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Copper in PDB 8zyg: Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/C106D Mutant) in Copper (Cu) Substituted Form

Protein crystallography data

The structure of Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/C106D Mutant) in Copper (Cu) Substituted Form, PDB code: 8zyg was solved by Y.Morita, H.Kubo, R.Matsumoto, N.Fujieda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.67, 57.57, 75.87, 90, 90, 90
R / Rfree (%) n/a / n/a

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/C106D Mutant) in Copper (Cu) Substituted Form (pdb code 8zyg). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/C106D Mutant) in Copper (Cu) Substituted Form, PDB code: 8zyg:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 8zyg

Go back to Copper Binding Sites List in 8zyg
Copper binding site 1 out of 2 in the Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/C106D Mutant) in Copper (Cu) Substituted Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/C106D Mutant) in Copper (Cu) Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:12.7
occ:0.90
O A:HOH378 1.8 37.0 1.0
NE2 A:HIS58 2.0 14.1 1.0
NE2 A:HIS54 2.1 12.4 1.0
NE2 A:HIS92 2.1 12.5 1.0
O A:HOH347 2.2 28.2 1.0
CE1 A:HIS92 3.0 12.7 1.0
CE1 A:HIS54 3.0 12.2 1.0
CD2 A:HIS58 3.0 13.1 1.0
CE1 A:HIS58 3.0 14.6 1.0
HE1 A:HIS92 3.1 15.3 1.0
CD2 A:HIS54 3.1 12.4 1.0
HE1 A:HIS54 3.1 14.6 1.0
CD2 A:HIS92 3.2 12.3 1.0
HD2 A:HIS58 3.2 15.7 1.0
HE1 A:HIS58 3.2 17.5 1.0
HD2 A:HIS54 3.4 14.9 1.0
HD2 A:HIS92 3.4 14.8 1.0
O A:HOH368 3.9 21.0 1.0
O A:HOH367 4.0 20.0 1.0
ND1 A:HIS92 4.1 11.7 1.0
ND1 A:HIS58 4.2 13.6 1.0
ND1 A:HIS54 4.2 11.7 1.0
CG A:HIS58 4.2 12.4 1.0
O A:HOH400 4.2 25.9 1.0
CG A:HIS54 4.2 12.1 1.0
CG A:HIS92 4.3 11.2 1.0
HE2 A:PHE94 4.6 26.0 1.0
O A:HOH305 4.7 61.9 1.0
HE1 A:TRP56 4.8 15.6 1.0
O A:HOH416 4.8 39.8 1.0
HD1 A:HIS92 4.9 14.0 1.0
HD1 A:HIS54 4.9 14.0 1.0
HD1 A:HIS58 4.9 16.3 1.0
HB3 A:ALA52 5.0 24.3 1.0

Copper binding site 2 out of 2 in 8zyg

Go back to Copper Binding Sites List in 8zyg
Copper binding site 2 out of 2 in the Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/C106D Mutant) in Copper (Cu) Substituted Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/C106D Mutant) in Copper (Cu) Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:13.4
occ:0.91
O B:HOH392 1.8 39.6 1.0
NE2 B:HIS58 2.0 12.7 1.0
NE2 B:HIS92 2.0 12.7 1.0
NE2 B:HIS54 2.1 13.5 1.0
CE1 B:HIS92 3.0 12.7 1.0
CE1 B:HIS54 3.0 12.6 1.0
CE1 B:HIS58 3.0 13.4 1.0
CD2 B:HIS58 3.1 12.8 1.0
HE1 B:HIS92 3.1 15.3 1.0
CD2 B:HIS92 3.1 12.9 1.0
CD2 B:HIS54 3.2 13.2 1.0
HE1 B:HIS54 3.2 15.1 1.0
HE1 B:HIS58 3.2 16.1 1.0
HD2 B:HIS58 3.2 15.3 1.0
HD2 B:HIS92 3.4 15.5 1.0
HD2 B:HIS54 3.4 15.8 1.0
O B:HOH374 3.9 25.5 1.0
O B:HOH377 4.1 26.8 1.0
ND1 B:HIS92 4.1 12.3 1.0
ND1 B:HIS58 4.1 13.2 1.0
ND1 B:HIS54 4.2 12.8 1.0
CG B:HIS58 4.2 11.4 1.0
CG B:HIS92 4.2 12.0 1.0
CG B:HIS54 4.3 12.5 1.0
HE2 B:PHE94 4.5 22.1 1.0
HB3 B:ALA52 4.8 30.8 1.0
HE1 B:TRP56 4.8 17.2 1.0
HD1 B:HIS92 4.9 14.8 1.0
HD1 B:HIS58 4.9 15.9 1.0
HD1 B:HIS54 4.9 15.3 1.0

Reference:

Y.Morita, H.Kubo, R.Matsumoto, N.Fujieda. Copper Center in Artificial Non-Heme Metalloenzyme To Be Published.
Page generated: Sat Sep 28 19:56:01 2024

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