 1 out of 4 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:32.3
occ:1.00
NE2 A:HIS273 2.0 28.4 1.0
NE2 A:HIS239 2.0 28.5 1.0
NE2 A:HIS243 2.0 29.3 1.0
O A:O403 2.1 35.2 1.0
CE1 A:HIS273 2.9 25.4 1.0
CE1 A:HIS243 2.9 27.5 1.0
HE1 A:HIS273 3.0 30.5 1.0
CD2 A:HIS239 3.0 25.9 1.0
CE1 A:HIS239 3.0 28.9 1.0
CD2 A:HIS243 3.0 30.0 1.0
HE1 A:HIS243 3.1 33.0 1.0
CD2 A:HIS273 3.1 26.8 1.0
HD2 A:HIS239 3.1 31.1 1.0
HE1 A:HIS239 3.2 34.6 1.0
HD2 A:HIS243 3.3 36.0 1.0
HD2 A:HIS273 3.4 32.2 1.0
HE2 A:PHE269 3.6 31.9 1.0
HE1 A:PHE113 3.9 31.5 1.0
HD2 A:HIS272 3.9 31.8 1.0
CU A:CU402 4.0 26.0 0.7
ND1 A:HIS273 4.0 26.9 1.0
ND1 A:HIS243 4.0 29.3 1.0
CE2 A:PHE269 4.1 26.6 1.0
ND1 A:HIS239 4.1 29.0 1.0
CG A:HIS239 4.1 27.3 1.0
CG A:HIS243 4.1 29.2 1.0
CG A:HIS273 4.2 26.4 1.0
HZ A:PHE269 4.2 31.8 1.0
NE2 A:HIS117 4.3 25.6 1.0
CZ A:PHE269 4.4 26.5 1.0
HE2 A:HIS272 4.4 33.0 1.0
CD2 A:HIS272 4.5 26.5 1.0
HZ A:PHE113 4.5 30.7 1.0
NE2 A:HIS87 4.6 33.9 1.0
CE1 A:PHE113 4.7 26.2 1.0
NE2 A:HIS272 4.7 27.5 1.0
CD2 A:HIS117 4.7 26.8 1.0
HD1 A:HIS273 4.8 32.3 1.0
HD2 A:HIS117 4.8 32.1 1.0
HD1 A:HIS243 4.8 35.2 1.0
CD2 A:PHE269 4.9 26.1 1.0
HD1 A:HIS239 4.9 34.8 1.0
CE1 A:HIS117 4.9 25.5 1.0
HE1 A:HIS87 4.9 38.2 1.0
HG21 A:VAL276 5.0 28.0 1.0

Copper binding site 2 out of 4 in 5ce9

Go back to Copper Binding Sites List in 5ce9
Copper binding site 2 out of 4 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:26.0
occ:0.70
NE2 A:HIS108 2.0 30.2 1.0
NE2 A:HIS87 2.0 33.9 1.0
NE2 A:HIS117 2.0 25.6 1.0
O A:O403 2.1 35.2 1.0
CE1 A:HIS117 2.7 25.5 1.0
HE1 A:HIS117 2.7 30.6 1.0
CD2 A:HIS87 2.8 33.3 1.0
HD2 A:HIS87 2.9 40.0 1.0
CE1 A:HIS108 2.9 29.2 1.0
CD2 A:HIS108 3.1 30.4 1.0
HE1 A:HIS108 3.1 35.0 1.0
CE1 A:HIS87 3.1 31.8 1.0
CD2 A:HIS117 3.2 26.8 1.0
HD2 A:HIS108 3.3 36.5 1.0
HE1 A:HIS87 3.4 38.2 1.0
HZ A:PHE269 3.5 31.8 1.0
HD11 A:ILE107 3.5 33.2 1.0
SG A:CYS91 3.6 31.0 1.0
HD2 A:HIS117 3.6 32.1 1.0
ND1 A:HIS117 4.0 24.8 1.0
CU A:CU401 4.0 32.3 1.0
CG A:HIS87 4.0 32.2 1.0
HE2 A:PHE269 4.1 31.9 1.0
ND1 A:HIS108 4.1 29.2 1.0
ND1 A:HIS87 4.1 31.6 1.0
HE1 A:PHE113 4.2 31.5 1.0
CG A:HIS108 4.2 30.1 1.0
CG A:HIS117 4.2 24.5 1.0
HE1 A:HIS273 4.2 30.5 1.0
NE2 A:HIS273 4.3 28.4 1.0
CZ A:PHE269 4.3 26.5 1.0
CD1 A:ILE107 4.4 27.6 1.0
CE1 A:HIS273 4.5 25.4 1.0
HD12 A:ILE107 4.5 33.2 1.0
HE2 A:PHE116 4.6 28.2 1.0
CE2 A:PHE269 4.6 26.6 1.0
HD1 A:PHE260 4.6 51.3 1.0
HD13 A:ILE107 4.6 33.2 1.0
HE1 A:PHE260 4.6 52.9 1.0
HD1 A:HIS117 4.7 29.8 1.0
HD2 A:PHE116 4.7 27.7 1.0
HD1 A:PHE113 4.8 31.0 1.0
HD1 A:HIS108 4.8 35.1 1.0
CE1 A:PHE113 4.9 26.2 1.0
HD1 A:HIS87 4.9 37.9 1.0
HE1 A:HIS239 4.9 34.6 1.0

