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Iron in PDB 5vsl: Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah)

Protein crystallography data

The structure of Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah), PDB code: 5vsl 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) 46.07 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.934, 73.854, 141.872, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 20

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah) (pdb code 5vsl). 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 and S- Adenosylhomocysteine (Sah), PDB code: 5vsl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5vsl

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Iron binding site 1 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah)


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 and S- Adenosylhomocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:23.9
occ:1.00
 FE1 A:SF4401 0.0 23.9 1.0
S2 A:SF4401 2.2 25.4 1.0
S4 A:SF4401 2.3 23.6 1.0
S3 A:SF4401 2.3 24.3 1.0
SG A:CYS84 2.4 27.4 1.0
FE4 A:SF4401 2.6 29.5 1.0
FE3 A:SF4401 2.7 24.4 1.0
FE2 A:SF4401 2.7 22.1 1.0
CB A:CYS84 3.3 31.0 1.0
S1 A:SF4401 3.8 24.0 1.0
N A:SAH402 3.9 28.1 1.0
CB A:TYR86 4.2 19.2 1.0
O A:HOH666 4.4 29.0 1.0
O A:TYR86 4.5 25.3 1.0
O A:HOH565 4.6 31.3 1.0
N A:TYR86 4.7 27.1 1.0
ND2 A:ASN158 4.7 22.7 1.0
C A:TYR86 4.7 26.4 1.0
CA A:CYS84 4.7 34.5 1.0
CA A:TYR86 4.8 22.5 1.0
O A:SAH402 4.8 32.5 1.0
O A:HOH530 4.8 27.9 1.0
SG A:CYS91 4.8 27.1 1.0
SG A:CYS88 4.9 24.3 1.0
O A:GLY126 4.9 29.4 1.0
C A:GLY126 4.9 28.4 1.0

Iron binding site 2 out of 8 in 5vsl

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Iron binding site 2 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah)


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 and S- Adenosylhomocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:22.1
occ:1.00
 FE2 A:SF4401 0.0 22.1 1.0
S1 A:SF4401 2.2 24.0 1.0
S3 A:SF4401 2.3 24.3 1.0
S4 A:SF4401 2.4 23.6 1.0
SG A:CYS88 2.4 24.3 1.0
FE3 A:SF4401 2.6 24.4 1.0
FE1 A:SF4401 2.7 23.9 1.0
FE4 A:SF4401 2.8 29.5 1.0
CB A:CYS88 3.1 21.8 1.0
NH1 A:ARG194 3.7 28.7 1.0
S2 A:SF4401 3.9 25.4 1.0
N A:CYS88 4.0 22.9 1.0
CA A:CYS88 4.2 23.2 1.0
CB A:TYR86 4.2 19.2 1.0
CZ A:ARG194 4.2 29.5 1.0
O A:SAH402 4.4 32.5 1.0
CB A:CYS91 4.6 21.5 1.0
NH2 A:ARG194 4.6 27.7 1.0
SG A:CYS84 4.8 27.4 1.0
NE A:ARG194 4.8 39.2 1.0
SG A:CYS91 4.8 27.1 1.0
CD2 A:TYR86 4.8 33.6 1.0
CD A:ARG194 5.0 45.5 1.0

Iron binding site 3 out of 8 in 5vsl

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Iron binding site 3 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah)


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 and S- Adenosylhomocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:24.4
occ:1.00
 FE3 A:SF4401 0.0 24.4 1.0
S1 A:SF4401 2.2 24.0 1.0
S2 A:SF4401 2.2 25.4 1.0
S4 A:SF4401 2.3 23.6 1.0
SG A:CYS91 2.5 27.1 1.0
FE2 A:SF4401 2.6 22.1 1.0
FE1 A:SF4401 2.7 23.9 1.0
FE4 A:SF4401 2.9 29.5 1.0
CB A:CYS91 3.1 21.5 1.0
S3 A:SF4401 3.9 24.3 1.0
O A:HOH666 4.0 29.0 1.0
CA A:CYS91 4.0 24.4 1.0
CB A:CYS88 4.6 21.8 1.0
O A:HOH530 4.7 27.9 1.0
SG A:CYS88 4.7 24.3 1.0
O A:HIS93 4.8 27.2 1.0
SD A:SAH402 4.8 43.4 1.0
SG A:CYS84 4.9 27.4 1.0
C A:CYS91 4.9 23.7 1.0
NH1 A:ARG265 5.0 39.0 1.0
N A:SAH402 5.0 28.1 1.0

