Iron in PDB 6q2q: Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine

The structure of Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine, PDB code: 6q2q was solved by M.K.Fenwick, M.Dong, H.Lin, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.30 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.455, 141.265, 143.488, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 18.2

The structure of Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Iron atom in the Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine (pdb code 6q2q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine, PDB code: 6q2q:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:7.4 occ:1.00 FE1 A:SF4401 0.0 7.4 1.0 S2 A:SF4401 2.2 6.8 1.0 S4 A:SF4401 2.3 7.7 1.0 S3 A:SF4401 2.3 7.1 1.0 SG A:CYS84 2.3 8.6 1.0 FE4 A:SF4401 2.6 12.4 1.0 FE3 A:SF4401 2.6 6.9 1.0 FE2 A:SF4401 2.6 8.5 1.0 CB A:CYS84 3.3 6.3 1.0 S1 A:SF4401 3.8 7.4 1.0 N A:SAH402 3.9 12.6 1.0 CB A:TYR86 4.2 7.5 1.0 O A:HOH822 4.3 11.1 1.0 O A:TYR86 4.4 10.0 1.0 N A:TYR86 4.6 10.2 1.0 C A:TYR86 4.6 10.8 1.0 O A:HOH643 4.7 5.1 1.0 SG A:CYS91 4.7 9.1 1.0 ND2 A:ASN158 4.7 8.0 1.0 CA A:CYS84 4.7 7.0 1.0 CA A:TYR86 4.7 10.1 1.0 O A:SAH402 4.7 13.9 1.0 O A:HOH529 4.8 10.9 1.0 SG A:CYS88 4.8 8.7 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:8.5 occ:1.00 FE2 A:SF4401 0.0 8.5 1.0 S1 A:SF4401 2.3 7.4 1.0 S3 A:SF4401 2.3 7.1 1.0 S4 A:SF4401 2.3 7.7 1.0 SG A:CYS88 2.4 8.7 1.0 FE3 A:SF4401 2.6 6.9 1.0 FE1 A:SF4401 2.6 7.4 1.0 FE4 A:SF4401 2.7 12.4 1.0 CB A:CYS88 3.2 7.3 1.0 NH1 A:ARG194 3.7 12.7 1.0 S2 A:SF4401 3.8 6.8 1.0 N A:CYS88 4.0 7.8 1.0 CB A:TYR86 4.2 7.5 1.0 CZ A:ARG194 4.2 17.2 1.0 CA A:CYS88 4.2 7.9 1.0 O A:SAH402 4.3 13.9 1.0 NH2 A:ARG194 4.6 20.0 1.0 CB A:CYS91 4.7 6.9 1.0 SG A:CYS91 4.7 9.1 1.0 SG A:CYS84 4.7 8.6 1.0 NE A:ARG194 4.8 16.2 1.0 CD2 A:TYR86 4.9 11.0 1.0 N A:SAH402 5.0 12.6 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:6.9 occ:1.00 FE3 A:SF4401 0.0 6.9 1.0 S4 A:SF4401 2.2 7.7 1.0 S2 A:SF4401 2.3 6.8 1.0 S1 A:SF4401 2.3 7.4 1.0 SG A:CYS91 2.3 9.1 1.0 FE1 A:SF4401 2.6 7.4 1.0 FE2 A:SF4401 2.6 8.5 1.0 FE4 A:SF4401 2.8 12.4 1.0 CB A:CYS91 3.1 6.9 1.0 S3 A:SF4401 3.9 7.1 1.0 O A:HOH822 3.9 11.1 1.0 CA A:CYS91 4.1 7.1 1.0 O A:HOH584 4.6 6.5 0.5 O A:HIS93 4.6 5.9 1.0 O A:HOH643 4.7 5.1 1.0 CB A:CYS88 4.7 7.3 1.0 SG A:CYS88 4.7 8.7 1.0 SD A:SAH402 4.8 13.8 1.0 SG A:CYS84 4.8 8.6 1.0 N A:SAH402 4.9 12.6 1.0 NH1 A:ARG265 4.9 15.8 0.4 C A:CYS91 5.0 10.6 1.0 CG A:SAH402 5.0 13.3 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.4 occ:1.00 FE4 A:SF4401 0.0 12.4 1.0 S3 A:SF4401 2.3 7.1 1.0 S1 A:SF4401 2.3 7.4 1.0 S2 A:SF4401 2.4 6.8 1.0 O A:SAH402 2.4 13.9 1.0 N A:SAH402 2.5 12.6 1.0 FE1 A:SF4401 2.6 7.4 1.0 FE2 A:SF4401 2.7 8.5 1.0 FE3 A:SF4401 2.8 6.9 1.0 C A:SAH402 3.1 9.4 1.0 CA A:SAH402 3.3 11.4 1.0 CG A:SAH402 3.5 13.3 1.0 SD A:SAH402 3.7 13.8 1.0 S4 A:SF4401 3.9 7.7 1.0 CB A:SAH402 3.9 13.8 1.0 NH1 A:ARG194 4.0 12.7 1.0 OXT A:SAH402 4.4 7.7 1.0 SG A:CYS84 4.4 8.6 1.0 O A:GLY126 4.5 7.1 1.0 C2' A:SAH402 4.9 10.6 1.0 SG A:CYS88 4.9 8.7 1.0 CZ A:ARG194 4.9 17.2 1.0 CB A:ASN158 5.0 7.5 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:7.0 occ:1.00 FE1 B:SF4401 0.0 7.0 1.0 S2 B:SF4401 2.2 5.2 1.0 S4 B:SF4401 2.3 6.2 1.0 S3 B:SF4401 2.3 7.1 1.0 SG B:CYS84 2.3 7.3 1.0 FE4 B:SF4401 2.6 13.2 1.0 FE3 B:SF4401 2.6 8.8 1.0 FE2 B:SF4401 2.7 8.1 1.0 CB B:CYS84 3.3 7.2 1.0 S1 B:SF4401 3.8 6.9 1.0 N B:SAH402 3.8 11.7 1.0 CB B:TYR86 4.2 8.5 1.0 O B:HOH824 4.4 12.2 1.0 O B:TYR86 4.6 9.4 1.0 N B:TYR86 4.7 8.9 1.0 O B:SAH402 4.7 16.0 1.0 C B:TYR86 4.7 11.3 1.0 ND2 B:ASN158 4.7 7.7 1.0 CA B:CYS84 4.7 7.7 1.0 O B:HOH586 4.7 9.6 1.0 SG B:CYS91 4.8 8.7 1.0 CA B:TYR86 4.8 10.8 1.0 O B:HOH571 4.8 11.0 1.0 SG B:CYS88 4.8 10.1 1.0 C B:GLY126 5.0 12.2 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:8.1 occ:1.00 FE2 B:SF4401 0.0 8.1 1.0 S1 B:SF4401 2.2 6.9 1.0 S3 B:SF4401 2.3 7.1 1.0 S4 B:SF4401 2.3 6.2 1.0 SG B:CYS88 2.4 10.1 1.0 FE3 B:SF4401 2.6 8.8 1.0 FE1 B:SF4401 2.7 7.0 1.0 FE4 B:SF4401 2.7 13.2 1.0 CB B:CYS88 3.2 7.5 1.0 NH1 B:ARG194 3.6 10.7 1.0 S2 B:SF4401 3.8 5.2 1.0 N B:CYS88 4.0 8.0 1.0 CA B:CYS88 4.2 8.0 1.0 CB B:TYR86 4.2 8.5 1.0 O B:SAH402 4.3 16.0 1.0 CZ B:ARG194 4.3 11.0 1.0 SG B:CYS84 4.7 7.3 1.0 CB B:CYS91 4.7 11.0 1.0 SG B:CYS91 4.8 8.7 1.0 NE B:ARG194 4.8 15.2 1.0 NH2 B:ARG194 4.8 12.1 1.0 CD B:ARG194 4.9 19.1 1.0 CD2 B:TYR86 4.9 12.6 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:8.8 occ:1.00 FE3 B:SF4401 0.0 8.8 1.0 S4 B:SF4401 2.2 6.2 1.0 S2 B:SF4401 2.3 5.2 1.0 S1 B:SF4401 2.3 6.9 1.0 SG B:CYS91 2.4 8.7 1.0 FE1 B:SF4401 2.6 7.0 1.0 FE2 B:SF4401 2.6 8.1 1.0 FE4 B:SF4401 2.8 13.2 1.0 CB B:CYS91 3.2 11.0 1.0 S3 B:SF4401 3.9 7.1 1.0 O B:HOH824 3.9 12.2 1.0 CA B:CYS91 4.1 6.9 1.0 O B:HOH510 4.6 21.1 1.0 O B:HIS93 4.6 9.8 1.0 CB B:CYS88 4.6 7.5 1.0 O B:HOH586 4.6 9.6 1.0 SG B:CYS88 4.7 10.1 1.0 SD B:SAH402 4.8 11.2 1.0 SG B:CYS84 4.8 7.3 1.0 N B:SAH402 4.9 11.7 1.0 C B:CYS91 5.0 11.4 1.0 O B:SAH402 5.0 16.0 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Mouse Viperin Bound to Uridine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:13.2 occ:1.00 FE4 B:SF4401 0.0 13.2 1.0 S3 B:SF4401 2.3 7.1 1.0 S1 B:SF4401 2.3 6.9 1.0 O B:SAH402 2.3 16.0 1.0 S2 B:SF4401 2.4 5.2 1.0 N B:SAH402 2.5 11.7 1.0 FE1 B:SF4401 2.6 7.0 1.0 FE2 B:SF4401 2.7 8.1 1.0 FE3 B:SF4401 2.8 8.8 1.0 C B:SAH402 3.1 10.5 1.0 CA B:SAH402 3.3 7.8 1.0 SD B:SAH402 3.6 11.2 1.0 CG B:SAH402 3.6 9.9 1.0 NH1 B:ARG194 3.8 10.7 1.0 S4 B:SF4401 3.9 6.2 1.0 CB B:SAH402 4.0 8.8 1.0 OXT B:SAH402 4.4 10.8 1.0 SG B:CYS84 4.5 7.3 1.0 O B:GLY126 4.5 7.6 1.0 C2' B:SAH402 4.8 7.2 1.0 SG B:CYS88 4.9 10.1 1.0

M.K.Fenwick, D.Su, M.Dong, H.Lin, S.E.Ealick. Structural Basis of Substrate Selectivity of Viperin. Biochemistry 2020.
ISSN: ISSN 0006-2960
PubMed: 31917549
DOI: 10.1021/ACS.BIOCHEM.9B00741