Cadmium in PDB 8h1g: The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain

The structure of The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain, PDB code: 8h1g was solved by K.Fukui, T.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.81 / 1.43
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	35.582, 35.582, 167.825, 90, 90, 90
R / Rfree (%)	19.3 / 22.1

The structure of The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cadmium atom in the The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain (pdb code 8h1g). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain, PDB code: 8h1g:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd503 b:18.0 occ:1.00 OXT A:TYR425 2.3 17.9 1.0 O A:TYR425 2.5 15.5 1.0 C A:TYR425 2.8 16.8 1.0 CA A:TYR425 4.3 16.7 1.0 CB A:ARG415 4.8 18.8 1.0 CD2 A:TYR425 4.9 15.6 1.0 N A:TYR425 4.9 16.6 1.0 CB A:TYR425 4.9 16.1 1.0

Cadmium binding site 2 out of 4 in the The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd504 b:21.2 occ:1.00 OE1 A:GLU357 2.2 20.6 1.0 O A:HOH647 2.3 21.4 1.0 ND1 A:HIS404 2.3 25.2 1.0 SG A:CYS402 2.5 21.0 1.0 O A:HOH661 2.6 31.1 1.0 CD A:GLU357 3.1 18.6 1.0 OE2 A:GLU357 3.2 18.8 1.0 CG A:HIS404 3.3 24.6 1.0 CE1 A:HIS404 3.3 25.8 1.0 CB A:CYS402 3.4 19.5 1.0 CB A:HIS404 3.5 24.1 1.0 CD2 A:LEU354 3.7 18.4 1.0 N A:HIS404 3.9 24.9 1.0 CD A:CD505 4.0 20.1 1.0 O A:HOH662 4.3 21.1 1.0 CD A:PRO403 4.3 22.7 1.0 CA A:HIS404 4.3 25.1 1.0 NE2 A:HIS404 4.4 26.0 1.0 CD2 A:HIS404 4.4 25.7 1.0 CG A:GLU357 4.4 18.0 1.0 N A:PRO403 4.5 22.2 1.0 CA A:CYS402 4.7 19.0 1.0 C A:CYS402 4.7 21.3 1.0

Cadmium binding site 3 out of 4 in the The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd505 b:20.1 occ:1.00 O A:HOH647 2.2 21.4 1.0 NE2 A:HIS353 2.4 19.1 1.0 OE2 A:GLU357 2.4 18.8 1.0 O A:HOH655 2.5 25.2 1.0 SG A:CYS371 2.6 21.2 1.0 O A:HOH662 2.8 21.1 1.0 CE1 A:HIS353 3.3 19.5 1.0 CD2 A:HIS353 3.4 19.1 1.0 CD A:GLU357 3.4 18.6 1.0 CB A:CYS371 3.5 18.7 1.0 CD A:CD506 3.7 34.9 1.0 OE1 A:GLU357 4.0 20.6 1.0 CD A:CD504 4.0 21.2 1.0 CA A:CYS371 4.2 17.8 1.0 O A:HOH661 4.2 31.1 1.0 CE1 A:HIS404 4.4 25.8 1.0 O A:HOH672 4.4 37.0 1.0 ND1 A:HIS353 4.5 17.5 1.0 CG A:GLU357 4.5 18.0 1.0 CG A:HIS353 4.5 17.2 1.0 ND1 A:HIS404 4.6 25.2 1.0 CB A:GLU357 4.9 16.6 1.0 C A:CYS371 4.9 16.5 1.0 O A:CYS371 4.9 18.4 1.0

Cadmium binding site 4 out of 4 in the The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of The R406T Mutant Form of the Aquifex Aeolicus Mutl Endonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd506 b:34.9 occ:1.00 O A:HOH662 2.5 21.1 1.0 O A:HOH666 2.6 40.2 1.0 SG A:CYS371 2.6 21.2 1.0 O A:HOH672 2.9 37.0 1.0 O A:HOH671 3.0 25.8 1.0 O A:HOH643 3.0 25.4 1.0 CB A:CYS371 3.5 18.7 1.0 CD A:CD505 3.7 20.1 1.0 O A:HOH655 4.0 25.2 1.0 CE1 A:HIS404 4.7 25.8 1.0 O A:HOH612 4.7 35.8 1.0 OE2 A:GLU357 4.9 18.8 1.0 NE2 A:HIS404 4.9 26.0 1.0 CA A:CYS371 4.9 17.8 1.0

K.Fukui, T.Yamamoto, T.Murakawa, S.Baba, T.Kumasaka, T.Yano. Catalytic Mechanism of the Zinc-Dependent Mutl Endonuclease Reaction. Life Sci Alliance V. 6 2023.
ISSN: ESSN 2575-1077
PubMed: 37487639
DOI: 10.26508/LSA.202302001