Samarium in PDB 5k97: Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+

The structure of Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+, PDB code: 5k97 was solved by S.E.Tsutakawa, A.S.Arvai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.85 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.236, 105.236, 104.548, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 21.9

The structure of Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+ also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Samarium atom in the Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+ (pdb code 5k97). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 8 binding sites of Samarium where determined in the Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+, PDB code: 5k97:
Jump to Samarium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Samarium binding site 1 out of 8 in the Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm401 b:58.7 occ:0.57 CG A:ASP181 2.3 83.2 1.0 O A:HOH689 2.3 81.1 1.0 OP1 E:DT7 2.3 90.0 1.0 OD2 A:ASP181 2.3 88.4 1.0 OD1 A:ASP181 2.4 73.7 1.0 SM A:SM403 2.5 45.5 0.6 OE2 A:GLU160 2.7 71.2 1.0 P E:DT7 3.1 73.2 1.0 CB A:ASP181 3.2 64.5 1.0 HB2 A:ASP181 3.2 77.4 1.0 OP3 E:DT7 3.2 66.4 1.0 HB3 A:ASP181 3.3 77.4 1.0 CD A:GLU160 3.3 80.7 1.0 N A:GLY2 3.4 54.8 1.0 OP2 E:DT7 3.4 73.3 1.0 SM A:SM404 3.5 41.2 0.5 OE1 A:GLU160 3.6 63.2 1.0 HD22 A:ASN233 3.7 90.9 1.0 HD21 A:ASN233 3.7 90.9 1.0 HB3 A:ASP179 4.0 73.5 1.0 ND2 A:ASN233 4.0 75.7 1.0 HG2 A:GLU160 4.3 82.9 1.0 HZ1 A:LYS93 4.3 0.1 1.0 HH A:TYR234 4.3 69.7 1.0 HA2 A:GLY2 4.4 66.8 1.0 CG A:GLU160 4.4 69.1 1.0 HE2 A:PHE185 4.4 46.3 1.0 HB2 A:GLU160 4.4 46.0 1.0 HZ2 A:LYS93 4.5 0.1 1.0 CA A:GLY2 4.5 55.7 1.0 O A:HOH651 4.6 51.7 1.0 O5' E:DT7 4.6 77.9 1.0 CA A:ASP181 4.6 51.6 1.0 CB A:ASP179 4.6 61.2 1.0 OD2 A:ASP179 4.6 96.2 1.0 HB2 A:ASP179 4.6 73.5 1.0 H A:ASP181 4.6 60.3 1.0 CG A:ASP179 4.7 93.1 1.0 OH A:TYR234 4.8 58.0 1.0 HA A:ASP181 4.8 61.9 1.0 NZ A:LYS93 4.9 92.6 1.0 CB A:GLU160 4.9 38.3 1.0 OE1 A:GLU158 4.9 83.5 1.0 H5' E:DT7 4.9 0.9 1.0 O E:HOH113 5.0 69.8 1.0

