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

Protein crystallography data

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

Other elements in 6q2p:

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

Iron Binding Sites:

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 6q2p

Go back to Iron Binding Sites List in 6q2p
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 6q2p

Go back to Iron Binding Sites List in 6q2p
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 6q2p

Go back to Iron Binding Sites List in 6q2p
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 6q2p

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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 6q2p

Go back to Iron Binding Sites List in 6q2p
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 6q2p

Go back to Iron Binding Sites List in 6q2p
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 6q2p

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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 6q2p

Go back to Iron Binding Sites List in 6q2p
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

Reference:

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
Page generated: Sun Dec 13 16:50:08 2020

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