Copper in PDB 8hjz: Crystal Structure of A Cupin Protein (TM1459, H52A/H58Q Mutant) in Copper (Cu) Substituted Form

Protein crystallography data

The structure of Crystal Structure of A Cupin Protein (TM1459, H52A/H58Q Mutant) in Copper (Cu) Substituted Form, PDB code: 8hjz was solved by R.Matsumoto, G.Kurisu, N.Fujieda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.00 / 1.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.1, 57.78, 74.98, 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, H52A/H58Q Mutant) in Copper (Cu) Substituted Form (pdb code 8hjz). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58Q Mutant) in Copper (Cu) Substituted Form, PDB code: 8hjz:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 8hjz

Go back to Copper Binding Sites List in 8hjz
Copper binding site 1 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58Q 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, H52A/H58Q Mutant) in Copper (Cu) Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:14.7
occ:0.77
 NE2 A:HIS92 2.0 14.4 1.0
NE2 A:HIS54 2.0 14.4 1.0
OE1 A:GLN58 2.1 27.1 1.0
O A:HOH376 2.2 30.6 1.0
CE1 A:HIS92 2.9 12.8 1.0
CE1 A:HIS54 3.0 14.2 1.0
HE1 A:HIS92 3.0 15.4 1.0
CD2 A:HIS54 3.1 14.0 1.0
HE21 A:GLN58 3.1 35.6 1.0
CD2 A:HIS92 3.1 12.5 1.0
CD A:GLN58 3.1 20.7 1.0
HE1 A:HIS54 3.2 17.1 1.0
HD2 A:HIS54 3.3 16.9 1.0
HD2 A:HIS92 3.3 14.9 1.0
NE2 A:GLN58 3.5 29.7 1.0
O A:HOH364 3.8 22.2 1.0
O A:HOH353 3.9 20.9 1.0
ND1 A:HIS92 4.1 11.6 1.0
O A:HOH393 4.1 48.6 1.0
ND1 A:HIS54 4.1 13.6 1.0
CG A:HIS54 4.2 12.9 1.0
CG A:HIS92 4.2 11.5 1.0
HE22 A:GLN58 4.3 35.6 1.0
HB2 A:GLN58 4.3 19.5 1.0
CG A:GLN58 4.5 19.3 1.0
HE2 A:PHE94 4.6 19.9 1.0
O A:HOH333 4.7 23.8 0.5
HD1 A:HIS92 4.8 14.0 1.0
HE1 A:TRP56 4.8 15.0 1.0
HB3 A:ALA52 4.9 25.6 1.0
HD1 A:HIS54 4.9 16.4 1.0
CB A:GLN58 4.9 16.2 1.0
HG3 A:GLN58 4.9 23.1 1.0

Copper binding site 2 out of 4 in 8hjz

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Copper binding site 2 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58Q 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, H52A/H58Q Mutant) in Copper (Cu) Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:18.4
occ:0.28
 OE2 A:GLU90 1.9 28.5 1.0
CD A:GLU90 2.7 22.9 1.0
OE1 A:GLU90 2.8 39.0 1.0
HA3 B:GLY0 3.1 34.1 1.0
O A:HOH343 3.9 27.1 1.0
H B:GLY0 3.9 35.6 1.0
CA B:GLY0 4.0 28.4 1.0
O A:HOH325 4.1 31.1 1.0
CG A:GLU90 4.2 15.0 1.0
N B:GLY0 4.2 29.7 1.0
HA A:GLU90 4.2 15.1 1.0
HB2 A:GLU90 4.2 17.2 1.0
OE2 A:GLU87 4.2 42.9 1.0
HA2 B:GLY0 4.5 34.1 1.0
OE1 A:GLU72 4.5 37.1 1.0
HG2 A:GLU90 4.5 18.0 1.0
CB A:GLU90 4.6 14.3 1.0
HG B:SER-1 4.7 102.9 1.0
HG3 A:GLU90 4.8 18.0 1.0
HG2 A:GLU87 4.8 39.0 1.0
HB2 B:SER-1 4.9 53.7 1.0
CA A:GLU90 4.9 12.5 1.0
C B:GLY0 5.0 25.4 1.0
CD A:GLU87 5.0 36.7 1.0