Samarium binding site 2 out of 8 in the Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm402 b:88.2 occ:0.54 SM A:SM404 2.0 41.2 0.5 OE1 A:GLU158 2.3 83.5 1.0 O E:HOH113 2.3 69.8 1.0 O A:HOH525 2.7 53.4 1.0 OE1 A:GLU160 3.1 63.2 1.0 OD1 A:ASP86 3.1 48.9 1.0 OD2 A:ASP86 3.1 54.7 1.0 CG A:ASP86 3.4 49.8 1.0 CD A:GLU158 3.4 90.3 1.0 HZ3 A:LYS93 3.4 0.1 1.0 O E:HOH103 3.6 73.7 1.0 H A:ALA159 3.7 40.8 1.0 O A:HOH689 3.8 81.1 1.0 HZ1 A:LYS93 3.8 0.1 1.0 OE2 A:GLU158 3.8 0.5 1.0 HZ2 A:LYS93 3.9 0.1 1.0 NZ A:LYS93 3.9 92.6 1.0 HA A:GLU158 3.9 56.4 1.0 CD A:GLU160 3.9 80.7 1.0 OP3 E:DT7 4.1 66.4 1.0 OE2 A:GLU160 4.1 71.2 1.0 OP2 E:DT7 4.2 73.3 1.0 HB3 A:GLU158 4.3 57.0 1.0 O G:HOH101 4.3 59.2 1.0 H A:GLU160 4.4 41.4 1.0 N A:ALA159 4.4 34.0 1.0 HB3 A:ALA159 4.5 43.2 1.0 OP1 G:DT6 4.5 91.8 0.5 H73 E:DT7 4.6 91.2 1.0 CG A:GLU158 4.6 68.8 1.0 CA A:GLU158 4.7 47.0 1.0 CB A:GLU158 4.7 47.5 1.0 CB A:ASP86 4.8 41.6 1.0 OD1 A:ASP34 4.8 57.2 1.0 HB3 A:ASP86 4.8 49.9 1.0 P E:DT7 4.9 73.2 1.0

Samarium binding site 3 out of 8 in the Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm403 b:45.5 occ:0.59 HB3 A:ASP179 2.0 73.5 1.0 OD2 A:ASP179 2.3 96.2 1.0 OD1 A:ASP181 2.3 73.7 1.0 CB A:ASP179 2.3 61.2 1.0 OP1 E:DT7 2.3 90.0 1.0 CG A:ASP179 2.3 93.1 1.0 HB2 A:ASP179 2.3 73.5 1.0 OE2 A:GLU160 2.3 71.2 1.0 SM A:SM401 2.5 58.7 0.6 OP3 E:DT7 2.7 66.4 1.0 P E:DT7 3.1 73.2 1.0 CG A:ASP181 3.1 83.2 1.0 HB2 A:ASP181 3.2 77.4 1.0 OD1 A:ASP179 3.2 97.7 1.0 CD A:GLU160 3.4 80.7 1.0 H5' E:DT7 3.5 0.9 1.0 HG2 A:GLU160 3.7 82.9 1.0 CB A:ASP181 3.7 64.5 1.0 CA A:ASP179 3.8 75.1 1.0 H A:ASP181 3.9 60.3 1.0 N A:GLY2 3.9 54.8 1.0 O A:HOH554 3.9 65.2 1.0 HA2 A:GLY2 4.0 66.8 1.0 OD2 A:ASP181 4.0 88.4 1.0 SM A:SM404 4.0 41.2 0.5 O5' E:DT7 4.1 77.9 1.0 C5' E:DT7 4.1 89.1 1.0 CG A:GLU160 4.1 69.1 1.0 HA A:ASP179 4.2 90.1 1.0 H5'' E:DT7 4.2 0.9 1.0 HE3 A:MET37 4.2 0.8 1.0 O E:HOH103 4.3 73.7 1.0 HB3 A:ASP181 4.3 77.4 1.0 OP2 E:DT7 4.3 73.3 1.0 OE1 A:GLU160 4.4 63.2 1.0 CA A:GLY2 4.4 55.7 1.0 H22 A:EDO410 4.5 88.2 1.0 C A:ASP179 4.5 76.7 1.0 H A:ASP179 4.5 85.2 1.0 O A:HOH689 4.6 81.1 1.0 N A:ASP181 4.6 50.3 1.0 N A:ASP179 4.7 71.0 1.0 HG3 A:GLU160 4.7 82.9 1.0 HA3 A:GLY2 4.7 66.8 1.0 HG1 A:THR177 4.8 0.7 1.0 CA A:ASP181 4.8 51.6 1.0 O A:ASP179 4.8 73.9 1.0 HE2 A:MET37 4.9 0.8 1.0 CE A:MET37 4.9 99.9 1.0 HE1 A:MET37 5.0 0.8 1.0

