Atomistry » Iron » PDB 6ppu-6q9k » 6q2p
Atomistry »
  Iron »
    PDB 6ppu-6q9k »
      6q2p »

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

Go back to Iron Binding Sites List in 6q2p
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

Go back to Iron Binding Sites List in 6q2p
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: Wed Aug 7 06:49:37 2024

Last articles

Cl in 2Y2G
Cl in 2Y2K
Cl in 2Y2H
Cl in 2Y2J
Cl in 2Y2I
Cl in 2Y1X
Cl in 2Y1G
Cl in 2Y1F
Cl in 2Y05
Cl in 2Y1K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy