Samarium in PDB 3q8k: Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Product 5'-Flap Dna, SM3+, and K+

The structure of Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Product 5'-Flap Dna, SM3+, and K+, PDB code: 3q8k 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)	34.46 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.438, 105.438, 105.064, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 21.3

The structure of Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Product 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 Product 5'-Flap Dna, SM3+, and K+ (pdb code 3q8k). 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 Product 5'-Flap Dna, SM3+, and K+, PDB code: 3q8k:
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 Product 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 Product 5'-Flap Dna, SM3+, and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm1001 b:48.0 occ:0.73 O A:HOH742 2.3 45.8 1.0 OP1 E:DT2 2.3 64.2 1.0 O A:HOH598 2.3 64.0 1.0 OD2 A:ASP86 2.4 64.5 1.0 O A:HOH693 2.4 60.5 1.0 OP2 E:DT2 2.5 63.1 1.0 OE1 A:GLU160 2.7 25.5 0.5 P E:DT2 2.8 77.9 1.0 OE1 A:GLU160 2.8 40.0 0.5 OE2 A:GLU160 2.8 26.5 0.5 OE2 A:GLU160 3.0 37.6 0.5 CD A:GLU160 3.2 29.8 0.5 CG A:ASP86 3.2 57.3 1.0 OD1 A:ASP86 3.2 55.7 1.0 CD A:GLU160 3.2 39.0 0.5 OP3 E:DT2 3.6 80.6 1.0 CG A:GLU158 3.9 62.7 1.0 SM A:SM1002 4.0 50.0 0.8 O E:HOH315 4.1 63.3 1.0 O5' E:DT2 4.1 79.8 1.0 OE1 A:GLU158 4.2 89.5 1.0 CD A:GLU158 4.3 88.4 1.0 OD2 A:ASP34 4.3 68.6 1.0 N A:ALA159 4.5 34.8 1.0 C5' E:DT2 4.5 89.5 1.0 CB A:ASP86 4.6 35.9 1.0 CG A:GLU160 4.7 32.9 0.5 CG A:GLU160 4.7 31.7 0.5 O A:HOH555 4.8 72.7 1.0 NZ A:LYS93 4.9 67.3 1.0 O E:HOH455 4.9 58.7 1.0 OD1 A:ASP34 4.9 65.0 1.0 CB A:GLU158 4.9 48.0 1.0 N A:GLU160 4.9 32.7 0.5 N A:GLU160 5.0 32.7 0.5 CA A:GLU158 5.0 44.0 1.0

Samarium binding site 2 out of 4 in the Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Product 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 Product 5'-Flap Dna, SM3+, and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm1002 b:50.0 occ:0.84 O A:OH347 2.0 60.4 1.0 OD2 A:ASP179 2.1 24.7 1.0 O A:HOH555 2.3 72.7 1.0 OD2 A:ASP181 2.3 56.9 1.0 OP1 E:DT2 2.3 64.2 1.0 OE2 A:GLU160 2.6 26.5 0.5 OE2 A:GLU160 2.7 37.6 0.5 CG A:ASP181 3.0 60.8 1.0 OD1 A:ASP181 3.1 56.5 1.0 CD A:GLU160 3.2 29.8 0.5 CG A:ASP179 3.3 55.8 1.0 O E:HOH455 3.3 58.7 1.0 CD A:GLU160 3.6 39.0 0.5 P E:DT2 3.7 77.9 1.0 OE1 A:GLU160 3.8 40.0 0.5 OD1 A:ASP179 3.9 61.2 1.0 CG A:GLU160 3.9 32.9 0.5 N A:GLY2 4.0 57.9 1.0 SM A:SM1001 4.0 48.0 0.7 O5' E:DT2 4.1 79.8 1.0 O A:HOH742 4.1 45.8 1.0 C5' E:DT2 4.2 89.5 1.0 OE1 A:GLU160 4.2 25.5 0.5 OD2 A:ASP233 4.3 71.7 1.0 OP3 E:DT2 4.3 80.6 1.0 CB A:ASP179 4.4 37.9 1.0 CG A:GLU160 4.4 31.7 0.5 CB A:ASP181 4.5 48.1 1.0 CG A:GLU158 4.5 62.7 1.0 NZ A:LYS93 4.6 67.3 1.0 OH A:TYR234 4.7 58.8 1.0 OE2 A:GLU158 4.8 90.0 1.0 CD A:GLU158 4.9 88.4 1.0 OP2 E:DT2 4.9 63.1 1.0 O A:HOH416 5.0 52.3 1.0

Samarium binding site 3 out of 4 in the Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Product 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 Product 5'-Flap Dna, SM3+, and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm1003 b:40.6 occ:1.00 OE1 A:GLU57 2.4 54.3 1.0 OE2 A:GLU57 2.4 46.8 1.0 OE1 A:GLU313 2.5 28.5 1.0 O A:HOH768 2.6 35.5 1.0 CD A:GLU57 2.7 49.8 1.0 O A:HOH767 3.0 44.8 1.0 O A:HOH769 3.0 48.5 1.0 CD A:GLU313 3.3 34.6 1.0 OE2 A:GLU313 3.4 37.9 1.0 SM A:SM1004 4.1 41.4 1.0 CG A:GLU57 4.2 55.1 1.0 O A:HOH591 4.4 76.9 1.0 O A:HOH770 4.6 63.2 1.0 O A:GLU313 4.6 37.0 1.0 O A:HOH610 4.7 36.8 1.0 CG A:GLU313 4.8 44.4 1.0 O A:HOH764 4.8 34.5 1.0 CA A:GLU313 4.9 35.8 1.0

Samarium binding site 4 out of 4 in the Crystal Structure of Human Flap Endonuclease FEN1 (Wt) in Complex with Product 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 Product 5'-Flap Dna, SM3+, and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm1004 b:41.4 occ:1.00 OE2 A:GLU59 2.3 50.4 1.0 OE1 A:GLU57 2.3 54.3 1.0 OE2 A:GLU313 2.4 37.9 1.0 OE1 A:GLU59 2.4 41.8 1.0 O A:HOH765 2.6 56.0 1.0 CD A:GLU59 2.7 48.7 1.0 O A:HOH764 2.9 34.5 1.0 O A:HOH766 3.1 46.5 1.0 CD A:GLU57 3.5 49.8 1.0 CD A:GLU313 3.5 34.6 1.0 OE1 A:GLU313 4.1 28.5 1.0 SM A:SM1003 4.1 40.6 1.0 CG A:GLU57 4.1 55.1 1.0 CG A:GLU59 4.2 49.2 1.0 OE2 A:GLU57 4.4 46.8 1.0 O A:HOH630 4.5 59.8 1.0 ND2 A:ASN55 4.6 34.2 1.0 CG A:GLU313 4.7 44.4 1.0 NZ A:LYS314 4.7 34.9 1.0 O A:HOH357 4.9 66.3 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