Cadmium in PDB 5b42: Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.

The structure of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl., PDB code: 5b42 was solved by K.Fukui, S.Baba, T.Kumasaka, T.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.70 / 1.35
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	35.349, 35.349, 161.560, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 18.3

The binding sites of Cadmium atom in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. (pdb code 5b42). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl., PDB code: 5b42:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:13.9 occ:0.89 NE2 A:HIS30 2.3 14.7 1.0 OE2 A:GLU34 2.3 16.6 1.0 O A:HOH373 2.4 16.5 1.0 O A:HOH369 2.4 22.4 1.0 SG A:CYS48 2.6 18.2 1.0 O A:HOH381 2.7 18.4 1.0 CE1 A:HIS30 3.3 13.3 1.0 CD2 A:HIS30 3.3 12.3 1.0 CD A:GLU34 3.4 13.8 1.0 CB A:CYS48 3.5 13.8 1.0 CD A:CD205 3.7 25.1 0.8 OE1 A:GLU34 3.9 17.1 1.0 CD A:CD202 3.9 14.3 0.8 O A:HOH345 4.2 21.4 1.0 CA A:CYS48 4.3 14.7 1.0 CE1 A:HIS81 4.4 21.5 1.0 ND1 A:HIS30 4.4 12.8 1.0 CG A:GLU34 4.4 14.6 1.0 CG A:HIS30 4.4 11.4 1.0 O A:HOH394 4.6 29.6 1.0 ND1 A:HIS81 4.6 21.6 1.0 CB A:GLU34 4.9 11.6 1.0

Cadmium binding site 2 out of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:14.3 occ:0.85 OE1 A:GLU34 2.3 17.1 1.0 ND1 A:HIS81 2.4 21.6 1.0 O A:HOH373 2.4 16.5 1.0 SG A:CYS79 2.5 15.4 1.0 O A:HOH345 2.5 21.4 1.0 CD A:GLU34 3.1 13.8 1.0 OE2 A:GLU34 3.2 16.6 1.0 CE1 A:HIS81 3.3 21.5 1.0 CG A:HIS81 3.3 20.1 1.0 CB A:CYS79 3.4 14.9 1.0 CB A:HIS81 3.6 17.7 1.0 CD2 A:LEU31 3.8 14.7 1.0 CD A:CD201 3.9 13.9 0.9 N A:HIS81 4.0 16.9 1.0 O A:HOH381 4.2 18.4 1.0 CD A:PRO80 4.2 18.2 1.0 CA A:HIS81 4.4 16.9 1.0 NE2 A:HIS81 4.4 24.6 1.0 CG A:GLU34 4.5 14.6 1.0 N A:PRO80 4.5 17.0 1.0 CD2 A:HIS81 4.5 26.5 1.0 CG A:PRO80 4.5 22.8 1.0 CA A:CYS79 4.6 14.5 1.0 C A:CYS79 4.7 16.6 1.0

Cadmium binding site 3 out of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:17.3 occ:0.94 OE2 A:GLU61 2.4 17.1 1.0 OE1 A:GLU61 2.5 18.5 1.0 O A:HOH380 2.5 10.9 1.0 O A:HOH376 2.5 11.2 1.0 CD A:GLU61 2.8 16.9 1.0 NE A:ARG64 4.1 20.3 1.0 CG A:GLU61 4.3 15.7 1.0 O A:HOH382 4.4 28.9 1.0 CG A:GLU65 4.5 21.9 1.0 CB A:ARG64 4.6 15.6 1.0 O A:GLU61 4.7 17.4 1.0 CD A:ARG64 4.8 18.9 1.0 OE2 A:GLU65 4.9 34.1 1.0 NH2 A:ARG64 5.0 21.6 1.0

Cadmium binding site 4 out of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:24.5 occ:0.52 OD2 A:ASP43 2.5 29.8 1.0 O A:HOH383 2.5 28.6 1.0 O A:HOH374 2.6 17.1 1.0 OD1 A:ASP43 2.7 27.6 1.0 CG A:ASP43 2.9 28.6 1.0 O A:HOH393 3.8 36.5 1.0 CB A:ASN45 4.2 24.2 1.0 O A:HOH359 4.3 29.4 1.0 N A:LEU46 4.4 19.1 1.0 CB A:ASP43 4.4 24.8 1.0 CB A:LEU46 4.7 19.1 1.0 OD1 A:ASN45 4.8 43.3 1.0

Cadmium binding site 5 out of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:25.1 occ:0.78 O A:HOH301 2.4 29.0 1.0 O A:HOH381 2.5 18.4 1.0 O A:HOH394 2.5 29.6 1.0 SG A:CYS48 2.6 18.2 1.0 O A:HOH370 2.7 24.8 1.0 CB A:CYS48 3.5 13.8 1.0 CD A:CD201 3.7 13.9 0.9 O A:HOH369 3.9 22.4 1.0 CE1 A:HIS81 4.5 21.5 1.0 ND2 A:ASN45 4.7 40.5 1.0 OE2 A:GLU34 4.7 16.6 1.0 NE2 A:HIS81 4.9 24.6 1.0 CA A:CYS48 4.9 14.7 1.0

Cadmium binding site 6 out of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:26.4 occ:0.51 OE1 A:GLU96 2.4 43.7 1.0 OE2 A:GLU96 2.6 34.9 1.0 O A:HOH371 2.7 36.9 1.0 OE1 A:GLU93 2.7 49.5 1.0 O A:HOH307 2.7 40.9 1.0 OE2 A:GLU93 2.8 44.3 1.0 CD A:GLU96 2.8 38.8 1.0 O A:HOH352 2.8 45.4 1.0 CD A:GLU93 3.1 44.3 1.0 CG A:GLU96 4.2 24.4 1.0 NE A:ARG92 4.5 31.1 1.0 CG A:GLU93 4.5 33.3 1.0 O A:HOH323 4.6 28.9 1.0 CA A:GLU93 4.7 15.1 1.0 NH2 A:ARG92 4.8 34.5 1.0

K.Fukui, S.Baba, T.Kumasaka, T.Yano. Structural Features and Functional Dependency on Beta-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease Mutl J.Biol.Chem. V. 291 16990 2016.
ISSN: ESSN 1083-351X
PubMed: 27369079
DOI: 10.1074/JBC.M116.739664