Manganese in PDB 6c33: Mycobacterium Smegmatis Dna Flap Endonuclease

The structure of Mycobacterium Smegmatis Dna Flap Endonuclease, PDB code: 6c33 was solved by S.Shuman, Y.Goldgur, A.Carl, M.L.Uson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.11 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.093, 39.828, 68.191, 90.00, 108.87, 90.00
R / Rfree (%)	17.5 / 20.5

The binding sites of Manganese atom in the Mycobacterium Smegmatis Dna Flap Endonuclease (pdb code 6c33). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Mycobacterium Smegmatis Dna Flap Endonuclease, PDB code: 6c33:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Mycobacterium Smegmatis Dna Flap Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mycobacterium Smegmatis Dna Flap Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:19.8 occ:1.00 O A:HOH687 2.0 16.7 1.0 O A:HOH531 2.2 21.0 1.0 O A:HOH590 2.2 19.1 1.0 O A:HOH544 2.2 24.5 1.0 OD1 A:ASP125 2.3 18.2 1.0 O A:HOH743 2.3 23.7 1.0 CG A:ASP125 3.3 20.0 1.0 OD2 A:ASP125 3.6 19.1 1.0 MN A:MN402 3.6 21.7 1.0 OD2 A:ASP146 3.9 23.7 1.0 O A:HOH706 4.0 33.1 1.0 OD2 A:ASP60 4.1 25.0 1.0 OE1 A:GLU123 4.1 20.0 1.0 O A:HOH733 4.1 41.2 1.0 OD2 A:ASP9 4.3 19.1 1.0 OD1 A:ASP9 4.3 20.8 1.0 OD1 A:ASP60 4.4 23.2 1.0 NZ A:LYS76 4.4 32.0 1.0 N A:ASP125 4.5 15.7 1.0 O A:HOH638 4.6 23.5 1.0 CB A:ASP125 4.6 20.4 1.0 CG A:ASP60 4.7 23.6 1.0 O A:HOH651 4.7 23.5 1.0 CG A:ASP9 4.7 19.3 1.0 O A:HOH693 4.8 45.0 1.0 CG A:ASP146 5.0 20.2 1.0 CB A:ALA124 5.0 19.2 1.0

Manganese binding site 2 out of 4 in the Mycobacterium Smegmatis Dna Flap Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mycobacterium Smegmatis Dna Flap Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:21.7 occ:1.00 O A:HOH687 2.0 16.7 1.0 OD2 A:ASP146 2.1 23.7 1.0 OD2 A:ASP125 2.2 19.1 1.0 OD2 A:ASP148 2.2 23.8 1.0 O A:HOH638 2.3 23.5 1.0 O A:HOH651 2.3 23.5 1.0 CG A:ASP146 3.2 20.2 1.0 CG A:ASP125 3.2 20.0 1.0 CG A:ASP148 3.3 28.4 1.0 OD1 A:ASP146 3.6 19.3 1.0 MN A:MN401 3.6 19.8 1.0 OD1 A:ASP125 3.6 18.2 1.0 O A:HOH544 3.7 24.5 1.0 CB A:ASP148 3.7 25.8 1.0 O A:HOH685 3.8 34.1 1.0 OD2 A:ASP208 4.0 33.1 1.0 MN A:MN403 4.1 27.5 1.0 OE1 A:GLU123 4.2 20.0 1.0 OD1 A:ASP148 4.3 21.7 1.0 O A:HOH562 4.4 34.2 1.0 CB A:ASP146 4.5 17.2 1.0 CB A:ASP125 4.5 20.4 1.0 NZ A:LYS76 4.5 32.0 1.0 OD1 A:ASP208 4.6 28.6 1.0 O A:HOH729 4.6 45.4 1.0 O A:HOH531 4.7 21.0 1.0 CG A:ASP208 4.7 34.0 1.0 O A:HOH743 4.8 23.7 1.0 CE A:LYS76 4.9 28.2 1.0 O A:HOH663 4.9 27.4 1.0

Manganese binding site 3 out of 4 in the Mycobacterium Smegmatis Dna Flap Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Mycobacterium Smegmatis Dna Flap Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:27.5 occ:1.00 O A:HOH562 1.9 34.2 1.0 OD2 A:ASP208 2.1 33.1 1.0 OD1 A:ASP148 2.2 21.7 1.0 OD2 A:ASP205 2.2 34.7 1.0 O A:HOH663 2.2 27.4 1.0 OD2 A:ASP148 2.3 23.8 1.0 CG A:ASP148 2.5 28.4 1.0 CG A:ASP208 3.0 34.0 1.0 CG A:ASP205 3.3 34.6 1.0 CB A:ASP208 3.7 25.4 1.0 OD1 A:ASP205 3.7 32.3 1.0 O A:HOH638 3.8 23.5 1.0 OD1 A:ASP208 3.8 28.6 1.0 O A:HOH602 3.9 25.6 1.0 O A:HOH651 4.0 23.5 1.0 CB A:ASP148 4.1 25.8 1.0 O A:HOH516 4.1 35.2 1.0 MN A:MN402 4.1 21.7 1.0 O A:HOH674 4.2 42.2 1.0 CB A:ASP205 4.5 26.3 1.0 O A:HOH658 4.5 31.9 1.0 OD1 A:ASP146 4.5 19.3 1.0 O A:HOH685 4.8 34.1 1.0 CA A:ASP148 4.9 27.0 1.0 CA A:ASP208 5.0 21.5 1.0

Manganese binding site 4 out of 4 in the Mycobacterium Smegmatis Dna Flap Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Mycobacterium Smegmatis Dna Flap Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:57.6 occ:1.00 O A:HOH509 1.9 51.1 1.0 O A:GLU84 2.2 33.5 1.0 O A:HOH548 2.2 48.6 1.0 O A:HOH506 2.4 40.3 1.0 OD1 A:ASP90 2.4 23.8 1.0 O A:HOH503 2.8 36.8 1.0 OE1 A:GLN66 3.2 58.0 1.0 CG A:ASP90 3.3 25.2 1.0 C A:GLU84 3.3 30.0 1.0 OD2 A:ASP90 3.5 27.3 1.0 O A:VAL88 3.7 26.9 1.0 N A:GLU84 3.8 23.7 1.0 O A:PRO85 4.0 30.7 1.0 CA A:GLU84 4.0 24.6 1.0 C A:PRO85 4.2 33.8 1.0 N A:PRO85 4.3 32.4 1.0 CD A:GLN66 4.4 48.5 1.0 CA A:PRO85 4.4 32.3 1.0 CB A:GLU84 4.5 23.0 1.0 N A:ASP90 4.5 24.3 1.0 CB A:ASP90 4.6 22.4 1.0 O A:HOH508 4.7 32.4 1.0 O A:HOH561 4.7 28.9 1.0 N A:ASP86 4.8 34.3 1.0 CA A:ASP90 4.8 22.6 1.0 C A:PRO83 4.9 24.7 1.0 O A:HOH668 4.9 46.1 1.0 C A:VAL88 5.0 22.1 1.0

M.L.Uson, A.Carl, Y.Goldgur, S.Shuman. Crystal Structure and Mutational Analysis of Mycobacterium Smegmatis Fena Highlight Active Site Amino Acids and Three Metal Ions Essential For Flap Endonuclease and 5' Exonuclease Activities. Nucleic Acids Res. V. 46 4164 2018.
ISSN: ESSN 1362-4962
PubMed: 29635474
DOI: 10.1093/NAR/GKY238