Iron in PDB 9dfw: X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam

The structure of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam, PDB code: 9dfw 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)	19.86 / 1.68
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	85.131, 85.131, 110.471, 90, 90, 120
R / Rfree (%)	15.5 / 18.8

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

Magnesium

(Mg)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam (pdb code 9dfw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam, PDB code: 9dfw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens 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 An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:20.6 occ:1.00 FE1 A:SF4401 0.0 20.6 1.0 S2 A:SF4401 2.3 19.4 1.0 SG A:CYS39 2.3 18.5 1.0 S4 A:SF4401 2.3 20.6 1.0 S3 A:SF4401 2.4 20.0 1.0 FE4 A:SF4401 2.7 19.6 1.0 FE2 A:SF4401 2.7 19.0 1.0 FE3 A:SF4401 2.9 21.0 1.0 CB A:CYS39 3.2 17.7 1.0 O A:HOH716 3.8 19.5 1.0 S1 A:SF4401 3.9 19.3 1.0 CE A:SAM402 4.0 30.7 1.0 CA A:CYS39 4.1 16.2 1.0 SD A:SAM402 4.6 27.5 1.0 CB A:CYS36 4.6 21.5 1.0 O A:HOH528 4.7 20.2 1.0 SG A:CYS36 4.7 20.4 1.0 O A:HIS41 4.7 18.0 1.0 OXT A:SAM402 4.8 20.6 1.0 N A:SAM402 4.8 20.8 1.0 SG A:CYS32 4.9 22.9 1.0

Iron binding site 2 out of 12 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens 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 An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:19.0 occ:1.00 FE2 A:SF4401 0.0 19.0 1.0 S1 A:SF4401 2.2 19.3 1.0 SG A:CYS36 2.3 20.4 1.0 S3 A:SF4401 2.3 20.0 1.0 S4 A:SF4401 2.3 20.6 1.0 FE4 A:SF4401 2.7 19.6 1.0 FE1 A:SF4401 2.7 20.6 1.0 FE3 A:SF4401 2.8 21.0 1.0 CB A:CYS36 3.1 21.5 1.0 NH1 A:ARG140 3.7 24.9 1.0 S2 A:SF4401 3.9 19.4 1.0 N A:CYS36 4.1 20.2 1.0 OXT A:SAM402 4.1 20.6 1.0 CA A:CYS36 4.2 20.8 1.0 CZ A:ARG140 4.3 26.2 1.0 CB A:LYS34 4.4 28.5 0.5 CB A:LYS34 4.5 25.9 0.5 NH2 A:ARG140 4.6 28.1 1.0 SG A:CYS32 4.7 22.9 1.0 SG A:CYS39 4.7 18.5 1.0 CB A:CYS39 4.8 17.7 1.0 N A:SAM402 5.0 20.8 1.0 CG A:ARG140 5.0 35.9 1.0

Iron binding site 3 out of 12 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens 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 An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.0 occ:1.00 FE3 A:SF4401 0.0 21.0 1.0 OXT A:SAM402 2.1 20.6 1.0 S4 A:SF4401 2.3 20.6 1.0 S1 A:SF4401 2.3 19.3 1.0 N A:SAM402 2.4 20.8 1.0 S2 A:SF4401 2.4 19.4 1.0 FE4 A:SF4401 2.7 19.6 1.0 FE2 A:SF4401 2.8 19.0 1.0 FE1 A:SF4401 2.9 20.6 1.0 C A:SAM402 3.0 21.1 1.0 CA A:SAM402 3.2 20.8 1.0 SD A:SAM402 3.4 27.5 1.0 CG A:SAM402 3.8 24.4 1.0 NH1 A:ARG140 3.9 24.9 1.0 CE A:SAM402 4.0 30.7 1.0 CB A:SAM402 4.0 22.0 1.0 S3 A:SF4401 4.0 20.0 1.0 O A:SAM402 4.2 22.4 1.0 SG A:CYS32 4.5 22.9 1.0 O A:GLY74 4.7 20.2 1.0 SG A:CYS36 4.9 20.4 1.0 C2' A:SAM402 4.9 21.2 1.0 CB A:ASN104 5.0 22.2 1.0 CZ A:ARG140 5.0 26.2 1.0

Iron binding site 4 out of 12 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens 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 An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:19.6 occ:1.00 FE4 A:SF4401 0.0 19.6 1.0 S3 A:SF4401 2.3 20.0 1.0 SG A:CYS32 2.3 22.9 1.0 S2 A:SF4401 2.3 19.4 1.0 S1 A:SF4401 2.3 19.3 1.0 FE2 A:SF4401 2.7 19.0 1.0 FE1 A:SF4401 2.7 20.6 1.0 FE3 A:SF4401 2.7 21.0 1.0 CB A:CYS32 3.3 21.3 1.0 S4 A:SF4401 3.8 20.6 1.0 N A:SAM402 3.9 20.8 1.0 O A:HOH716 4.1 19.5 1.0 CB A:LYS34 4.3 28.5 0.5 CB A:LYS34 4.4 25.9 0.5 O A:HOH534 4.4 24.8 1.0 O A:LYS34 4.5 25.1 0.5 O A:LYS34 4.6 25.7 0.5 SG A:CYS39 4.7 18.5 1.0 CA A:CYS32 4.7 21.6 1.0 N A:LYS34 4.7 28.3 0.5 C A:LYS34 4.7 24.9 0.5 OXT A:SAM402 4.7 20.6 1.0 N A:LYS34 4.7 27.1 0.5 ND2 A:ASN104 4.7 22.2 1.0 C A:LYS34 4.7 25.7 0.5 SG A:CYS36 4.8 20.4 1.0 O A:HOH528 4.8 20.2 1.0 CA A:LYS34 4.8 26.6 0.5 CA A:LYS34 4.8 25.1 0.5

Iron binding site 5 out of 12 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens 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 5 of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:19.3 occ:1.00 FE1 B:SF4401 0.0 19.3 1.0 S2 B:SF4401 2.2 20.6 1.0 SG B:CYS36 2.3 21.4 1.0 S4 B:SF4401 2.3 20.6 1.0 S3 B:SF4401 2.3 20.8 1.0 FE3 B:SF4401 2.7 20.4 1.0 FE2 B:SF4401 2.8 22.3 1.0 FE4 B:SF4401 2.8 21.1 1.0 CB B:CYS36 3.2 21.2 1.0 NH1 B:ARG140 3.7 28.0 1.0 S1 B:SF4401 3.9 20.2 1.0 N B:CYS36 4.1 21.7 1.0 CZ B:ARG140 4.1 27.0 1.0 O B:SAM402 4.1 21.0 1.0 CA B:CYS36 4.2 21.1 1.0 NH2 B:ARG140 4.4 26.8 1.0 CB B:LYS34 4.5 22.1 1.0 SG B:CYS32 4.6 21.6 1.0 NE B:ARG140 4.7 26.6 1.0 SG B:CYS39 4.8 21.1 1.0 CB B:CYS39 4.8 20.9 1.0 N B:SAM402 4.8 24.5 1.0

Iron binding site 6 out of 12 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens 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 6 of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:22.3 occ:1.00 FE2 B:SF4401 0.0 22.3 1.0 S1 B:SF4401 2.2 20.2 1.0 SG B:CYS39 2.3 21.1 1.0 S4 B:SF4401 2.3 20.6 1.0 S3 B:SF4401 2.3 20.8 1.0 FE3 B:SF4401 2.7 20.4 1.0 FE1 B:SF4401 2.8 19.3 1.0 FE4 B:SF4401 2.9 21.1 1.0 CB B:CYS39 3.2 20.9 1.0 O B:HOH719 3.8 25.3 1.0 CE B:SAM402 3.9 40.7 1.0 S2 B:SF4401 3.9 20.6 1.0 CA B:CYS39 4.1 19.4 1.0 O B:HOH550 4.5 24.4 1.0 SD B:SAM402 4.6 30.8 1.0 N B:SAM402 4.7 24.5 1.0 O B:HIS41 4.7 24.2 1.0 SG B:CYS36 4.7 21.4 1.0 CB B:CYS36 4.8 21.2 1.0 SG B:CYS32 4.8 21.6 1.0 O B:SAM402 4.9 21.0 1.0 NH1 B:ARG209 5.0 24.6 1.0

Iron binding site 7 out of 12 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens 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 7 of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:20.4 occ:1.00 FE3 B:SF4401 0.0 20.4 1.0 S4 B:SF4401 2.2 20.6 1.0 SG B:CYS32 2.2 21.6 1.0 S1 B:SF4401 2.3 20.2 1.0 S2 B:SF4401 2.3 20.6 1.0 FE2 B:SF4401 2.7 22.3 1.0 FE4 B:SF4401 2.7 21.1 1.0 FE1 B:SF4401 2.7 19.3 1.0 CB B:CYS32 3.3 19.8 1.0 N B:SAM402 3.8 24.5 1.0 S3 B:SF4401 3.8 20.8 1.0 O B:HOH719 4.1 25.3 1.0 O B:HOH569 4.3 25.5 1.0 CB B:LYS34 4.4 22.1 1.0 O B:LYS34 4.6 23.4 1.0 CA B:CYS32 4.6 18.8 1.0 SG B:CYS39 4.7 21.1 1.0 C B:LYS34 4.7 22.5 1.0 ND2 B:ASN104 4.7 18.3 1.0 O B:HOH550 4.7 24.4 1.0 N B:LYS34 4.7 22.8 1.0 O B:SAM402 4.7 21.0 1.0 SG B:CYS36 4.8 21.4 1.0 CA B:LYS34 4.8 21.8 1.0

