Samarium in PDB 3q8l: Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+

The structure of Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+, PDB code: 3q8l was solved by S.E.Tsutakawa, S.Classen, B.R.Chapados, A.Arvai, D.L.Finger, G.Guenther, C.G.Tomlinson, P.Thompson, A.H.Sarker, B.Shen, P.K.Cooper, J.A.Grasby, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.48 / 2.32
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.140, 105.140, 104.050, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 20.2

The structure of Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+ also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Samarium atom in the Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+ (pdb code 3q8l). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 4 binding sites of Samarium where determined in the Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+, PDB code: 3q8l:
Jump to Samarium binding site number: 1; 2; 3; 4;

Samarium binding site 1 out of 4 in the Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm1001 b:53.1 occ:0.36 O A:HOH376 2.3 55.2 1.0 O A:HOH361 2.3 61.9 1.0 O A:HOH422 2.5 46.9 1.0 O2 A:SO41201 2.5 85.0 0.7 O A:HOH683 2.7 52.5 1.0 OD1 A:ASP86 3.0 54.4 1.0 OD2 A:ASP86 3.2 61.3 1.0 CG A:ASP86 3.4 48.5 1.0 OE1 A:GLU158 3.5 82.7 1.0 CG A:GLU158 3.7 59.5 1.0 S A:SO41201 3.8 87.7 0.7 OE1 A:GLU160 3.8 64.7 1.0 CD A:GLU158 3.9 72.6 1.0 O A:HOH379 3.9 58.5 1.0 OE2 A:GLU160 3.9 62.4 1.0 CD A:GLU160 4.0 61.0 1.0 OD2 A:ASP34 4.1 44.8 1.0 O4 A:SO41201 4.2 91.8 0.7 O3 A:SO41201 4.3 87.1 0.7 N A:ALA159 4.4 34.3 1.0 SM A:SM1002 4.6 48.1 0.9 NZ A:LYS93 4.7 51.2 1.0 O A:HOH414 4.7 0.2 1.0 N A:GLU160 4.8 31.3 1.0 CB A:GLU158 4.8 33.5 1.0 OE2 A:GLU158 4.9 69.4 1.0 O1 A:SO41201 4.9 84.2 0.7 CA A:GLU158 4.9 33.4 1.0 CB A:ASP86 4.9 41.7 1.0 CB A:ALA159 4.9 27.9 1.0 O A:HOH356 5.0 65.0 1.0 CG A:ASP34 5.0 42.3 1.0

Samarium binding site 2 out of 4 in the Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm1002 b:48.1 occ:0.93 OD2 A:ASP179 2.3 33.7 1.0 OD2 A:ASP181 2.3 59.8 1.0 O A:HOH356 2.3 65.0 1.0 OD1 A:ASP181 2.4 59.9 1.0 O A:HOH422 2.5 46.9 1.0 OE2 A:GLU160 2.6 62.4 1.0 OE1 A:GLU160 2.7 64.7 1.0 CG A:ASP181 2.7 58.2 1.0 CD A:GLU160 2.9 61.0 1.0 O A:HOH379 2.9 58.5 1.0 O E:HOH277 3.1 49.0 1.0 CG A:ASP179 3.3 47.5 1.0 OD1 A:ASP179 3.6 46.5 1.0 O3 A:SO41201 3.6 87.1 0.7 OD2 A:ASP233 4.0 49.5 1.0 O2 A:SO41201 4.1 85.0 0.7 O A:HOH376 4.2 55.2 1.0 CB A:ASP181 4.2 58.1 1.0 CG A:GLU160 4.3 47.7 1.0 O A:HOH414 4.4 0.2 1.0 S A:SO41201 4.4 87.7 0.7 CB A:ASP179 4.5 41.3 1.0 O A:HOH361 4.6 61.9 1.0 O A:HOH687 4.6 82.5 1.0 SM A:SM1001 4.6 53.1 0.4 N A:GLY2 4.7 68.2 1.0 CA A:GLY2 4.7 58.2 1.0 O A:HOH612 4.8 44.3 1.0 O1 A:SO41201 4.9 84.2 0.7 OH A:TYR234 5.0 46.5 1.0

Samarium binding site 3 out of 4 in the Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm1003 b:41.6 occ:1.00 OE1 A:GLU57 2.4 45.3 1.0 OE2 A:GLU57 2.4 41.7 1.0 OE1 A:GLU313 2.5 39.2 1.0 O A:HOH575 2.5 31.3 1.0 CD A:GLU57 2.7 39.7 1.0 O A:HOH574 2.9 42.9 1.0 O A:HOH605 2.9 44.8 1.0 CD A:GLU313 3.4 31.1 1.0 OE2 A:GLU313 3.6 40.8 1.0 SM A:SM1004 4.1 42.5 1.0 CG A:GLU57 4.2 36.8 1.0 O A:GLU313 4.4 42.6 1.0 O A:HOH578 4.7 46.8 1.0 CG A:GLU313 4.8 35.3 1.0 CA A:GLU313 4.8 31.8 1.0 O A:HOH455 4.8 42.6 1.0 O A:HOH576 5.0 40.5 1.0

Samarium binding site 4 out of 4 in the Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Substrate 5'-Flap Dna, SM3+, and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm1004 b:42.5 occ:1.00 OE2 A:GLU59 2.3 47.4 1.0 OE1 A:GLU57 2.3 45.3 1.0 OE2 A:GLU313 2.4 40.8 1.0 OE1 A:GLU59 2.4 44.1 1.0 O A:HOH577 2.5 44.1 1.0 CD A:GLU59 2.7 37.9 1.0 O A:HOH658 2.8 36.7 1.0 O A:HOH576 2.9 40.5 1.0 CD A:GLU57 3.3 39.7 1.0 CD A:GLU313 3.4 31.1 1.0 CG A:GLU57 3.8 36.8 1.0 OE1 A:GLU313 3.9 39.2 1.0 SM A:SM1003 4.1 41.6 1.0 CG A:GLU59 4.2 29.8 1.0 OE2 A:GLU57 4.2 41.7 1.0 NZ A:LYS314 4.5 37.8 1.0 O A:HOH659 4.5 57.7 1.0 CG A:GLU313 4.6 35.3 1.0 O A:HOH565 4.7 65.3 1.0 ND2 A:ASN55 4.7 37.3 1.0 O A:HOH578 4.8 46.8 1.0 O A:HOH563 4.8 45.4 1.0

S.E.Tsutakawa, S.Classen, B.R.Chapados, A.S.Arvai, L.D.Finger, G.Guenther, C.G.Tomlinson, P.Thompson, A.H.Sarker, B.Shen, P.K.Cooper, J.A.Grasby, J.A.Tainer. Human Flap Endonuclease Structures, Dna Double-Base Flipping, and A Unified Understanding of the FEN1 Superfamily. Cell(Cambridge,Mass.) V. 145 198 2011.
ISSN: ISSN 0092-8674
PubMed: 21496641
DOI: 10.1016/J.CELL.2011.03.004