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Copper in PDB 6rek: Crystal Structure of PIZZA6-Sh with CU2+

Protein crystallography data

The structure of Crystal Structure of PIZZA6-Sh with CU2+, PDB code: 6rek was solved by H.Noguchi, D.E.Clarke, J.L.Gryspeerdt, S.D.Feyter, A.R.D.Voet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.14 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 32.708, 69.547, 48.266, 90.00, 109.16, 90.00
R / Rfree (%) 14.1 / 16.3

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of PIZZA6-Sh with CU2+ (pdb code 6rek). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of PIZZA6-Sh with CU2+, PDB code: 6rek:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 6rek

Go back to Copper Binding Sites List in 6rek
Copper binding site 1 out of 3 in the Crystal Structure of PIZZA6-Sh with CU2+


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 PIZZA6-Sh with CU2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:13.3
occ:1.00
ND1 A:HIS157 2.0 14.4 1.0
NE2 A:HIS115 2.0 10.9 1.0
NE2 A:HIS142 2.0 19.4 0.4
NE2 A:HIS142 2.2 19.9 0.6
CD2 A:HIS142 2.9 18.1 0.4
CE1 A:HIS157 3.0 14.7 1.0
CE1 A:HIS115 3.0 11.1 1.0
CG A:HIS157 3.0 11.4 1.0
CD2 A:HIS115 3.0 10.8 1.0
CE1 A:HIS142 3.1 20.8 0.4
CE1 A:HIS142 3.1 21.1 0.6
CD2 A:HIS142 3.2 17.1 0.6
CB A:HIS157 3.3 11.4 1.0
O A:HOH552 3.7 19.6 1.0
CB A:THR140 3.8 10.2 1.0
NE2 A:HIS157 4.1 15.4 1.0
CG A:HIS142 4.1 17.9 0.4
ND1 A:HIS115 4.1 10.7 1.0
CD2 A:HIS157 4.1 12.8 1.0
CG A:HIS115 4.2 9.8 1.0
ND1 A:HIS142 4.2 21.3 0.4
O A:THR140 4.2 9.9 1.0
OG1 A:THR140 4.2 11.3 1.0
ND1 A:HIS142 4.2 21.6 0.6
CG A:HIS142 4.3 16.8 0.6
CG2 A:THR140 4.4 11.6 1.0
CA A:HIS157 4.8 10.9 1.0
O A:HOH582 4.8 41.0 1.0
C A:THR140 4.9 8.9 1.0
CA A:THR140 4.9 10.4 1.0

Copper binding site 2 out of 3 in 6rek

Go back to Copper Binding Sites List in 6rek
Copper binding site 2 out of 3 in the Crystal Structure of PIZZA6-Sh with CU2+


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 PIZZA6-Sh with CU2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:12.9
occ:1.00
NE2 A:HIS31 2.0 10.9 1.0
ND1 A:HIS73 2.0 11.2 1.0
NE2 A:HIS58 2.1 13.9 0.4
NE2 A:HIS58 2.2 15.8 0.6
O A:HOH646 2.6 17.5 1.0
CG A:HIS73 3.0 9.4 1.0
CE1 A:HIS31 3.0 10.4 1.0
CD2 A:HIS58 3.0 14.3 0.4
CE1 A:HIS73 3.0 13.0 1.0
CD2 A:HIS31 3.0 10.2 1.0
CE1 A:HIS58 3.1 15.4 0.6
CE1 A:HIS58 3.2 15.6 0.4
CB A:HIS73 3.2 10.1 1.0
CD2 A:HIS58 3.3 13.7 0.6
CB A:THR56 3.9 10.2 1.0
O A:THR56 4.1 9.0 1.0
NE2 A:HIS73 4.1 12.0 1.0
ND1 A:HIS31 4.1 11.3 1.0
CD2 A:HIS73 4.1 11.8 1.0
CG A:HIS31 4.1 9.9 1.0
CG A:HIS58 4.2 13.8 0.4
ND1 A:HIS58 4.2 17.1 0.4
ND1 A:HIS58 4.3 16.4 0.6
OG1 A:THR56 4.3 11.1 1.0
CG A:HIS58 4.4 11.8 0.6
CG2 A:THR56 4.5 11.6 1.0
CA A:HIS73 4.8 8.8 1.0
C A:THR56 4.8 8.2 1.0
CA A:THR56 4.9 8.4 1.0

Copper binding site 3 out of 3 in 6rek

Go back to Copper Binding Sites List in 6rek
Copper binding site 3 out of 3 in the Crystal Structure of PIZZA6-Sh with CU2+


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 PIZZA6-Sh with CU2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu303

b:17.4
occ:1.00
ND1 A:HIS241 2.0 15.7 1.0
NE2 A:HIS199 2.0 14.8 1.0
NE2 A:HIS226 2.2 20.8 0.6
O A:HOH587 2.3 32.2 1.0
NE2 A:HIS226 2.3 21.9 0.4
OG1 A:THR224 2.7 16.1 1.0
CE1 A:HIS241 2.9 17.4 1.0
CD2 A:HIS226 3.0 21.4 0.4
CD2 A:HIS199 3.0 14.0 1.0
CE1 A:HIS199 3.0 14.3 1.0
CG A:HIS241 3.0 13.2 1.0
CD2 A:HIS226 3.2 21.7 0.6
CE1 A:HIS226 3.2 20.9 0.6
CB A:HIS241 3.4 13.1 1.0
CE1 A:HIS226 3.5 21.7 0.4
CB A:THR224 3.6 14.8 1.0
NE2 A:HIS241 4.0 17.2 1.0
O A:HOH635 4.0 43.7 1.0
ND1 A:HIS199 4.1 14.7 1.0
CD2 A:HIS241 4.1 15.5 1.0
CG A:HIS199 4.1 13.2 1.0
CG A:HIS226 4.2 19.7 0.4
O A:THR224 4.3 16.7 1.0
ND1 A:HIS226 4.3 22.8 0.6
CG A:HIS226 4.3 19.8 0.6
ND1 A:HIS226 4.4 22.7 0.4
CG2 A:THR224 4.4 15.7 1.0
C A:THR224 4.7 13.0 1.0
CA A:THR224 4.8 13.3 1.0
CA A:HIS241 4.9 12.8 1.0

Reference:

D.E.Clarke, H.Noguchi, J.A.G.Gryspeerdt, S.De Feyter, A.R.D.Voet. Artificial Beta-Propeller Protein-Based Hydrolases. Chem.Commun.(Camb.) V. 55 8880 2019.
ISSN: ESSN 1364-548X
PubMed: 31321399
DOI: 10.1039/C9CC04388H
Page generated: Sun Dec 13 11:25:14 2020

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