Cadmium in PDB 6z0l: Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix

The structure of Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix, PDB code: 6z0l was solved by A.G.Mcewen, P.Poussin-Courmontagne, E.A.Naudin, W.F.Degrado, V.Torbeev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.77 / 2.33
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.669, 49.952, 53.043, 105.09, 92.49, 110.15
R / Rfree (%)	22.3 / 28.3

The structure of Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cadmium atom in the Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix (pdb code 6z0l). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix, PDB code: 6z0l:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:45.9 occ:0.50 O A:HOH209 3.6 27.9 1.0 NH1 A:ARG35 3.7 38.0 1.0 OE1 B:GLU35 4.0 79.2 1.0 NH2 G:ARG28 4.1 54.7 1.0 OE2 B:GLU35 4.2 59.4 1.0 CD B:GLU35 4.2 76.1 1.0 CB A:ALA31 4.2 40.5 1.0 CD G:ARG28 4.5 51.4 1.0 CZ G:ARG28 4.9 54.7 1.0 CD A:ARG35 4.9 31.3 1.0 CD A:ARG28 4.9 40.7 1.0 CZ A:ARG35 5.0 22.8 1.0

Cadmium binding site 2 out of 5 in the Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd102 b:31.1 occ:0.50 O A:HOH207 2.9 21.3 1.0 O A:HOH201 2.9 42.1 1.0 O H:HOH103 3.1 32.3 1.0 NH2 A:ARG28 3.3 52.4 1.0 NH1 A:ARG21 3.9 44.7 1.0 NH1 G:ARG35 4.1 36.2 1.0 CZ A:ARG28 4.3 68.4 1.0 CB G:ALA31 4.3 46.0 1.0 OE2 H:GLU35 4.3 65.8 1.0 CD H:GLU35 4.4 56.5 1.0 NE A:ARG28 4.5 63.6 1.0 OE1 H:GLU35 4.6 44.1 1.0 CD G:ARG35 4.9 25.4 1.0 CB A:ALA24 5.0 33.0 1.0

Cadmium binding site 3 out of 5 in the Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd101 b:30.6 occ:0.50 O E:HOH210 2.9 21.4 1.0 NH1 C:ARG28 3.7 44.1 1.0 NH1 E:ARG35 4.2 33.8 1.0 CD C:ARG28 4.3 32.5 1.0 CZ C:ARG28 4.4 42.0 1.0 OE1 F:GLU35 4.4 63.2 1.0 CG E:ARG28 4.6 39.1 1.0 NE C:ARG28 4.6 30.6 1.0 CB E:ALA31 4.8 19.7 1.0 OE2 D:GLU42 4.9 59.5 1.0 CZ E:ARG35 4.9 22.1 1.0

Cadmium binding site 4 out of 5 in the Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd102 b:31.7 occ:0.50 OE2 C:GLU20 2.8 47.1 1.0 OE1 C:GLU20 2.9 21.8 1.0 O C:HOH208 2.9 14.8 1.0 CD C:GLU20 3.2 32.4 1.0 CD C:PRO19 3.8 12.5 1.0 OG C:SER18 4.3 11.9 1.0 O C:HOH213 4.4 23.6 1.0 CG C:PRO19 4.6 8.9 1.0 CG C:GLU20 4.7 27.2 1.0 N C:PRO19 4.7 22.3 1.0 CA C:SER18 4.9 28.9 1.0

Cadmium binding site 5 out of 5 in the Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix within 5.0Å range: probe atom residue distance (Å) B Occ E:Cd101 b:58.0 occ:0.50 NH2 E:ARG28 2.9 77.1 1.0 NH1 C:ARG35 3.2 50.0 1.0 NH1 E:ARG28 3.4 53.4 1.0 CZ E:ARG28 3.6 62.5 1.0 O E:HOH207 3.8 23.8 1.0 OE2 F:GLU42 4.1 47.3 1.0 CB C:ALA31 4.3 14.4 1.0 CZ C:ARG35 4.5 47.1 1.0 OE2 D:GLU35 4.5 62.2 1.0 CD C:ARG35 4.5 48.5 1.0 NE E:ARG28 4.8 57.0 1.0 NE C:ARG35 5.0 39.3 1.0

E.A.Naudin, A.G.Mcewen, S.K.Tan, P.Poussin-Courmontagne, J.L.Schmitt, C.Birck, W.F.Degrado, V.Torbeev. Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of Alpha-Helix As Oxyanion-Binding Site. J.Am.Chem.Soc. 2021.
ISSN: ESSN 1520-5126
PubMed: 33635059
DOI: 10.1021/JACS.0C10053