Samarium in PDB 5um9: Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+

The structure of Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+, PDB code: 5um9 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)	19.67 / 2.81
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.846, 105.846, 100.709, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 26.6

The structure of Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+ also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Samarium atom in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+ (pdb code 5um9). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 5 binding sites of Samarium where determined in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+, PDB code: 5um9:
Jump to Samarium binding site number: 1; 2; 3; 4; 5;

Samarium binding site 1 out of 5 in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna 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) D86N with 5'-Flap Substrate Dna and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm402 b:86.8 occ:1.00 O A:HOH502 2.2 88.3 1.0 OP1 E:DT7 2.2 96.7 1.0 OD2 A:ASP181 2.3 88.6 1.0 OD2 A:ASP179 2.3 0.5 1.0 O A:HOH506 2.3 0.6 1.0 OD1 A:ASP179 2.6 91.5 1.0 CG A:ASP179 2.7 95.4 1.0 OD1 A:ASP181 2.9 97.7 1.0 CG A:ASP181 2.9 79.3 1.0 OE1 A:GLU160 3.1 92.1 1.0 P E:DT7 3.4 97.8 1.0 CD A:GLU160 3.5 0.6 1.0 HA2 A:GLY2 3.6 0.3 1.0 HG2 A:GLU160 3.7 0.9 1.0 O5' E:DT7 3.8 0.4 1.0 OE2 A:GLU160 3.9 0.5 1.0 HH A:TYR234 3.9 0.6 1.0 H5' E:DT7 4.1 0.3 1.0 OP2 E:DT7 4.1 0.8 1.0 CG A:GLU160 4.1 0.6 1.0 CB A:ASP179 4.2 0.8 1.0 HZ2 A:LYS93 4.3 0.8 1.0 CA A:GLY2 4.4 92.7 1.0 HE2 A:PHE185 4.4 0.5 1.0 HB3 A:ASP179 4.4 0.7 1.0 CB A:ASP181 4.4 88.8 1.0 HZ1 A:LYS93 4.4 0.8 1.0 OH A:TYR234 4.4 0.8 1.0 N A:GLY2 4.5 98.8 1.0 C5' E:DT7 4.5 0.3 1.0 O3' E:DT6 4.6 0.8 1.0 HB3 A:ASP181 4.6 0.6 1.0 HB2 A:ASP179 4.6 0.7 1.0 HB2 A:GLU160 4.6 0.1 1.0 OE1 A:GLU158 4.7 0.8 1.0 H A:ASP181 4.7 0.1 1.0 HA3 A:GLY2 4.7 0.3 1.0 NZ A:LYS93 4.8 0.0 1.0 HB2 A:ASP181 4.8 0.6 1.0 HG3 A:GLU160 4.9 0.9 1.0 HE3 A:LYS93 4.9 0.4 1.0 CB A:GLU160 5.0 83.4 1.0 HA A:ASP179 5.0 0.0 1.0

Samarium binding site 2 out of 5 in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna 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) D86N with 5'-Flap Substrate Dna and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm403 b:0.9 occ:1.00 OE2 A:GLU57 1.9 0.1 1.0 OE1 A:GLU313 2.3 0.6 1.0 CD A:GLU57 2.8 0.8 1.0 CD A:GLU313 3.2 0.1 1.0 OE2 A:GLU313 3.3 97.3 1.0 OE1 A:GLU57 3.4 0.2 1.0 HG3 A:GLU57 3.8 0.8 1.0 HA A:GLU313 3.9 0.1 1.0 CG A:GLU57 4.0 0.0 1.0 SM A:SM404 4.2 96.2 1.0 HG2 A:GLU57 4.4 0.8 1.0 O A:GLU313 4.5 96.5 1.0 CG A:GLU313 4.6 76.9 1.0 CA A:GLU313 4.7 95.1 1.0 HB2 A:GLU313 4.8 0.1 1.0 HD22 A:ASN55 4.8 0.7 1.0 CB A:GLU313 5.0 84.2 1.0

Samarium binding site 3 out of 5 in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna 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) D86N with 5'-Flap Substrate Dna and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm404 b:96.2 occ:1.00 OE2 A:GLU313 2.3 97.3 1.0 OE2 A:GLU59 2.3 99.1 1.0 OE1 A:GLU57 2.5 0.2 1.0 OE1 A:GLU59 2.8 0.7 1.0 CD A:GLU59 2.9 91.2 1.0 CD A:GLU313 3.3 0.1 1.0 CD A:GLU57 3.6 0.8 1.0 OE1 A:GLU313 3.9 0.6 1.0 OE2 A:GLU57 4.0 0.1 1.0 HZ2 A:LYS314 4.0 0.6 1.0 HD21 A:ASN55 4.1 0.7 1.0 SM A:SM403 4.2 0.9 1.0 HB2 A:GLU57 4.2 0.4 1.0 CG A:GLU59 4.4 0.9 1.0 HG2 A:GLU313 4.4 92.2 1.0 CG A:GLU313 4.4 76.9 1.0 HG3 A:GLU313 4.5 92.2 1.0 HB3 A:GLU57 4.7 0.4 1.0 HG3 A:GLU59 4.7 0.5 1.0 HG2 A:GLU59 4.7 0.5 1.0 CG A:GLU57 4.7 0.0 1.0 CB A:GLU57 4.8 0.4 1.0 ND2 A:ASN55 4.8 96.5 1.0 HZ3 A:LYS314 4.8 0.6 1.0 NZ A:LYS314 4.8 1.0 1.0 HD22 A:ASN55 4.9 0.7 1.0

Samarium binding site 4 out of 5 in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna 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) D86N with 5'-Flap Substrate Dna and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm405 b:0.6 occ:0.81 O D:HOH107 2.3 0.4 1.0 O A:HOH517 2.3 0.3 1.0 OE2 A:GLU106 3.7 0.3 1.0 OE1 A:GLU106 4.0 0.7 1.0 OP1 D:DC8 4.1 0.2 1.0 CD A:GLU106 4.3 0.5 1.0 OP2 D:DC8 4.8 0.2 1.0 P D:DC8 4.9 0.5 1.0

Samarium binding site 5 out of 5 in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna 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) D86N with 5'-Flap Substrate Dna and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm406 b:0.4 occ:0.36 OE2 A:GLU338 2.3 0.6 1.0 O A:HOH518 2.3 0.4 1.0 O A:HOH507 2.3 0.3 1.0 CD A:GLU338 2.7 0.3 1.0 OE1 A:GLU338 3.0 0.9 1.0 HG2 A:GLU338 3.6 0.8 1.0 HH22 A:ARG332 3.7 0.8 1.0 CG A:GLU338 3.8 0.8 1.0 NH2 A:ARG332 4.3 0.9 1.0 HH21 A:ARG332 4.4 0.8 1.0 HB3 A:GLU338 4.4 0.2 1.0 HG3 A:GLU338 4.5 0.8 1.0 CB A:GLU338 4.7 0.3 1.0 HB2 A:GLU300 4.8 0.9 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