Iron binding site 4 out of 8 in 5vsl

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Iron binding site 4 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah)


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 and S- Adenosylhomocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:29.5
occ:1.00
 FE4 A:SF4401 0.0 29.5 1.0
S3 A:SF4401 2.2 24.3 1.0
O A:SAH402 2.4 32.5 1.0
S1 A:SF4401 2.4 24.0 1.0
S2 A:SF4401 2.5 25.4 1.0
N A:SAH402 2.5 28.1 1.0
FE1 A:SF4401 2.6 23.9 1.0
FE2 A:SF4401 2.8 22.1 1.0
FE3 A:SF4401 2.9 24.4 1.0
C A:SAH402 3.2 31.1 1.0
CA A:SAH402 3.4 31.4 1.0
SD A:SAH402 3.5 43.4 1.0
CG A:SAH402 3.7 43.8 1.0
NH1 A:ARG194 3.9 28.7 1.0
S4 A:SF4401 4.0 23.6 1.0
CB A:SAH402 4.0 31.9 1.0
OXT A:SAH402 4.4 30.5 1.0
O A:GLY126 4.5 29.4 1.0
SG A:CYS84 4.5 27.4 1.0
C2' A:SAH402 4.7 37.1 1.0
CZ A:ARG194 4.9 29.5 1.0
SG A:CYS88 4.9 24.3 1.0

Iron binding site 5 out of 8 in 5vsl

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Iron binding site 5 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah)


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 and S- Adenosylhomocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:23.4
occ:1.00
 FE1 B:SF4401 0.0 23.4 1.0
S2 B:SF4401 2.1 22.7 1.0
S4 B:SF4401 2.3 21.9 1.0
S3 B:SF4401 2.3 24.2 1.0
SG B:CYS84 2.4 28.7 1.0
FE3 B:SF4401 2.6 26.4 1.0
FE4 B:SF4401 2.6 29.4 1.0
FE2 B:SF4401 2.7 22.5 1.0
CB B:CYS84 3.3 24.6 1.0
S1 B:SF4401 3.7 24.3 1.0
N B:SAH402 3.9 22.9 1.0
CB B:TYR86 4.0 25.9 0.4
O B:TYR86 4.3 26.0 0.6
O B:HOH531 4.5 30.0 1.0
CB B:TYR86 4.5 28.5 0.6
O B:HOH698 4.5 30.0 1.0
C B:TYR86 4.6 31.0 0.6
ND2 B:ASN158 4.7 22.9 1.0
CA B:CYS84 4.7 25.7 1.0
N B:TYR86 4.7 26.1 0.4
O B:HOH541 4.7 25.8 1.0
CA B:TYR86 4.7 28.1 0.4
N B:TYR86 4.7 25.7 0.6
C B:TYR86 4.8 30.5 0.4
O B:TYR86 4.8 27.6 0.4
O B:GLY126 4.9 24.7 1.0
O B:SAH402 4.9 24.5 1.0
CA B:TYR86 4.9 27.5 0.6
SG B:CYS91 4.9 33.5 1.0
SG B:CYS88 4.9 23.4 1.0
C B:GLY126 4.9 25.1 1.0

Iron binding site 6 out of 8 in 5vsl

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Iron binding site 6 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah)


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 and S- Adenosylhomocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:22.5
occ:1.00
 FE2 B:SF4401 0.0 22.5 1.0
S1 B:SF4401 2.1 24.3 1.0
S3 B:SF4401 2.3 24.2 1.0
S4 B:SF4401 2.4 21.9 1.0
SG B:CYS88 2.4 23.4 1.0
FE3 B:SF4401 2.6 26.4 1.0
FE4 B:SF4401 2.7 29.4 1.0
FE1 B:SF4401 2.7 23.4 1.0
CB B:CYS88 3.1 25.2 1.0
NH1 B:ARG194 3.6 23.7 1.0
S2 B:SF4401 3.8 22.7 1.0
N B:CYS88 4.0 23.4 1.0
CB B:TYR86 4.1 25.9 0.4
CA B:CYS88 4.2 25.1 1.0
CZ B:ARG194 4.2 25.5 1.0
O B:SAH402 4.3 24.5 1.0
CB B:TYR86 4.6 28.5 0.6
CB B:CYS91 4.6 29.5 1.0
CD1 B:TYR86 4.6 23.8 0.4
NH2 B:ARG194 4.8 20.9 1.0
NE B:ARG194 4.8 29.3 1.0
SG B:CYS84 4.8 28.7 1.0
CD B:ARG194 4.9 33.2 1.0
SG B:CYS91 4.9 33.5 1.0
CG B:TYR86 4.9 28.2 0.4

Iron binding site 7 out of 8 in 5vsl

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Iron binding site 7 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah)


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 and S- Adenosylhomocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:26.4
occ:1.00
 FE3 B:SF4401 0.0 26.4 1.0
S2 B:SF4401 2.2 22.7 1.0
S4 B:SF4401 2.2 21.9 1.0
S1 B:SF4401 2.3 24.3 1.0
FE1 B:SF4401 2.6 23.4 1.0
FE2 B:SF4401 2.6 22.5 1.0
SG B:CYS91 2.6 33.5 1.0
FE4 B:SF4401 2.9 29.4 1.0
CB B:CYS91 3.1 29.5 1.0
S3 B:SF4401 3.9 24.2 1.0
O B:HOH698 4.0 30.0 1.0
CA B:CYS91 4.1 33.4 1.0
CB B:CYS88 4.6 25.2 1.0
O B:HOH541 4.7 25.8 1.0
SG B:CYS88 4.7 23.4 1.0
NH1 B:ARG265 4.8 33.3 1.0
O B:HIS93 4.9 31.7 1.0
SG B:CYS84 4.9 28.7 1.0
SD B:SAH402 5.0 31.5 1.0

Iron binding site 8 out of 8 in 5vsl

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Iron binding site 8 out of 8 in the Crystal Structure of Viperin with Bound [4FE-4S] Cluster and S- Adenosylhomocysteine (Sah)


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 and S- Adenosylhomocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:29.4
occ:1.00
 FE4 B:SF4401 0.0 29.4 1.0
S3 B:SF4401 2.2 24.2 1.0
S1 B:SF4401 2.4 24.3 1.0
S2 B:SF4401 2.5 22.7 1.0
O B:SAH402 2.5 24.5 1.0
N B:SAH402 2.5 22.9 1.0
FE1 B:SF4401 2.6 23.4 1.0
FE2 B:SF4401 2.7 22.5 1.0
FE3 B:SF4401 2.9 26.4 1.0
C B:SAH402 3.2 26.8 1.0
CA B:SAH402 3.3 25.8 1.0
CG B:SAH402 3.6 28.2 1.0
SD B:SAH402 3.8 31.5 1.0
NH1 B:ARG194 3.8 23.7 1.0
CB B:SAH402 3.9 25.4 1.0
S4 B:SF4401 4.0 21.9 1.0
OXT B:SAH402 4.3 23.0 1.0
O B:GLY126 4.4 24.7 1.0
SG B:CYS84 4.5 28.7 1.0
C2' B:SAH402 4.8 28.0 1.0
CB B:ASN158 4.9 20.8 1.0
SG B:CYS88 4.9 23.4 1.0
CZ B:ARG194 5.0 25.5 1.0

Reference:

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
Page generated: Tue Aug 6 10:32:32 2024

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