Cadmium in PDB 6ggv: Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima

The structure of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima, PDB code: 6ggv was solved by G.Smaldone, R.Berisio, N.Balasco, S.D'auria, L.Vitagliano, A.Ruggiero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.69
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	30.700, 52.139, 221.343, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Cadmium atom in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima (pdb code 6ggv). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 22 binding sites of Cadmium where determined in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima, PDB code: 6ggv:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 22 in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:40.3 occ:1.00 OD1 A:ASP178 2.5 16.9 1.0 O A:HOH509 2.5 14.1 1.0 OD2 A:ASP178 2.6 19.2 1.0 CG A:ASP178 2.9 17.9 1.0 O A:HOH444 4.0 23.8 1.0 CB A:ASP178 4.4 16.2 1.0 OG1 A:THR138 4.6 17.5 1.0 N A:THR138 4.6 15.3 1.0 CD A:LYS137 4.6 19.7 1.0 CB A:THR138 4.9 15.8 1.0

Cadmium binding site 2 out of 22 in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:84.2 occ:1.00 OD2 A:ASP219 2.3 34.5 1.0 OD1 A:ASP219 2.6 34.8 1.0 CG A:ASP219 2.8 33.9 1.0 O A:HOH418 2.9 15.7 1.0 CB A:ASP219 4.3 30.9 1.0 CD A:CD305 4.3 78.8 1.0 O A:HOH488 4.4 27.8 1.0 OD1 A:ASP217 4.5 33.3 1.0 O A:GLU216 4.7 30.0 1.0 N A:ASP219 4.9 31.0 1.0 CA A:ASP217 4.9 31.1 1.0

Cadmium binding site 3 out of 22 in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:99.0 occ:1.00 OE2 A:GLU171 3.2 25.2 1.0 OE1 A:GLU171 3.3 26.0 1.0 CD A:GLU171 3.6 23.9 1.0 NH1 A:ARG176 3.9 32.9 1.0 CD A:ARG176 4.5 26.9 1.0 CZ A:ARG176 4.8 31.1 1.0 CG A:GLU171 5.0 20.7 1.0

Cadmium binding site 4 out of 22 in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:78.8 occ:1.00 O A:HOH549 2.7 20.8 1.0 OD2 A:ASP219 2.8 34.5 1.0 O A:HOH556 2.9 38.1 1.0 CG A:ASP219 3.6 33.9 1.0 CB A:ASP219 3.8 30.9 1.0 CD A:CD303 4.3 84.2 1.0 OD1 A:ASP219 4.7 34.8 1.0

Cadmium binding site 5 out of 22 in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:46.0 occ:1.00 O A:LYS153 2.4 20.1 1.0 O B:HOH432 2.6 16.6 1.0 OD2 B:ASP77 2.7 24.7 1.0 OD2 A:ASP155 3.1 26.1 1.0 OD1 B:ASP163 3.3 22.8 1.0 C A:LYS153 3.5 20.1 1.0 CG B:ASP77 3.7 20.0 1.0 CB B:ASP77 3.8 18.6 1.0 OG1 B:THR75 4.0 18.2 1.0 CG A:ASP155 4.1 22.8 1.0 CA A:LYS153 4.3 20.1 1.0 CG B:ASP163 4.4 21.0 1.0 N A:TYR154 4.4 19.9 1.0 N A:ASP155 4.4 19.6 1.0 CA A:TYR154 4.5 19.6 1.0 OD1 A:ASP155 4.7 24.7 1.0 CB B:THR75 4.8 17.2 1.0 OD2 B:ASP163 4.8 21.9 1.0 OD1 B:ASP77 4.8 21.2 1.0 C A:TYR154 4.8 19.5 1.0 CB A:LYS153 4.9 20.1 1.0 CG2 B:THR75 5.0 17.9 1.0 CG2 B:ILE143 5.0 9.3 1.0

Cadmium binding site 6 out of 22 in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd307 b:80.8 occ:1.00 OD1 A:ASP163 2.4 23.0 1.0 O A:HOH460 2.4 36.3 1.0 O A:HOH489 2.6 31.7 1.0 CG A:ASP163 3.4 22.2 1.0 OG1 A:THR75 3.7 17.4 1.0 OD2 A:ASP163 3.9 24.6 1.0 O A:HOH404 3.9 8.8 1.0 CB A:ASP77 4.2 18.7 1.0 CB A:THR75 4.4 17.1 1.0 OD2 A:ASP77 4.4 24.6 1.0 O A:HOH439 4.4 4.3 1.0 CD1 A:ILE143 4.5 20.9 1.0 CB A:ASP163 4.6 20.5 1.0 CG2 A:THR75 4.7 17.4 1.0 CG A:ASP77 4.8 20.1 1.0

Cadmium binding site 7 out of 22 in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd308 b:75.5 occ:1.00 OD2 A:ASP125 2.5 29.6 1.0 CG A:ASP125 3.3 28.3 1.0 CB A:ASP125 3.9 25.8 1.0 OD1 A:ASP125 4.1 31.9 1.0 N A:ASP125 4.2 25.3 1.0 CA A:ASP125 4.7 24.9 1.0

Cadmium binding site 8 out of 22 in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd309 b:41.6 occ:1.00 CD A:CD310 2.4 48.5 1.0 OE2 A:GLU99 2.4 21.1 1.0 OE1 A:GLU99 2.4 25.2 1.0 CD A:GLU99 2.7 23.9 1.0 NH2 B:ARG176 3.3 27.4 1.0 O B:HOH403 3.5 37.2 1.0 CG A:GLU99 4.1 22.0 1.0 CZ B:ARG176 4.2 27.8 1.0 O A:HOH453 4.6 11.7 1.0 NH1 B:ARG176 4.7 26.6 1.0 CE A:LYS102 4.8 19.6 1.0 NE B:ARG176 5.0 27.1 1.0 CB A:GLU99 5.0 20.2 1.0

Cadmium binding site 9 out of 22 in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd310 b:48.5 occ:1.00 CD A:CD309 2.4 41.6 1.0 OE2 A:GLU99 2.5 21.1 1.0 CE A:LYS102 3.3 19.6 1.0 CD A:GLU99 3.4 23.9 1.0 OE1 A:GLU99 3.6 25.2 1.0 NZ A:LYS102 3.9 19.2 1.0 O A:HOH420 3.9 15.5 1.0 NH2 B:ARG176 4.4 27.4 1.0 CD A:LYS102 4.6 20.8 1.0 O B:HOH403 4.7 37.2 1.0 CG A:GLU99 4.8 22.0 1.0

Cadmium binding site 10 out of 22 in the Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of the Arginine-Bound Form of Truncated (Residues 20-233) Argbp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd311 b:0.2 occ:1.00 OE1 A:GLU222 2.9 33.5 1.0 OE2 A:GLU222 3.0 28.9 1.0 CD A:GLU222 3.3 30.0 1.0 CG A:GLU222 4.8 28.6 1.0 O A:HOH556 4.9 38.1 1.0 O A:HOH435 4.9 4.3 1.0

G.Smaldone, R.Berisio, N.Balasco, S.D'auria, L.Vitagliano, A.Ruggiero. Domain Swapping Dissection in Thermotoga Maritima Arginine Binding Protein: How Structural Flexibility May Compensate Destabilization. Biochim. Biophys. Acta V.1866 952 2018.
ISSN: ISSN 0006-3002
PubMed: 29860047
DOI: 10.1016/J.BBAPAP.2018.05.016