Zinc in PDB 8h1f: Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking

The structure of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking, PDB code: 8h1f 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)	34.75 / 1.22
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	35.529, 35.529, 167.288, 90, 90, 90
R / Rfree (%)	15.7 / 17.5

The structure of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking (pdb code 8h1f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking, PDB code: 8h1f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:9.1 occ:1.00 OE1 A:GLU384 2.3 13.7 1.0 OE2 A:GLU384 2.4 13.5 1.0 CL A:CL509 2.5 15.9 1.0 CL A:CL510 2.5 13.6 1.0 CD A:GLU384 2.7 13.1 1.0 CG A:GLU384 4.3 14.1 1.0 O A:HOH714 4.3 22.6 1.0 NE A:ARG387 4.3 16.6 1.0 CG A:GLU388 4.4 17.1 1.0 O A:GLU384 4.7 13.7 1.0 CB A:ARG387 4.8 14.3 1.0 NH2 A:ARG387 4.8 16.6 1.0 OE2 A:GLU388 4.9 18.3 1.0

Zinc binding site 2 out of 5 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:25.0 occ:1.00 O A:HOH611 2.3 26.2 1.0 O A:HOH605 2.4 30.0 1.0 OD2 A:ASP366 2.4 28.0 1.0 O A:HOH687 2.6 25.6 1.0 O A:HOH678 2.7 17.9 1.0 OD1 A:ASP366 2.7 22.3 1.0 CG A:ASP366 2.9 24.1 1.0 ND2 A:ASN368 4.1 35.7 1.0 O A:HOH602 4.2 27.2 1.0 CB A:ASN368 4.3 23.1 1.0 N A:LEU369 4.3 15.0 1.0 CB A:ASP366 4.4 21.1 1.0 CB A:LEU369 4.6 17.4 1.0 CG A:ASN368 4.7 30.8 1.0 N A:ASN368 5.0 17.9 1.0 CA A:ASN368 5.0 17.6 1.0

Zinc binding site 3 out of 5 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:24.3 occ:1.00 O A:HOH703 2.2 25.4 1.0 SG A:CYS371 2.5 17.0 1.0 O A:HOH688 2.5 19.4 1.0 O A:HOH720 2.5 26.1 1.0 O A:HOH718 2.8 20.2 1.0 O A:HOH666 3.1 24.9 1.0 CB A:CYS371 3.5 13.9 1.0 ZN A:ZN505 3.7 11.1 1.0 O A:HOH671 3.8 21.1 1.0 O A:HOH620 4.5 24.0 1.0 CE1 A:HIS404 4.7 21.6 1.0 OE2 A:GLU357 4.8 16.9 1.0 CA A:CYS371 4.9 13.3 1.0

Zinc binding site 4 out of 5 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:12.4 occ:1.00 OE1 A:GLU357 2.1 17.3 1.0 O A:HOH675 2.2 21.8 1.0 ND1 A:HIS404 2.3 18.5 1.0 SG A:CYS402 2.4 15.8 1.0 O A:HOH663 2.4 18.1 1.0 CD A:GLU357 3.0 14.9 1.0 OE2 A:GLU357 3.2 16.9 1.0 CE1 A:HIS404 3.2 21.6 1.0 CG A:HIS404 3.3 19.5 1.0 CB A:CYS402 3.4 15.1 1.0 CB A:HIS404 3.6 20.6 1.0 CD2 A:LEU354 3.8 13.8 1.0 N A:HIS404 3.9 20.6 1.0 ZN A:ZN505 4.0 11.1 1.0 O A:HOH688 4.2 19.4 1.0 CA A:HIS404 4.4 21.0 1.0 CG A:GLU357 4.4 13.4 1.0 NE2 A:HIS404 4.4 23.7 1.0 CD2 A:HIS404 4.4 22.5 1.0 CD A:PRO403 4.4 17.8 1.0 N A:PRO403 4.5 17.7 1.0 CG A:PRO403 4.6 23.0 1.0 CA A:CYS402 4.6 15.3 1.0 C A:CYS402 4.7 16.3 1.0 CD A:ARG406 4.9 28.0 1.0

Zinc binding site 5 out of 5 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Zinc Ions After Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:11.1 occ:1.00 O A:HOH663 2.2 18.1 1.0 OE2 A:GLU357 2.3 16.9 1.0 NE2 A:HIS353 2.3 15.9 1.0 O A:HOH671 2.4 21.1 1.0 SG A:CYS371 2.5 17.0 1.0 O A:HOH688 2.7 19.4 1.0 CE1 A:HIS353 3.2 14.2 1.0 CD A:GLU357 3.4 14.9 1.0 CD2 A:HIS353 3.4 14.7 1.0 CB A:CYS371 3.5 13.9 1.0 ZN A:ZN503 3.7 24.3 1.0 OE1 A:GLU357 3.9 17.3 1.0 ZN A:ZN504 4.0 12.4 1.0 CA A:CYS371 4.2 13.3 1.0 O A:HOH675 4.3 21.8 1.0 O A:HOH720 4.3 26.1 1.0 ND1 A:HIS353 4.4 13.6 1.0 CE1 A:HIS404 4.4 21.6 1.0 CG A:GLU357 4.4 13.4 1.0 CG A:HIS353 4.5 12.3 1.0 O A:HOH695 4.6 22.6 1.0 ND1 A:HIS404 4.6 18.5 1.0 CB A:GLU357 4.9 12.2 1.0 C A:CYS371 5.0 12.1 1.0 O A:CYS371 5.0 13.5 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