Samarium binding site 4 out of 8 in the Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm404 b:41.2 occ:0.52 SM A:SM402 2.0 88.2 0.5 OE1 A:GLU160 2.3 63.2 1.0 OP3 E:DT7 2.3 66.4 1.0 O E:HOH113 2.3 69.8 1.0 O E:HOH103 2.3 73.7 1.0 OE2 A:GLU160 2.3 71.2 1.0 CD A:GLU160 2.6 80.7 1.0 O A:HOH525 2.9 53.4 1.0 O A:HOH689 3.2 81.1 1.0 OP2 E:DT7 3.3 73.3 1.0 P E:DT7 3.3 73.2 1.0 OE1 A:GLU158 3.4 83.5 1.0 SM A:SM401 3.5 58.7 0.6 HZ1 A:LYS93 3.9 0.1 1.0 OD1 A:ASP34 3.9 57.2 1.0 CG A:GLU160 4.0 69.1 1.0 SM A:SM403 4.0 45.5 0.6 OP1 E:DT7 4.1 90.0 1.0 HG3 A:GLU160 4.2 82.9 1.0 HZ3 A:LYS93 4.2 0.1 1.0 HZ2 A:LYS93 4.3 0.1 1.0 NZ A:LYS93 4.3 92.6 1.0 H73 E:DT7 4.3 91.2 1.0 H A:GLU160 4.4 41.4 1.0 OD2 A:ASP86 4.4 54.7 1.0 HG2 A:GLU160 4.5 82.9 1.0 HE2 A:MET37 4.5 0.8 1.0 CD A:GLU158 4.6 90.3 1.0 OD1 A:ASP86 4.6 48.9 1.0 O5' E:DT7 4.6 77.9 1.0 HB2 A:GLU160 4.6 46.0 1.0 O A:HOH554 4.8 65.2 1.0 H A:ALA159 4.9 40.8 1.0 CB A:GLU160 4.9 38.3 1.0 OD2 A:ASP179 4.9 96.2 1.0 CG A:ASP86 4.9 49.8 1.0 HB3 A:ALA159 5.0 43.2 1.0 CG A:ASP34 5.0 49.0 1.0 HB3 A:GLU158 5.0 57.0 1.0

Samarium binding site 5 out of 8 in the Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 5 of Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm406 b:37.6 occ:1.00 OE2 A:GLU57 2.3 59.1 1.0 OE1 A:GLU313 2.4 37.5 1.0 O A:HOH588 2.4 36.2 1.0 OE1 A:GLU57 2.4 58.2 1.0 CD A:GLU57 2.6 46.3 1.0 CD A:GLU313 3.3 37.3 1.0 OE2 A:GLU313 3.5 49.5 1.0 HA A:GLU313 3.9 45.0 1.0 CG A:GLU57 4.0 49.5 1.0 HG3 A:GLU57 4.1 59.4 1.0 SM A:SM407 4.1 38.5 1.0 O A:HOH743 4.2 69.0 1.0 HG2 A:GLU57 4.4 59.4 1.0 O A:GLU313 4.5 34.6 1.0 CG A:GLU313 4.7 41.0 1.0 CA A:GLU313 4.8 37.5 1.0 O A:HOH549 4.8 46.7 1.0 HB2 A:GLU313 4.9 40.1 1.0 HB2 A:GLU57 4.9 63.5 1.0

