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Copper in PDB 5ns5: Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+

Enzymatic activity of Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+

All present enzymatic activity of Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+:
3.4.13.19;

Protein crystallography data

The structure of Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+, PDB code: 5ns5 was solved by M.Groll, E.M.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.000, 99.000, 106.490, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 18.9

Other elements in 5ns5:

The structure of Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+ also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+ (pdb code 5ns5). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+, PDB code: 5ns5:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 5ns5

Go back to Copper Binding Sites List in 5ns5
Copper binding site 1 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:68.1
occ:0.50
ZN A:ZN402 0.1 67.1 0.5
OE1 A:GLU134 2.0 46.8 1.0
OD1 A:ASP25 2.1 51.1 1.0
NE2 A:HIS23 2.1 40.5 1.0
CG A:ASP25 2.7 48.6 1.0
OD2 A:ASP25 2.7 49.6 1.0
CD A:GLU134 2.9 45.0 1.0
CE1 A:HIS23 3.1 41.2 1.0
CD2 A:HIS23 3.1 39.6 1.0
OE2 A:GLU134 3.2 46.0 1.0
OG A:SER69 3.6 43.2 1.0
ZN A:ZN401 3.9 59.8 0.5
O A:HOH638 3.9 69.7 1.0
CU A:CU404 3.9 52.4 0.5
OD1 A:ASP294 4.0 48.2 1.0
ND1 A:HIS23 4.2 40.7 1.0
CB A:SER69 4.2 43.7 1.0
CB A:ASP25 4.2 45.1 1.0
CG A:GLU134 4.2 47.7 1.0
CG A:HIS23 4.2 39.8 1.0
CB A:PHE71 4.3 44.1 1.0
NE2 A:HIS224 4.6 38.1 1.0
CB A:GLU134 4.6 47.3 1.0
CG A:PHE71 4.6 45.9 1.0
CE1 A:HIS224 4.8 39.1 1.0
CD1 A:PHE71 4.9 47.1 1.0

Copper binding site 2 out of 2 in 5ns5

Go back to Copper Binding Sites List in 5ns5
Copper binding site 2 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:52.4
occ:0.50
ZN A:ZN401 0.0 59.8 0.5
NE2 A:HIS203 2.0 48.6 1.0
OE2 A:GLU134 2.1 46.0 1.0
O A:HOH586 2.2 50.0 1.0
NE2 A:HIS224 2.2 38.1 1.0
O A:HOH638 2.9 69.7 1.0
CE1 A:HIS203 2.9 47.0 1.0
CD2 A:HIS203 3.0 49.1 1.0
CE1 A:HIS224 3.1 39.1 1.0
CD2 A:HIS224 3.2 36.2 1.0
CD A:GLU134 3.3 45.0 1.0
OE1 A:GLU134 3.8 46.8 1.0
ZN A:ZN402 3.9 67.1 0.5
CU A:CU403 3.9 68.1 0.5
ND1 A:HIS203 4.0 48.1 1.0
NH1 A:ARG235 4.0 51.5 1.0
CG A:HIS203 4.1 49.1 1.0
NE2 A:HIS161 4.1 54.9 1.0
CD2 A:HIS161 4.2 55.5 1.0
ND1 A:HIS224 4.3 38.7 1.0
OD1 A:ASP294 4.3 48.2 1.0
CG A:HIS224 4.3 38.2 1.0
OD2 A:ASP294 4.4 49.0 1.0
NE2 A:HIS23 4.4 40.5 1.0
CG A:GLU134 4.4 47.7 1.0
CG A:ASP294 4.6 47.9 1.0
CD2 A:HIS23 4.8 39.6 1.0
O A:HOH623 4.8 60.3 1.0
CZ A:ARG235 4.9 52.0 1.0
CE1 A:HIS23 4.9 41.2 1.0
NE A:ARG235 5.0 53.0 1.0

Reference:

A.Marion, M.Groll, D.H.Scharf, K.Scherlach, M.Glaser, H.Sievers, M.Schuster, C.Hertweck, A.A.Brakhage, I.Antes, E.M.Huber. Gliotoxin Biosynthesis: Structure, Mechanism, and Metal Promiscuity of Carboxypeptidase Glij. Acs Chem. Biol. V. 12 1874 2017.
ISSN: ESSN 1554-8937
PubMed: 28525266
DOI: 10.1021/ACSCHEMBIO.6B00847
Page generated: Sun Dec 13 11:19:08 2020

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