Manganese in PDB 8h1e: Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions

The structure of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions, PDB code: 8h1e 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)	32.80 / 1.22
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	35.631, 35.631, 167.819, 90, 90, 90
R / Rfree (%)	20 / 22.1

The binding sites of Manganese atom in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions (pdb code 8h1e). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions, PDB code: 8h1e:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:15.1 occ:1.00 OE1 A:GLU357 2.1 26.7 1.0 ND1 A:HIS404 2.2 27.6 1.0 O A:HOH648 2.2 36.4 1.0 O A:HOH641 2.3 21.6 1.0 SG A:CYS402 2.5 21.9 1.0 CD A:GLU357 3.0 23.6 1.0 CE1 A:HIS404 3.2 27.0 1.0 OE2 A:GLU357 3.2 23.7 1.0 CG A:HIS404 3.2 28.1 1.0 CB A:CYS402 3.4 23.5 1.0 CB A:HIS404 3.6 25.1 1.0 CD2 A:LEU354 3.7 20.3 1.0 N A:HIS404 3.9 25.2 1.0 MN A:MN503 4.0 13.9 1.0 NE2 A:HIS404 4.3 28.1 1.0 O A:HOH659 4.3 22.8 1.0 CD2 A:HIS404 4.4 31.2 1.0 CA A:HIS404 4.4 24.2 1.0 CG A:GLU357 4.4 22.3 1.0 CD A:PRO403 4.5 22.2 1.0 N A:PRO403 4.5 23.5 1.0 CA A:CYS402 4.7 21.5 1.0 C A:CYS402 4.8 22.5 1.0 CG A:PRO403 4.8 26.9 1.0

Manganese binding site 2 out of 6 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:13.9 occ:1.00 O A:HOH645 2.2 26.0 1.0 OE2 A:GLU357 2.3 23.7 1.0 NE2 A:HIS353 2.3 22.2 1.0 O A:HOH641 2.3 21.6 1.0 SG A:CYS371 2.5 21.7 1.0 O A:HOH659 2.7 22.8 1.0 CE1 A:HIS353 3.2 22.2 1.0 CD A:GLU357 3.3 23.6 1.0 CD2 A:HIS353 3.4 20.9 1.0 CB A:CYS371 3.5 20.4 1.0 MN A:MN504 3.7 26.1 1.0 OE1 A:GLU357 3.9 26.7 1.0 MN A:MN502 4.0 15.1 1.0 CA A:CYS371 4.2 19.3 1.0 O A:HOH670 4.3 36.9 1.0 CE1 A:HIS404 4.3 27.0 1.0 O A:HOH648 4.3 36.4 1.0 O A:HOH661 4.3 31.1 1.0 ND1 A:HIS353 4.4 19.9 1.0 CG A:GLU357 4.4 22.3 1.0 CG A:HIS353 4.5 17.6 1.0 ND1 A:HIS404 4.6 27.6 1.0 CB A:GLU357 4.9 18.5 1.0 O A:CYS371 5.0 20.7 1.0 C A:CYS371 5.0 18.2 1.0

Manganese binding site 3 out of 6 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn504 b:26.1 occ:1.00 O A:HOH666 2.2 36.7 1.0 O A:HOH670 2.2 36.9 1.0 O A:HOH659 2.5 22.8 1.0 SG A:CYS371 2.6 21.7 1.0 O A:HOH651 2.8 31.3 1.0 O A:HOH668 3.1 31.3 1.0 CB A:CYS371 3.5 20.4 1.0 MN A:MN503 3.7 13.9 1.0 O A:HOH645 3.8 26.0 1.0 O A:HOH625 4.5 42.2 1.0 CE1 A:HIS404 4.7 27.0 1.0 OE2 A:GLU357 4.8 23.7 1.0 NE2 A:HIS404 4.9 28.1 1.0 CA A:CYS371 5.0 19.3 1.0

Manganese binding site 4 out of 6 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn505 b:13.1 occ:1.00 OE2 A:GLU384 2.4 20.9 1.0 OE1 A:GLU384 2.4 23.3 1.0 O A:HOH658 2.5 14.7 1.0 O A:HOH652 2.5 12.5 1.0 CD A:GLU384 2.7 21.7 1.0 CG A:GLU384 4.3 22.2 1.0 NE A:ARG387 4.3 22.7 1.0 CG A:GLU388 4.5 23.6 1.0 O A:GLU384 4.7 19.8 1.0 NH2 A:ARG387 4.8 24.4 1.0 CB A:ARG387 4.8 19.3 1.0 OE2 A:GLU388 4.9 25.3 1.0 O A:HOH660 5.0 27.6 1.0

Manganese binding site 5 out of 6 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn506 b:37.0 occ:1.00 OD2 A:ASP366 2.1 29.4 1.0 OD1 A:ASP366 2.7 28.2 1.0 O A:HOH654 2.7 23.8 1.0 CG A:ASP366 2.7 25.2 1.0 CB A:ASP366 4.2 24.9 1.0 CB A:ASN368 4.2 26.7 1.0 N A:LEU369 4.4 21.9 1.0 CB A:LEU369 4.5 22.7 1.0 ND2 A:ASN368 4.9 35.6 1.0

Manganese binding site 6 out of 6 in the Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Aquifex Aeolicus Mutl Endonuclease Domain Complexed with Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn507 b:32.7 occ:1.00 OE2 A:GLU419 2.0 38.4 1.0 OE2 A:GLU416 2.4 40.9 1.0 CD A:GLU419 2.9 35.7 1.0 CD A:GLU416 3.1 40.1 1.0 OE1 A:GLU419 3.1 34.5 1.0 OE1 A:GLU416 3.2 45.7 1.0 CG A:GLU419 4.3 27.8 1.0 CG A:GLU416 4.5 33.4 1.0 O A:HOH613 4.6 28.3 1.0 CA A:GLU416 4.8 21.6 1.0 CB A:GLU416 4.9 25.8 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