Iron in PDB 5vsm: Crystal Structure of Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine

The structure of Crystal Structure of Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine, PDB code: 5vsm was solved by M.K.Fenwick, Y.Li, P.Cresswell, Y.Modis, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.364, 73.264, 141.939, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.5

The binding sites of Iron atom in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine (pdb code 5vsm). 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 Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine, PDB code: 5vsm:
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 Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine


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 Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:23.3 occ:1.00 FE1 A:SF4401 0.0 23.3 1.0 S2 A:SF4401 2.2 23.6 1.0 S4 A:SF4401 2.2 22.0 1.0 S3 A:SF4401 2.3 21.4 1.0 SG A:CYS84 2.4 24.7 1.0 FE3 A:SF4401 2.6 23.5 1.0 FE2 A:SF4401 2.6 21.7 1.0 FE4 A:SF4401 2.8 24.2 1.0 CB A:CYS84 3.3 24.0 1.0 S1 A:SF4401 3.8 23.6 1.0 N A:MET403 3.8 22.5 1.0 CB A:TYR86 4.0 25.6 1.0 O A:HOH729 4.3 27.4 1.0 ND2 A:ASN158 4.6 20.2 1.0 O A:TYR86 4.6 25.3 1.0 O A:HOH532 4.6 26.9 1.0 N A:TYR86 4.6 22.4 1.0 CA A:TYR86 4.7 22.9 1.0 C A:TYR86 4.7 24.8 1.0 CA A:CYS84 4.7 28.3 1.0 O A:MET403 4.7 25.4 1.0 SG A:CYS91 4.8 23.8 1.0 O A:HOH548 4.8 27.6 1.0 SG A:CYS88 4.8 22.9 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine


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 Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.7 occ:1.00 FE2 A:SF4401 0.0 21.7 1.0 S1 A:SF4401 2.2 23.6 1.0 S3 A:SF4401 2.2 21.4 1.0 S4 A:SF4401 2.3 22.0 1.0 SG A:CYS88 2.4 22.9 1.0 FE1 A:SF4401 2.6 23.3 1.0 FE3 A:SF4401 2.7 23.5 1.0 FE4 A:SF4401 2.9 24.2 1.0 CB A:CYS88 3.1 22.6 1.0 NH1 A:ARG194 3.6 24.2 1.0 S2 A:SF4401 3.9 23.6 1.0 N A:CYS88 4.0 23.2 1.0 CB A:TYR86 4.1 25.6 1.0 O A:MET403 4.2 25.4 1.0 CA A:CYS88 4.2 23.5 1.0 CZ A:ARG194 4.3 26.0 1.0 CB A:CYS91 4.7 26.8 1.0 CD2 A:TYR86 4.7 24.3 1.0 SG A:CYS84 4.7 24.7 1.0 SG A:CYS91 4.8 23.8 1.0 NE A:ARG194 4.8 27.5 1.0 CD A:ARG194 4.9 26.1 1.0 NH2 A:ARG194 4.9 24.6 1.0 N A:MET403 4.9 22.5 1.0 CG A:TYR86 4.9 25.9 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine


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 Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:23.5 occ:1.00 FE3 A:SF4401 0.0 23.5 1.0 S1 A:SF4401 2.2 23.6 1.0 S2 A:SF4401 2.2 23.6 1.0 S4 A:SF4401 2.3 22.0 1.0 SG A:CYS91 2.4 23.8 1.0 FE1 A:SF4401 2.6 23.3 1.0 FE2 A:SF4401 2.7 21.7 1.0 FE4 A:SF4401 2.8 24.2 1.0 CB A:CYS91 3.1 26.8 1.0 O A:HOH729 3.7 27.4 1.0 CE A:MET403 3.8 24.2 1.0 S3 A:SF4401 3.9 21.4 1.0 CA A:CYS91 4.1 24.0 1.0 SD A:MET403 4.2 29.1 1.0 O A:HOH548 4.5 27.6 1.0 O A:HIS93 4.6 27.3 1.0 CB A:CYS88 4.6 22.6 1.0 SG A:CYS88 4.7 22.9 1.0 N A:MET403 4.8 22.5 1.0 SG A:CYS84 4.9 24.7 1.0 O A:MET403 4.9 25.4 1.0 C A:CYS91 4.9 28.8 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine


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 Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:24.2 occ:1.00 FE4 A:SF4401 0.0 24.2 1.0 O A:MET403 2.3 25.4 1.0 N A:MET403 2.4 22.5 1.0 S2 A:SF4401 2.4 23.6 1.0 S1 A:SF4401 2.4 23.6 1.0 S3 A:SF4401 2.4 21.4 1.0 SD A:MET403 2.7 29.1 1.0 FE1 A:SF4401 2.8 23.3 1.0 FE3 A:SF4401 2.8 23.5 1.0 FE2 A:SF4401 2.9 21.7 1.0 C A:MET403 3.0 26.7 1.0 CA A:MET403 3.1 23.9 1.0 CG A:MET403 3.5 29.1 1.0 CE A:MET403 3.7 24.2 1.0 CB A:MET403 3.8 25.2 1.0 NH1 A:ARG194 3.9 24.2 1.0 S4 A:SF4401 4.1 22.0 1.0 OXT A:MET403 4.3 23.7 1.0 O A:GLY126 4.6 25.6 1.0 SG A:CYS84 4.7 24.7 1.0 C2' A:5AD402 4.8 26.9 1.0 SG A:CYS91 5.0 23.8 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine


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 Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:23.3 occ:1.00 FE1 B:SF4401 0.0 23.3 1.0 S2 B:SF4401 2.2 22.4 1.0 S4 B:SF4401 2.3 21.8 1.0 S3 B:SF4401 2.3 21.0 1.0 SG B:CYS84 2.4 27.2 1.0 FE3 B:SF4401 2.6 24.9 1.0 FE2 B:SF4401 2.6 22.8 1.0 FE4 B:SF4401 2.7 24.0 1.0 CB B:CYS84 3.3 28.8 1.0 S1 B:SF4401 3.7 23.5 1.0 N B:MET403 3.8 23.2 1.0 CB B:TYR86 4.0 23.6 1.0 O B:HOH737 4.3 28.4 1.0 O B:HOH558 4.5 29.3 1.0 O B:TYR86 4.6 28.6 1.0 ND2 B:ASN158 4.6 23.2 1.0 N B:TYR86 4.7 25.5 1.0 C B:TYR86 4.7 27.7 1.0 CA B:TYR86 4.7 24.3 1.0 CA B:CYS84 4.8 28.2 1.0 O B:MET403 4.8 22.4 1.0 SG B:CYS88 4.8 24.6 1.0 SG B:CYS91 4.9 28.9 1.0 O B:HOH543 4.9 25.7 1.0 C B:GLY126 5.0 26.1 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine


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 Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:22.8 occ:1.00 FE2 B:SF4401 0.0 22.8 1.0 S1 B:SF4401 2.2 23.5 1.0 S3 B:SF4401 2.2 21.0 1.0 S4 B:SF4401 2.3 21.8 1.0 SG B:CYS88 2.4 24.6 1.0 FE3 B:SF4401 2.6 24.9 1.0 FE1 B:SF4401 2.6 23.3 1.0 FE4 B:SF4401 2.8 24.0 1.0 CB B:CYS88 3.2 23.2 1.0 NH1 B:ARG194 3.6 23.7 1.0 S2 B:SF4401 3.8 22.4 1.0 N B:CYS88 4.1 23.7 1.0 CB B:TYR86 4.1 23.6 1.0 O B:MET403 4.2 22.4 1.0 CA B:CYS88 4.2 22.4 1.0 CZ B:ARG194 4.3 20.8 1.0 CB B:CYS91 4.7 29.3 1.0 SG B:CYS84 4.7 27.2 1.0 CD B:ARG194 4.7 21.2 1.0 NE B:ARG194 4.8 20.3 1.0 CD2 B:TYR86 4.8 24.5 1.0 SG B:CYS91 4.8 28.9 1.0 NH2 B:ARG194 4.9 26.1 1.0 N B:MET403 4.9 23.2 1.0 CG B:TYR86 5.0 26.1 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine


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 Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:24.9 occ:1.00 FE3 B:SF4401 0.0 24.9 1.0 S2 B:SF4401 2.2 22.4 1.0 S1 B:SF4401 2.2 23.5 1.0 S4 B:SF4401 2.3 21.8 1.0 SG B:CYS91 2.5 28.9 1.0 FE1 B:SF4401 2.6 23.3 1.0 FE2 B:SF4401 2.6 22.8 1.0 FE4 B:SF4401 2.8 24.0 1.0 CB B:CYS91 3.2 29.3 1.0 CE B:MET403 3.8 27.4 1.0 S3 B:SF4401 3.8 21.0 1.0 O B:HOH737 3.8 28.4 1.0 CA B:CYS91 4.1 28.0 1.0 SD B:MET403 4.1 27.5 1.0 O B:HOH543 4.6 25.7 1.0 CB B:CYS88 4.6 23.2 1.0 O B:HIS93 4.7 27.7 1.0 SG B:CYS88 4.8 24.6 1.0 SG B:CYS84 4.9 27.2 1.0 N B:MET403 4.9 23.2 1.0 O B:MET403 5.0 22.4 1.0 NH1 B:ARG265 5.0 33.4 1.0 C B:CYS91 5.0 29.8 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine


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 Viperin with Bound [4FE-4S] Cluster, 5'- Deoxyadenosine, and L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:24.0 occ:1.00 FE4 B:SF4401 0.0 24.0 1.0 S3 B:SF4401 2.3 21.0 1.0 O B:MET403 2.3 22.4 1.0 S2 B:SF4401 2.4 22.4 1.0 S1 B:SF4401 2.4 23.5 1.0 N B:MET403 2.4 23.2 1.0 FE1 B:SF4401 2.7 23.3 1.0 SD B:MET403 2.7 27.5 1.0 FE3 B:SF4401 2.8 24.9 1.0 FE2 B:SF4401 2.8 22.8 1.0 C B:MET403 3.0 32.4 1.0 CA B:MET403 3.2 27.3 1.0 CG B:MET403 3.4 25.4 1.0 CE B:MET403 3.7 27.4 1.0 CB B:MET403 3.8 26.0 1.0 NH1 B:ARG194 3.9 23.7 1.0 S4 B:SF4401 4.1 21.8 1.0 OXT B:MET403 4.3 24.6 1.0 O B:GLY126 4.6 25.4 1.0 SG B:CYS84 4.6 27.2 1.0 C2' B:5AD402 4.8 25.3 1.0 O2' B:5AD402 4.9 27.1 1.0

M.K.Fenwick, Y.Li, P.Cresswell, Y.Modis, S.E.Ealick. Structural Studies of Viperin, An Antiviral Radical Sam Enzyme. Proc. Natl. Acad. Sci. V. 114 6806 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28607080
DOI: 10.1073/PNAS.1705402114