Iron in PDB 9dfu: X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam

The structure of X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam, PDB code: 9dfu was solved by J.C.Lachowicz, J.B.Bonanno, T.L.Grove, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.66 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.137, 55.959, 152.81, 90, 90, 90
R / Rfree (%)	22.6 / 26

The structure of X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam (pdb code 9dfu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam, PDB code: 9dfu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:17.2 occ:1.00 FE1 A:SF4402 0.0 17.2 1.0 SG A:CYS49 2.0 15.7 1.0 S3 A:SF4402 2.1 23.3 1.0 S2 A:SF4402 2.1 18.1 1.0 S4 A:SF4402 2.1 24.3 1.0 FE4 A:SF4402 3.0 19.3 1.0 FE2 A:SF4402 3.0 18.2 1.0 FE3 A:SF4402 3.1 18.3 1.0 CB A:CYS49 3.2 14.9 1.0 NH1 A:ARG153 3.7 19.1 1.0 S1 A:SF4402 3.7 19.6 1.0 N A:CYS49 3.9 18.7 1.0 CZ A:ARG153 4.2 17.8 1.0 CA A:CYS49 4.2 15.2 1.0 NH2 A:ARG153 4.4 20.3 1.0 CB A:LYS47 4.6 17.4 1.0 CG A:ARG153 4.7 22.7 1.0 OXT A:SAM403 4.7 15.0 1.0 SG A:CYS45 4.7 19.0 1.0 SG A:CYS52 4.9 14.6 1.0 NE A:ARG153 5.0 18.6 1.0

Iron binding site 2 out of 4 in the X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:18.2 occ:1.00 FE2 A:SF4402 0.0 18.2 1.0 S4 A:SF4402 2.1 24.3 1.0 S3 A:SF4402 2.1 23.3 1.0 S1 A:SF4402 2.1 19.6 1.0 N A:SAM403 2.6 15.6 1.0 OXT A:SAM403 2.7 15.0 1.0 CG A:SAM403 3.0 20.0 1.0 FE4 A:SF4402 3.0 19.3 1.0 FE1 A:SF4402 3.0 17.2 1.0 SD A:SAM403 3.1 23.5 1.0 FE3 A:SF4402 3.1 18.3 1.0 CA A:SAM403 3.3 17.3 1.0 C A:SAM403 3.4 14.3 1.0 CB A:SAM403 3.7 15.4 1.0 S2 A:SF4402 3.7 18.1 1.0 CE A:SAM403 3.7 21.2 1.0 NH1 A:ARG153 4.1 19.1 1.0 O A:GLY87 4.3 18.2 1.0 O A:SAM403 4.5 19.0 1.0 C5' A:SAM403 4.6 20.8 1.0 SG A:CYS45 4.6 19.0 1.0 C2' A:SAM403 4.8 14.5 1.0 C3' A:SAM403 4.8 18.8 1.0 SG A:CYS49 4.9 15.7 1.0 C A:GLY87 4.9 18.0 1.0 OE1 A:GLU88 5.0 13.9 1.0

Iron binding site 3 out of 4 in the X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:18.3 occ:1.00 FE3 A:SF4402 0.0 18.3 1.0 SG A:CYS52 2.1 14.6 1.0 S4 A:SF4402 2.1 24.3 1.0 S2 A:SF4402 2.1 18.1 1.0 S1 A:SF4402 2.1 19.6 1.0 FE4 A:SF4402 3.0 19.3 1.0 FE1 A:SF4402 3.1 17.2 1.0 FE2 A:SF4402 3.1 18.2 1.0 CB A:CYS52 3.2 15.0 1.0 O A:HOH582 3.6 15.5 1.0 S3 A:SF4402 3.8 23.3 1.0 CE A:SAM403 3.9 21.2 1.0 CA A:CYS52 4.2 18.2 1.0 O A:HIS54 4.5 18.8 1.0 SD A:SAM403 4.5 23.5 1.0 SG A:CYS49 4.7 15.7 1.0 CG A:SAM403 4.8 20.0 1.0 C8 A:SAM403 4.8 13.7 1.0

Iron binding site 4 out of 4 in the X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Crystal Structure of the Second Viperin-Like Enzyme From T. Virens Variant F40H with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:19.3 occ:1.00 FE4 A:SF4402 0.0 19.3 1.0 SG A:CYS45 2.1 19.0 1.0 S1 A:SF4402 2.1 19.6 1.0 S3 A:SF4402 2.1 23.3 1.0 S2 A:SF4402 2.1 18.1 1.0 FE2 A:SF4402 3.0 18.2 1.0 FE1 A:SF4402 3.0 17.2 1.0 FE3 A:SF4402 3.0 18.3 1.0 CB A:CYS45 3.1 15.6 1.0 S4 A:SF4402 3.6 24.3 1.0 O A:HOH582 4.2 15.5 1.0 O A:LYS47 4.3 18.2 1.0 N A:SAM403 4.3 15.6 1.0 O A:HOH543 4.3 19.9 1.0 CB A:LYS47 4.5 17.4 1.0 CA A:CYS45 4.5 17.1 1.0 C A:LYS47 4.6 19.0 1.0 ND2 A:ASN117 4.6 12.8 1.0 N A:LYS47 4.7 22.2 1.0 C A:GLY87 4.7 18.0 1.0 SG A:CYS49 4.8 15.7 1.0 CA A:LYS47 4.8 21.3 1.0 O A:GLY87 4.8 18.2 1.0 SG A:CYS52 4.9 14.6 1.0 CA A:GLY87 4.9 18.3 1.0

J.C.Lachowicz, S.Grudman, J.B.Bonanno, A.Fiser, T.L.Grove. Structural Insights From Active Site Variants and B-8 Loop Interactions in Viperin-Like Enzymes To Be Published.