Copper binding site 3 out of 4 in 8hjz

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Copper binding site 3 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58Q 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 3 of Crystal Structure of A Cupin Protein (TM1459, H52A/H58Q Mutant) in Copper (Cu) Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:15.7
occ:0.50
 CU B:CU201 0.0 15.7 0.5
CU B:CU201 1.2 21.7 0.4
NE2 B:HIS92 1.9 18.9 1.0
OE1 B:GLN58 2.1 30.8 0.5
NE2 B:HIS54 2.1 14.5 0.5
NE2 B:HIS54 2.1 16.7 0.5
O B:HOH373 2.3 36.7 1.0
HD2 B:HIS54 2.4 18.8 0.5
OE1 B:GLN58 2.5 33.6 0.5
CD2 B:HIS54 2.6 15.7 0.5
CD B:GLN58 2.7 22.7 0.5
CE1 B:HIS92 2.8 16.3 1.0
HE21 B:GLN58 2.9 24.4 0.5
HE1 B:HIS92 3.0 19.6 1.0
CD2 B:HIS92 3.0 17.2 1.0
CE1 B:HIS54 3.0 12.7 0.5
HE21 B:GLN58 3.1 30.9 0.5
CD2 B:HIS54 3.1 13.4 0.5
NE2 B:GLN58 3.1 20.4 0.5
HE1 B:HIS54 3.2 15.2 0.5
O B:HOH382 3.2 38.4 1.0
HD2 B:HIS54 3.3 16.0 0.5
HD2 B:HIS92 3.3 20.6 1.0
CD B:GLN58 3.3 20.8 0.5
CE1 B:HIS54 3.4 18.8 0.5
NE2 B:GLN58 3.5 25.7 0.5
O B:HOH354 3.8 24.4 1.0
HG3 B:GLN58 3.8 16.9 0.5
HE22 B:GLN58 3.8 24.4 0.5
HE1 B:HIS54 3.8 22.5 0.5
CG B:GLN58 3.9 14.1 0.5
CG B:HIS54 3.9 13.2 0.5
ND1 B:HIS92 4.0 13.7 1.0
CG B:HIS92 4.1 13.7 1.0
ND1 B:HIS54 4.1 11.7 0.5
CG B:HIS54 4.2 12.5 0.5
HG2 B:GLN58 4.2 16.9 0.5
ND1 B:HIS54 4.2 16.8 0.5
HE22 B:GLN58 4.3 30.9 0.5
O B:HOH345 4.3 19.0 1.0
HB2 B:GLN58 4.5 22.2 0.5
HE2 B:PHE94 4.5 17.8 1.0
CG B:GLN58 4.7 18.9 0.5
HD1 B:HIS92 4.7 16.5 1.0
HE1 B:TRP56 4.7 16.4 1.0
HG3 B:GLN58 4.9 22.6 0.5
HB3 B:ALA52 4.9 25.1 1.0
HD1 B:HIS54 4.9 14.1 0.5

Copper binding site 4 out of 4 in 8hjz

Go back to Copper Binding Sites List in 8hjz
Copper binding site 4 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58Q 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 4 of Crystal Structure of A Cupin Protein (TM1459, H52A/H58Q Mutant) in Copper (Cu) Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:21.7
occ:0.38
 CU B:CU201 0.0 21.7 0.4
CU B:CU201 1.2 15.7 0.5
O B:HOH373 1.7 36.7 1.0
NE2 B:HIS54 2.0 16.7 0.5
O B:HOH382 2.0 38.4 1.0
NE2 B:HIS92 2.2 18.9 1.0
NE2 B:HIS54 2.7 14.5 0.5
CD2 B:HIS54 3.0 15.7 0.5
CE1 B:HIS54 3.0 18.8 0.5
OE1 B:GLN58 3.1 30.8 0.5
HD2 B:HIS54 3.1 16.0 0.5
CE1 B:HIS92 3.1 16.3 1.0
HD2 B:HIS54 3.2 18.8 0.5
HE1 B:HIS54 3.2 22.5 0.5
CD2 B:HIS92 3.2 17.2 1.0
CD2 B:HIS54 3.3 13.4 0.5
HE1 B:HIS92 3.3 19.6 1.0
O B:HOH345 3.3 19.0 1.0
HD2 B:HIS92 3.4 20.6 1.0
HE21 B:GLN58 3.6 24.4 0.5
HE21 B:GLN58 3.7 30.9 0.5
OE1 B:GLN58 3.7 33.6 0.5
CD B:GLN58 3.8 22.7 0.5
HB3 B:ALA52 3.9 25.1 1.0
CE1 B:HIS54 3.9 12.7 0.5
NE2 B:GLN58 4.0 20.4 0.5
ND1 B:HIS54 4.1 16.8 0.5
CG B:HIS54 4.1 13.2 0.5
O B:HOH354 4.2 24.4 1.0
ND1 B:HIS92 4.2 13.7 1.0
NE2 B:GLN58 4.3 25.7 0.5
HE1 B:HIS54 4.3 15.2 0.5
CD B:GLN58 4.3 20.8 0.5
CG B:HIS92 4.3 13.7 1.0
HE2 B:PHE94 4.5 17.8 1.0
CG B:HIS54 4.5 12.5 0.5
CB B:ALA52 4.8 16.7 1.0
HE22 B:GLN58 4.8 24.4 0.5
O B:HOH386 4.8 41.1 1.0
ND1 B:HIS54 4.8 11.7 0.5
HG23 B:ILE49 4.9 23.3 1.0
HD1 B:HIS54 4.9 20.1 0.5
HB1 B:ALA52 4.9 25.1 1.0
O B:HOH397 4.9 49.6 1.0
HD1 B:HIS92 5.0 16.5 1.0

Reference:

R.Matsumoto, S.Yoshioka, M.Yuasa, Y.Morita, G.Kurisu, N.Fujieda. An Artificial Metallolyase with Pliable 2-His-1-Carboxylate Facial Triad For Stereoselective Michael Addition. Chem Sci V. 14 3932 2023.
ISSN: ISSN 2041-6520
PubMed: 37035687
DOI: 10.1039/D2SC06809E
Page generated: Wed Jul 26 17:38:02 2023

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