Samarium binding site 6 out of 8 in the Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 6 of Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm407 b:38.5 occ:1.00 OE2 A:GLU59 2.3 43.1 1.0 OE2 A:GLU313 2.3 49.5 1.0 OE1 A:GLU59 2.6 36.7 1.0 CD A:GLU59 2.8 37.9 1.0 OE1 A:GLU57 2.9 58.2 1.0 CD A:GLU313 3.4 37.3 1.0 HZ2 A:LYS314 3.8 49.6 1.0 CD A:GLU57 3.8 46.3 1.0 OE1 A:GLU313 3.9 37.5 1.0 HD21 A:ASN55 3.9 46.6 1.0 SM A:SM406 4.1 37.6 1.0 O A:HOH562 4.2 55.0 1.0 CG A:GLU59 4.3 39.6 1.0 OE2 A:GLU57 4.3 59.1 1.0 HB2 A:GLU57 4.4 63.5 1.0 CG A:GLU313 4.5 41.0 1.0 HG2 A:GLU313 4.5 49.2 1.0 HG3 A:GLU59 4.5 47.6 1.0 HB3 A:GLU57 4.6 63.5 1.0 O A:HOH830 4.6 70.6 1.0 NZ A:LYS314 4.6 41.3 1.0 HZ3 A:LYS314 4.6 49.6 1.0 HG2 A:GLU59 4.7 47.6 1.0 HG3 A:GLU313 4.7 49.2 1.0 ND2 A:ASN55 4.7 38.9 1.0 CB A:GLU57 4.8 52.9 1.0 HD22 A:ASN55 4.9 46.6 1.0 CG A:GLU57 4.9 49.5 1.0 HB2 A:GLU59 5.0 52.7 1.0

Samarium binding site 7 out of 8 in the Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 7 of Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm408 b:0.4 occ:0.55 O A:HOH803 2.3 84.4 1.0 OD2 A:ASP51 2.9 0.3 1.0 O A:GLY49 3.0 83.0 1.0 O A:HOH724 3.1 77.8 1.0 OD1 A:ASP51 3.1 0.1 1.0 CG A:ASP51 3.3 0.7 1.0 C A:GLY49 4.2 80.1 1.0 HA3 A:GLY50 4.2 99.1 1.0 O A:HOH503 4.6 72.3 1.0 CB A:ASP51 4.6 82.3 1.0 N A:ASP51 4.7 73.6 1.0 C A:GLY50 4.7 73.0 1.0 H A:ASP51 4.7 88.3 1.0 O A:HOH937 4.7 80.5 1.0 HB2 A:ASP51 4.7 98.8 1.0 CA A:GLY50 4.8 82.5 1.0 HA3 A:GLY49 4.9 94.1 1.0 N A:GLY50 5.0 81.0 1.0

Samarium binding site 8 out of 8 in the Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 8 of Flap Endonuclease 1 (FEN1) D233N with Cleaved Product Fragment and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm409 b:0.8 occ:1.00 O A:HOH545 2.3 0.6 1.0 O A:HOH901 2.9 0.4 1.0 O A:HOH848 3.3 0.1 1.0 OE2 A:GLU102 3.4 0.9 1.0 HG2 A:LYS99 3.6 0.9 1.0 OE1 A:GLU102 3.7 0.3 1.0 CD A:GLU102 3.9 0.1 1.0 HD3 A:LYS99 4.3 1.0 1.0 CG A:LYS99 4.5 0.5 1.0 O A:HOH711 4.6 83.4 1.0 CD A:LYS99 4.8 0.5 1.0 HG3 A:LYS99 4.8 0.9 1.0 HD2 A:LYS99 4.9 1.0 1.0 HA A:LYS99 5.0 0.3 1.0

S.E.Tsutakawa, M.J.Thompson, A.S.Arvai, A.J.Neil, S.J.Shaw, S.I.Algasaier, J.C.Kim, L.D.Finger, E.Jardine, V.J.B.Gotham, A.H.Sarker, M.Z.Her, F.Rashid, S.M.Hamdan, S.M.Mirkin, J.A.Grasby, J.A.Tainer. Phosphate Steering By Flap Endonuclease 1 Promotes 5'-Flap Specificity and Incision to Prevent Genome Instability. Nat Commun V. 8 15855 2017.
ISSN: ESSN 2041-1723
PubMed: 28653660
DOI: 10.1038/NCOMMS15855