Iron binding site 8 out of 12 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens 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 8 of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:21.1 occ:1.00 FE4 B:SF4401 0.0 21.1 1.0 N B:SAM402 2.3 24.5 1.0 O B:SAM402 2.3 21.0 1.0 S3 B:SF4401 2.3 20.8 1.0 S2 B:SF4401 2.3 20.6 1.0 S1 B:SF4401 2.4 20.2 1.0 FE3 B:SF4401 2.7 20.4 1.0 FE1 B:SF4401 2.8 19.3 1.0 FE2 B:SF4401 2.9 22.3 1.0 C B:SAM402 3.0 24.1 1.0 CA B:SAM402 3.1 23.0 1.0 SD B:SAM402 3.3 30.8 1.0 CG B:SAM402 3.8 27.8 1.0 CE B:SAM402 3.9 40.7 1.0 S4 B:SF4401 3.9 20.6 1.0 CB B:SAM402 4.0 24.6 1.0 NH1 B:ARG140 4.2 28.0 1.0 OXT B:SAM402 4.2 22.2 1.0 SG B:CYS32 4.5 21.6 1.0 O B:GLY74 4.7 21.9 1.0 SG B:CYS36 4.9 21.4 1.0 CZ B:ARG140 4.9 27.0 1.0 C2' B:SAM402 4.9 26.4 1.0

Iron binding site 9 out of 12 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens 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 9 of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:20.8 occ:1.00 FE1 C:SF4401 0.0 20.8 1.0 S2 C:SF4401 2.2 20.8 1.0 SG C:CYS32 2.3 23.9 1.0 S4 C:SF4401 2.3 20.2 1.0 S3 C:SF4401 2.3 22.8 1.0 FE4 C:SF4401 2.7 21.5 1.0 FE2 C:SF4401 2.7 22.9 1.0 FE3 C:SF4401 2.7 22.7 1.0 CB C:CYS32 3.3 20.9 1.0 S1 C:SF4401 3.8 22.7 1.0 N C:SAM402 3.9 22.4 1.0 O C:HOH692 4.1 23.8 1.0 O C:HOH588 4.3 25.8 1.0 CB C:LYS34 4.4 29.4 1.0 O C:LYS34 4.6 27.6 1.0 N C:LYS34 4.7 26.9 1.0 O C:SAM402 4.7 22.5 1.0 ND2 C:ASN104 4.7 25.2 1.0 CA C:CYS32 4.7 22.5 1.0 SG C:CYS39 4.7 21.3 1.0 SG C:CYS36 4.7 25.2 1.0 C C:LYS34 4.7 24.0 1.0 CA C:LYS34 4.8 27.0 1.0 O C:HOH522 4.8 22.0 1.0

Iron binding site 10 out of 12 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens 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 10 of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:22.9 occ:1.00 FE2 C:SF4401 0.0 22.9 1.0 S1 C:SF4401 2.2 22.7 1.0 S4 C:SF4401 2.3 20.2 1.0 SG C:CYS39 2.3 21.3 1.0 S3 C:SF4401 2.3 22.8 1.0 FE1 C:SF4401 2.7 20.8 1.0 FE4 C:SF4401 2.7 21.5 1.0 FE3 C:SF4401 2.9 22.7 1.0 CB C:CYS39 3.2 20.9 1.0 O C:HOH692 3.8 23.8 1.0 S2 C:SF4401 3.9 20.8 1.0 CE C:SAM402 3.9 33.5 1.0 CA C:CYS39 4.1 21.3 1.0 SD C:SAM402 4.5 31.3 1.0 O C:HIS41 4.6 22.1 1.0 O C:HOH522 4.7 22.0 1.0 SG C:CYS36 4.7 25.2 1.0 CB C:CYS36 4.8 26.1 1.0 O C:SAM402 4.8 22.5 1.0 N C:SAM402 4.9 22.4 1.0 SG C:CYS32 4.9 23.9 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.