Samarium in PDB 5kse: Flap Endonuclease 1 (FEN1) R100A with 5'-Flap Substrate Dna and SM3+

The structure of Flap Endonuclease 1 (FEN1) R100A with 5'-Flap Substrate Dna and SM3+, PDB code: 5kse 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)	37.00 / 2.11
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.235, 105.235, 104.064, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 24.5

The structure of Flap Endonuclease 1 (FEN1) R100A 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) R100A with 5'-Flap Substrate Dna and SM3+ (pdb code 5kse). 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) R100A with 5'-Flap Substrate Dna and SM3+, PDB code: 5kse:
Jump to Samarium binding site number: 1; 2; 3; 4; 5;

Samarium binding site 1 out of 5 in the Flap Endonuclease 1 (FEN1) R100A 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) R100A with 5'-Flap Substrate Dna and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm401 b:97.1 occ:0.88 O A:HOH512 2.2 0.2 1.0 OD2 A:ASP181 2.3 86.9 1.0 O A:HOH550 2.3 86.5 1.0 OD2 A:ASP179 2.3 85.0 1.0 O E:HOH102 2.3 0.9 1.0 OE2 A:GLU160 2.3 0.4 1.0 CG A:ASP179 3.1 76.7 1.0 CG A:ASP181 3.1 90.1 1.0 CD A:GLU160 3.2 94.3 1.0 OD1 A:ASP179 3.3 82.8 1.0 OD1 A:ASP181 3.3 90.5 1.0 HG2 A:GLU160 3.4 0.6 1.0 OP2 E:DT6 3.5 0.6 1.0 OD2 A:ASP233 3.7 0.1 1.0 CG A:GLU160 3.9 83.8 1.0 N A:GLY2 3.9 78.9 1.0 O E:HOH103 4.1 64.5 1.0 OE1 A:GLU160 4.1 0.5 1.0 HA2 A:GLY2 4.3 89.8 1.0 OE2 A:GLU158 4.3 0.1 1.0 CB A:ASP179 4.4 69.4 1.0 SM A:SM403 4.4 0.2 0.7 HB2 A:GLU160 4.4 80.3 1.0 HB3 A:ASP179 4.4 83.4 1.0 SM A:SM402 4.5 0.4 0.8 CB A:ASP181 4.5 75.0 1.0 HH A:TYR234 4.6 0.7 1.0 H5' E:DT6 4.6 0.8 1.0 HE2 A:PHE185 4.6 71.2 1.0 HG3 A:GLU160 4.6 0.6 1.0 HB3 A:ASP181 4.7 90.0 1.0 CB A:GLU160 4.7 66.8 1.0 HB2 A:ASP179 4.7 83.4 1.0 CA A:GLY2 4.7 74.7 1.0 O E:HOH106 4.7 0.0 1.0 HB2 A:ASP181 4.7 90.0 1.0 HB3 A:GLU160 4.8 80.3 1.0 CD A:GLU158 4.9 0.1 1.0 OE1 A:GLU158 4.9 90.7 1.0 P E:DT6 4.9 0.2 1.0 CG A:ASP233 5.0 0.1 1.0

Samarium binding site 2 out of 5 in the Flap Endonuclease 1 (FEN1) R100A 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) R100A with 5'-Flap Substrate Dna and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm402 b:0.4 occ:0.81 O A:HOH617 2.1 0.3 1.0 O A:HOH518 2.2 81.8 1.0 OE1 A:GLU158 2.3 90.7 1.0 OE1 A:GLU160 2.3 0.5 1.0 O E:HOH103 2.4 64.5 1.0 OE2 A:GLU160 2.8 0.4 1.0 OD1 A:ASP86 2.8 84.1 1.0 CD A:GLU160 2.9 94.3 1.0 O E:HOH102 3.3 0.9 1.0 CD A:GLU158 3.4 0.1 1.0 CG A:ASP86 3.6 78.2 1.0 OD2 A:ASP86 3.6 89.6 1.0 OE2 A:GLU158 3.7 0.1 1.0 HZ2 A:LYS93 3.9 0.8 1.0 H A:ALA159 4.1 85.3 1.0 OD2 A:ASP34 4.1 74.9 1.0 H A:GLU160 4.1 80.9 1.0 HZ1 A:LYS93 4.1 0.8 1.0 CG A:GLU160 4.4 83.8 1.0 NZ A:LYS93 4.4 0.2 1.0 HB3 A:GLU158 4.4 86.0 1.0 HB3 A:ALA159 4.4 66.1 1.0 HA A:GLU158 4.5 91.0 1.0 SM A:SM401 4.5 97.1 0.9 O A:HOH512 4.6 0.2 1.0 HZ3 A:LYS93 4.6 0.8 1.0 HG3 A:GLU160 4.6 0.6 1.0 CG A:GLU158 4.7 91.4 1.0 OP2 E:DT6 4.7 0.6 1.0 N A:ALA159 4.7 71.0 1.0 HB2 A:GLU160 4.9 80.3 1.0 HG2 A:GLU160 4.9 0.6 1.0 CB A:GLU158 4.9 71.5 1.0 CG A:ASP34 4.9 75.7 1.0 O E:HOH106 4.9 0.0 1.0 OD1 A:ASP34 4.9 73.2 1.0 CB A:ASP86 4.9 68.1 1.0 N A:GLU160 4.9 67.3 1.0 OD2 A:ASP179 5.0 85.0 1.0 HB3 A:ASP86 5.0 81.8 1.0