Copper binding site 3 out of 4 in 5ce9

Go back to Copper Binding Sites List in 5ce9
Copper binding site 3 out of 4 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:37.3
occ:1.00
NE2 B:HIS243 2.0 27.5 1.0
NE2 B:HIS239 2.0 24.6 1.0
NE2 B:HIS273 2.0 29.1 1.0
O B:O403 2.1 30.1 1.0
CE1 B:HIS273 2.9 27.9 1.0
CE1 B:HIS243 2.9 27.2 1.0
CD2 B:HIS239 3.0 24.3 1.0
HE1 B:HIS273 3.0 33.5 1.0
CE1 B:HIS239 3.0 26.1 1.0
HE1 B:HIS243 3.1 32.7 1.0
CD2 B:HIS243 3.1 28.0 1.0
CD2 B:HIS273 3.1 26.4 1.0
HD2 B:HIS239 3.1 29.2 1.0
HE1 B:HIS239 3.3 31.3 1.0
HD2 B:HIS243 3.3 33.6 1.0
HD2 B:HIS273 3.4 31.7 1.0
HE2 B:PHE269 3.6 27.8 1.0
HD2 B:HIS272 3.9 30.5 1.0
HE1 B:PHE113 4.0 27.2 1.0
CU B:CU402 4.0 30.9 0.7
ND1 B:HIS273 4.0 27.1 1.0
ND1 B:HIS243 4.0 28.7 1.0
CE2 B:PHE269 4.1 23.2 1.0
ND1 B:HIS239 4.1 27.2 1.0
CG B:HIS239 4.1 27.7 1.0
CG B:HIS243 4.1 26.9 1.0
CG B:HIS273 4.1 25.2 1.0
HZ B:PHE269 4.3 27.6 1.0
NE2 B:HIS117 4.3 23.8 1.0
HE2 B:HIS272 4.4 30.0 1.0
CD2 B:HIS272 4.5 25.4 1.0
CZ B:PHE269 4.5 23.0 1.0
HZ B:PHE113 4.5 26.4 1.0
NE2 B:HIS87 4.6 29.7 1.0
NE2 B:HIS272 4.7 25.0 1.0
CD2 B:HIS117 4.7 22.7 1.0
CE1 B:PHE113 4.8 22.7 1.0
HD2 B:HIS117 4.8 27.2 1.0
HD1 B:HIS273 4.8 32.5 1.0
HD1 B:HIS243 4.8 34.4 1.0
HD1 B:HIS239 4.9 32.6 1.0
CD2 B:PHE269 4.9 22.6 1.0
CE1 B:HIS117 5.0 23.0 1.0
HE1 B:PHE260 5.0 49.2 1.0

Copper binding site 4 out of 4 in 5ce9

Go back to Copper Binding Sites List in 5ce9
Copper binding site 4 out of 4 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:30.9
occ:0.70
NE2 B:HIS87 2.0 29.7 1.0
NE2 B:HIS108 2.0 23.0 1.0
NE2 B:HIS117 2.1 23.8 1.0
O B:O403 2.1 30.1 1.0
CD2 B:HIS87 2.8 28.4 1.0
CE1 B:HIS117 2.8 23.0 1.0
HD2 B:HIS87 2.8 34.0 1.0
HE1 B:HIS117 2.9 27.6 1.0
CE1 B:HIS108 2.9 25.4 1.0
HE1 B:HIS108 3.0 30.4 1.0
CD2 B:HIS108 3.1 25.6 1.0
CE1 B:HIS87 3.2 30.3 1.0
CD2 B:HIS117 3.2 22.7 1.0
HD2 B:HIS108 3.4 30.8 1.0
HE1 B:HIS87 3.5 36.3 1.0
SG B:CYS91 3.5 26.4 1.0
HD2 B:HIS117 3.5 27.2 1.0
HZ B:PHE269 3.6 27.6 1.0
HD11 B:ILE107 3.6 29.8 1.0
CG B:HIS87 4.0 28.4 1.0
CU B:CU401 4.0 37.3 1.0
ND1 B:HIS117 4.0 22.1 1.0
ND1 B:HIS108 4.1 23.7 1.0
HE2 B:PHE269 4.1 27.8 1.0
ND1 B:HIS87 4.1 29.6 1.0
CG B:HIS108 4.2 23.8 1.0
CG B:HIS117 4.2 21.9 1.0
NE2 B:HIS273 4.3 29.1 1.0
HE1 B:HIS273 4.3 33.5 1.0
HE1 B:PHE113 4.4 27.2 1.0
CZ B:PHE269 4.4 23.0 1.0
CD1 B:ILE107 4.4 24.8 1.0
HE2 B:PHE116 4.4 25.9 1.0
HE1 B:PHE260 4.5 49.2 1.0
HD12 B:ILE107 4.5 29.8 1.0
CE1 B:HIS273 4.5 27.9 1.0
HD1 B:PHE260 4.6 50.2 1.0
CE2 B:PHE269 4.6 23.2 1.0
HD13 B:ILE107 4.6 29.8 1.0
HD2 B:PHE116 4.7 24.9 1.0
HD1 B:HIS117 4.8 26.5 1.0
CE1 B:PHE260 4.8 41.0 1.0
HD1 B:HIS108 4.8 28.4 1.0
CD1 B:PHE260 4.9 41.8 1.0
HD1 B:HIS87 4.9 35.6 1.0
HE1 B:HIS239 5.0 31.3 1.0
HD1 B:PHE113 5.0 27.4 1.0
HB3 B:CYS91 5.0 29.8 1.0
CB B:CYS91 5.0 24.8 1.0

Reference:

A.Bijelic, M.Pretzler, C.Molitor, F.Zekiri, A.Rompel. The Structure of A Plant Tyrosinase From Walnut Leaves Reveals the Importance of """"Substrate-Guiding Residues"""" For Enzymatic Specificity. Angew.Chem.Int.Ed.Engl. V. 54 14677 2015.
ISSN: ESSN 1521-3773
PubMed: 26473311
DOI: 10.1002/ANIE.201506994
Page generated: Sun Dec 13 11:17:20 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy