Iron in PDB 6q2p: Crystal Structure of Mouse Viperin Bound to Cytidine Triphosphate and S-Adenosylhomocysteine

The structure of Crystal Structure of Mouse Viperin Bound to Cytidine Triphosphate and S-Adenosylhomocysteine, PDB code: 6q2p 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)	39.77 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.483, 142.588, 143.732, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 16

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

Chlorine

(Cl)

3 atoms

The binding sites of Iron atom in the Crystal Structure of Mouse Viperin Bound to Cytidine Triphosphate and S-Adenosylhomocysteine (pdb code 6q2p). 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 Cytidine Triphosphate and S-Adenosylhomocysteine, PDB code: 6q2p:
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 Cytidine 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 Cytidine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:6.2 occ:1.00 FE1 A:SF4401 0.0 6.2 1.0 S4 A:SF4401 2.2 6.5 1.0 S2 A:SF4401 2.3 5.7 1.0 SG A:CYS84 2.3 5.8 1.0 S3 A:SF4401 2.3 6.6 1.0 FE3 A:SF4401 2.7 6.2 1.0 FE4 A:SF4401 2.7 7.7 1.0 FE2 A:SF4401 2.7 6.4 1.0 CB A:CYS84 3.3 7.1 1.0 N A:SAH402 3.8 6.8 1.0 S1 A:SF4401 3.8 6.6 1.0 CB A:TYR86 4.1 5.9 1.0 O A:HOH914 4.3 6.5 1.0 O A:TYR86 4.5 8.2 1.0 ND2 A:ASN158 4.6 7.1 1.0 N A:TYR86 4.6 7.6 1.0 CA A:CYS84 4.7 6.5 1.0 C A:TYR86 4.7 8.5 1.0 SG A:CYS91 4.7 6.1 1.0 O A:HOH623 4.7 5.2 1.0 O A:SAH402 4.7 6.8 1.0 CA A:TYR86 4.7 5.9 1.0 O A:HOH581 4.8 8.4 1.0 SG A:CYS88 4.8 7.0 1.0 C A:GLY126 5.0 5.9 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Mouse Viperin Bound to Cytidine 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 Cytidine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:6.4 occ:1.00 FE2 A:SF4401 0.0 6.4 1.0 S3 A:SF4401 2.2 6.6 1.0 S1 A:SF4401 2.3 6.6 1.0 S4 A:SF4401 2.3 6.5 1.0 SG A:CYS88 2.3 7.0 1.0 FE1 A:SF4401 2.7 6.2 1.0 FE3 A:SF4401 2.7 6.2 1.0 FE4 A:SF4401 2.8 7.7 1.0 CB A:CYS88 3.2 7.1 1.0 NH1 A:ARG194 3.6 9.0 1.0 S2 A:SF4401 3.9 5.7 1.0 N A:CYS88 4.0 6.6 1.0 CZ A:ARG194 4.1 9.5 1.0 O A:SAH402 4.1 6.8 1.0 CB A:TYR86 4.2 5.9 1.0 CA A:CYS88 4.2 8.5 1.0 NH2 A:ARG194 4.6 10.1 1.0 NE A:ARG194 4.7 11.3 1.0 SG A:CYS84 4.7 5.8 1.0 SG A:CYS91 4.8 6.1 1.0 CB A:CYS91 4.8 4.3 1.0 CD2 A:TYR86 4.9 7.5 1.0 N A:SAH402 4.9 6.8 1.0 CD A:ARG194 4.9 16.7 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Mouse Viperin Bound to Cytidine 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 Cytidine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:6.2 occ:1.00 FE3 A:SF4401 0.0 6.2 1.0 S2 A:SF4401 2.2 5.7 1.0 S1 A:SF4401 2.3 6.6 1.0 S4 A:SF4401 2.3 6.5 1.0 SG A:CYS91 2.3 6.1 1.0 FE1 A:SF4401 2.7 6.2 1.0 FE2 A:SF4401 2.7 6.4 1.0 FE4 A:SF4401 2.9 7.7 1.0 CB A:CYS91 3.2 4.3 1.0 O A:HOH914 3.9 6.5 1.0 S3 A:SF4401 3.9 6.6 1.0 CA A:CYS91 4.1 6.7 1.0 O A:HOH516 4.5 13.3 1.0 O A:HIS93 4.6 5.1 1.0 CB A:CYS88 4.7 7.1 1.0 O A:HOH623 4.7 5.2 1.0 SG A:CYS88 4.7 7.0 1.0 N A:SAH402 4.8 6.8 1.0 SD A:SAH402 4.8 7.7 1.0 SG A:CYS84 4.8 5.8 1.0 O A:SAH402 4.9 6.8 1.0 C8 A:SAH402 5.0 5.2 1.0 C A:CYS91 5.0 5.3 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Mouse Viperin Bound to Cytidine 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 Cytidine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:7.7 occ:1.00 FE4 A:SF4401 0.0 7.7 1.0 O A:SAH402 2.2 6.8 1.0 N A:SAH402 2.3 6.8 1.0 S3 A:SF4401 2.3 6.6 1.0 S1 A:SF4401 2.4 6.6 1.0 S2 A:SF4401 2.4 5.7 1.0 FE1 A:SF4401 2.7 6.2 1.0 FE2 A:SF4401 2.8 6.4 1.0 FE3 A:SF4401 2.9 6.2 1.0 C A:SAH402 2.9 7.2 1.0 CA A:SAH402 3.1 5.7 1.0 SD A:SAH402 3.6 7.7 1.0 CG A:SAH402 3.6 7.3 1.0 CB A:SAH402 3.9 7.0 1.0 S4 A:SF4401 4.0 6.5 1.0 NH1 A:ARG194 4.0 9.0 1.0 OXT A:SAH402 4.2 7.5 1.0 SG A:CYS84 4.5 5.8 1.0 O A:GLY126 4.6 5.6 1.0 C2' A:SAH402 4.8 5.5 1.0 SG A:CYS88 4.9 7.0 1.0 CZ A:ARG194 5.0 9.5 1.0 CB A:ASN158 5.0 6.4 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Mouse Viperin Bound to Cytidine 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 Cytidine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:6.4 occ:1.00 FE1 B:SF4402 0.0 6.4 1.0 S4 B:SF4402 2.2 6.9 1.0 S2 B:SF4402 2.3 6.6 1.0 SG B:CYS84 2.3 6.4 1.0 S3 B:SF4402 2.3 6.6 1.0 FE3 B:SF4402 2.7 6.7 1.0 FE2 B:SF4402 2.7 6.8 1.0 FE4 B:SF4402 2.7 7.7 1.0 CB B:CYS84 3.3 7.1 1.0 N B:SAH403 3.8 7.0 1.0 S1 B:SF4402 3.8 7.5 1.0 CB B:TYR86 4.1 7.4 1.0 O B:HOH911 4.3 7.4 1.0 O B:TYR86 4.6 9.4 1.0 ND2 B:ASN158 4.6 6.9 1.0 CA B:CYS84 4.7 7.2 1.0 N B:TYR86 4.7 6.6 1.0 C B:TYR86 4.7 9.2 1.0 O B:HOH656 4.7 7.5 1.0 SG B:CYS91 4.7 7.0 1.0 CA B:TYR86 4.7 6.1 1.0 O B:SAH403 4.7 8.6 1.0 O B:HOH565 4.8 7.9 1.0 SG B:CYS88 4.8 7.6 1.0 C B:GLY126 5.0 6.4 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Mouse Viperin Bound to Cytidine 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 Cytidine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:6.8 occ:1.00 FE2 B:SF4402 0.0 6.8 1.0 S3 B:SF4402 2.2 6.6 1.0 S1 B:SF4402 2.3 7.5 1.0 S4 B:SF4402 2.3 6.9 1.0 SG B:CYS88 2.3 7.6 1.0 FE1 B:SF4402 2.7 6.4 1.0 FE3 B:SF4402 2.7 6.7 1.0 FE4 B:SF4402 2.8 7.7 1.0 CB B:CYS88 3.1 8.2 1.0 NH1 B:ARG194 3.5 10.3 1.0 S2 B:SF4402 3.9 6.6 1.0 N B:CYS88 4.0 7.0 1.0 CZ B:ARG194 4.2 8.5 1.0 O B:SAH403 4.2 8.6 1.0 CB B:TYR86 4.2 7.4 1.0 CA B:CYS88 4.2 6.4 1.0 NE B:ARG194 4.7 10.0 1.0 SG B:CYS84 4.7 6.4 1.0 NH2 B:ARG194 4.7 10.7 1.0 CD B:ARG194 4.8 15.6 1.0 SG B:CYS91 4.8 7.0 1.0 CB B:CYS91 4.8 5.9 1.0 CD2 B:TYR86 4.8 7.5 1.0 N B:SAH403 4.9 7.0 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Mouse Viperin Bound to Cytidine 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 Cytidine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:6.7 occ:1.00 FE3 B:SF4402 0.0 6.7 1.0 S2 B:SF4402 2.2 6.6 1.0 S1 B:SF4402 2.3 7.5 1.0 S4 B:SF4402 2.3 6.9 1.0 SG B:CYS91 2.3 7.0 1.0 FE1 B:SF4402 2.7 6.4 1.0 FE2 B:SF4402 2.7 6.8 1.0 FE4 B:SF4402 2.9 7.7 1.0 CB B:CYS91 3.2 5.9 1.0 O B:HOH911 3.9 7.4 1.0 S3 B:SF4402 3.9 6.6 1.0 CA B:CYS91 4.1 5.5 1.0 O B:HIS93 4.6 7.2 1.0 O B:HOH510 4.6 15.8 1.0 CB B:CYS88 4.6 8.2 1.0 O B:HOH656 4.7 7.5 1.0 SG B:CYS88 4.7 7.6 1.0 N B:SAH403 4.8 7.0 1.0 SD B:SAH403 4.8 8.2 1.0 SG B:CYS84 4.8 6.4 1.0 O B:SAH403 4.9 8.6 1.0 C B:CYS91 5.0 5.5 1.0 C8 B:SAH403 5.0 6.2 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Mouse Viperin Bound to Cytidine 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 Cytidine Triphosphate and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:7.7 occ:1.00 FE4 B:SF4402 0.0 7.7 1.0 O B:SAH403 2.2 8.6 1.0 N B:SAH403 2.3 7.0 1.0 S3 B:SF4402 2.4 6.6 1.0 S1 B:SF4402 2.4 7.5 1.0 S2 B:SF4402 2.4 6.6 1.0 FE1 B:SF4402 2.7 6.4 1.0 FE2 B:SF4402 2.8 6.8 1.0 FE3 B:SF4402 2.9 6.7 1.0 C B:SAH403 3.0 9.4 1.0 CA B:SAH403 3.1 6.5 1.0 SD B:SAH403 3.6 8.2 1.0 CG B:SAH403 3.6 7.2 1.0 NH1 B:ARG194 3.8 10.3 1.0 CB B:SAH403 3.9 8.4 1.0 S4 B:SF4402 4.0 6.9 1.0 OXT B:SAH403 4.2 7.9 1.0 SG B:CYS84 4.5 6.4 1.0 O B:GLY126 4.6 6.5 1.0 C2' B:SAH403 4.8 6.8 1.0 SG B:CYS88 5.0 7.6 1.0 CZ B:ARG194 5.0 8.5 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