Samarium binding site 3 out of 5 in the Flap Endonuclease 1 (FEN1) R100A 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) R100A with 5'-Flap Substrate Dna and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm403 b:0.2 occ:0.74 O A:HOH529 2.3 0.8 1.0 O A:HOH584 2.3 1.0 1.0 OD2 A:ASP233 2.3 0.1 1.0 OD1 A:ASP233 2.3 0.1 1.0 O E:HOH106 2.4 0.0 1.0 CG A:ASP233 2.5 0.1 1.0 O E:HOH102 3.4 0.9 1.0 O3' E:DT5 3.4 0.2 1.0 N A:GLY2 3.7 78.9 1.0 HE3 A:LYS93 3.8 0.3 1.0 CB A:ASP233 3.8 87.8 1.0 H5'' E:DT6 3.9 0.8 1.0 HB3 A:ASP233 3.9 0.5 1.0 H3' E:DT5 4.0 0.1 1.0 OP2 E:DT6 4.1 0.6 1.0 HZ1 A:LYS93 4.2 0.8 1.0 HB2 A:ASP233 4.2 0.5 1.0 C3' E:DT5 4.3 0.5 1.0 SM A:SM401 4.4 97.1 0.9 P E:DT6 4.4 0.2 1.0 CE A:LYS93 4.5 98.5 1.0 HE2 A:LYS93 4.5 0.3 1.0 OP1 E:DT5 4.6 0.6 1.0 H5' E:DT6 4.6 0.8 1.0 C5' E:DT6 4.7 0.7 1.0 O A:HOH550 4.7 86.5 1.0 NZ A:LYS93 4.8 0.2 1.0 HA A:ASP233 4.9 93.6 1.0 H2'' E:DT5 4.9 0.0 1.0

Samarium binding site 4 out of 5 in the Flap Endonuclease 1 (FEN1) R100A 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) R100A with 5'-Flap Substrate Dna and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm405 b:66.8 occ:1.00 O A:HOH544 2.2 62.7 1.0 OE2 A:GLU57 2.3 93.6 1.0 OE1 A:GLU313 2.3 63.2 1.0 CD A:GLU57 2.7 75.8 1.0 OE1 A:GLU57 3.0 77.5 1.0 CD A:GLU313 3.1 57.2 1.0 OE2 A:GLU313 3.2 72.7 1.0 HG3 A:GLU57 3.9 85.8 1.0 CG A:GLU57 3.9 71.4 1.0 HA A:GLU313 3.9 73.0 1.0 SM A:SM406 4.1 63.6 1.0 HG2 A:GLU57 4.2 85.8 1.0 O A:HOH515 4.4 62.1 1.0 O A:GLU313 4.5 68.7 1.0 CG A:GLU313 4.6 69.4 1.0 CA A:GLU313 4.8 60.7 1.0 O A:HOH504 4.8 65.0 1.0 HB2 A:GLU313 4.9 64.2 1.0 HD22 A:ASN55 5.0 77.5 1.0

Samarium binding site 5 out of 5 in the Flap Endonuclease 1 (FEN1) R100A 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) R100A with 5'-Flap Substrate Dna and SM3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sm406 b:63.6 occ:1.00 O A:HOH507 2.3 63.8 1.0 OE2 A:GLU59 2.3 56.9 1.0 OE2 A:GLU313 2.3 72.7 1.0 O A:HOH515 2.3 62.1 1.0 O A:HOH548 2.3 67.7 1.0 OE1 A:GLU57 2.4 77.5 1.0 OE1 A:GLU59 2.4 61.1 1.0 CD A:GLU59 2.6 59.2 1.0 CD A:GLU57 3.4 75.8 1.0 CD A:GLU313 3.5 57.2 1.0 HZ2 A:LYS314 3.7 72.7 1.0 OE2 A:GLU57 3.8 93.6 1.0 HD21 A:ASN55 4.0 77.5 1.0 SM A:SM405 4.1 66.8 1.0 OE1 A:GLU313 4.1 63.2 1.0 CG A:GLU59 4.1 57.3 1.0 HB2 A:GLU57 4.4 86.3 1.0 HG3 A:GLU59 4.4 68.9 1.0 HZ3 A:LYS314 4.4 72.7 1.0 NZ A:LYS314 4.5 60.4 1.0 CG A:GLU313 4.5 69.4 1.0 HG2 A:GLU313 4.5 83.4 1.0 HG2 A:GLU59 4.6 68.9 1.0 HG3 A:GLU313 4.6 83.4 1.0 O A:HOH567 4.7 67.3 1.0 CG A:GLU57 4.7 71.4 1.0 HB3 A:GLU57 4.7 86.3 1.0 ND2 A:ASN55 4.7 64.5 1.0 CB A:GLU57 4.8 71.8 1.0 HB2 A:GLU59 4.8 74.8 1.0 HD22 A:ASN55 4.9 77.5 1.0 HZ1 A:LYS314 5.0 72.7 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