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Fluorine in PDB 7ckf: The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer

Protein crystallography data

The structure of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer, PDB code: 7ckf was solved by W.Cui, H.T.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.79 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.326, 79.329, 140.192, 90, 90, 90
R / Rfree (%) 21.2 / 25.9

Other elements in 7ckf:

The structure of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer also contains other interesting chemical elements:

Aluminium (Al) 2 atoms
Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer (pdb code 7ckf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer, PDB code: 7ckf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7ckf

Go back to Fluorine Binding Sites List in 7ckf
Fluorine binding site 1 out of 6 in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:39.5
occ:1.00
 F1 A:AF3403 0.0 39.5 1.0
AL A:AF3403 1.5 52.2 1.0
O1B A:GDP402 2.3 31.9 1.0
MG A:MG401 2.4 40.5 1.0
F2 A:AF3403 2.6 40.0 1.0
F3 A:AF3403 2.8 41.7 1.0
O2B A:GDP402 2.9 39.8 1.0
OG1 A:THR75 3.1 36.2 1.0
PB A:GDP402 3.2 35.2 1.0
CB A:THR75 3.3 33.6 1.0
N A:THR75 3.4 34.9 1.0
CA A:THR75 3.9 33.0 1.0
NH2 A:ARG48 4.0 37.1 1.0
O3B A:GDP402 4.1 37.3 1.0
N A:HIS74 4.2 35.9 1.0
O A:THR75 4.3 37.0 1.0
N A:GLY100 4.4 34.0 1.0
NZ A:LYS51 4.4 34.0 1.0
C A:HIS74 4.4 35.3 1.0
O3A A:GDP402 4.4 37.2 1.0
O1A A:GDP402 4.5 35.4 1.0
O A:THR98 4.6 31.3 1.0
C A:THR75 4.6 34.7 1.0
CG2 A:THR75 4.6 26.0 1.0
CB A:HIS74 4.6 35.8 1.0
CA A:HIS74 4.6 34.2 1.0
CE A:LYS51 4.7 33.8 1.0
OG A:SER52 4.7 30.6 1.0
N A:ARG48 4.9 36.4 1.0
O A:HOH580 5.0 35.8 1.0
NE A:ARG48 5.0 40.1 1.0
CZ A:ARG48 5.0 35.1 1.0

Fluorine binding site 2 out of 6 in 7ckf

Go back to Fluorine Binding Sites List in 7ckf
Fluorine binding site 2 out of 6 in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:40.0
occ:1.00
 F2 A:AF3403 0.0 40.0 1.0
AL A:AF3403 1.6 52.2 1.0
NZ A:LYS51 2.5 34.0 1.0
F1 A:AF3403 2.6 39.5 1.0
F3 A:AF3403 2.7 41.7 1.0
O1B A:GDP402 2.8 31.9 1.0
N A:GLY100 2.9 34.0 1.0
CA A:GLY100 2.9 39.1 1.0
CA A:TYR47 3.1 34.7 1.0
CE A:LYS51 3.2 33.8 1.0
CB A:TYR47 3.4 35.1 1.0
N A:ARG48 3.6 36.4 1.0
O3B A:GDP402 3.6 37.3 1.0
PB A:GDP402 3.6 35.2 1.0
C A:TYR47 3.9 37.7 1.0
O A:HOH580 4.0 35.8 1.0
N A:TYR47 4.0 34.7 1.0
O2B A:GDP402 4.1 39.8 1.0
C A:GLY100 4.1 39.7 1.0
O A:LEU46 4.1 33.4 1.0
C A:GLU99 4.1 36.5 1.0
MG A:MG401 4.3 40.5 1.0
O A:THR98 4.4 31.3 1.0
C A:LEU46 4.4 33.7 1.0
O A:GLY100 4.6 37.7 1.0
CD A:LYS51 4.6 30.0 1.0
CA A:GLU99 4.8 36.8 1.0
CG A:TYR47 4.9 35.0 1.0
CA A:ARG48 4.9 35.1 1.0
N A:LEU101 4.9 38.0 1.0
O A:GLY45 5.0 38.6 1.0

Fluorine binding site 3 out of 6 in 7ckf

Go back to Fluorine Binding Sites List in 7ckf
Fluorine binding site 3 out of 6 in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:41.7
occ:1.00
 F3 A:AF3403 0.0 41.7 1.0
AL A:AF3403 1.6 52.2 1.0
O1B A:GDP402 2.6 31.9 1.0
F2 A:AF3403 2.7 40.0 1.0
F1 A:AF3403 2.8 39.5 1.0
NE A:ARG48 3.0 40.1 1.0
CB A:TYR47 3.1 35.1 1.0
N A:ARG48 3.2 36.4 1.0
NH2 A:ARG48 3.5 37.1 1.0
CA A:SER73 3.5 33.6 1.0
CA A:TYR47 3.6 34.7 1.0
N A:HIS74 3.7 35.9 1.0
O A:HOH580 3.7 35.8 1.0
CZ A:ARG48 3.7 35.1 1.0
CB A:SER73 3.8 32.6 1.0
C A:TYR47 3.9 37.7 1.0
CD2 A:TYR47 3.9 34.4 1.0
CG A:TYR47 4.0 35.0 1.0
CA A:ARG48 4.0 35.1 1.0
CD A:ARG48 4.0 31.2 1.0
CG A:ARG48 4.1 34.7 1.0
C A:SER73 4.1 38.7 1.0
PB A:GDP402 4.1 35.2 1.0
N A:SER73 4.6 35.8 1.0
CB A:ARG48 4.7 33.0 1.0
O3B A:GDP402 4.8 37.3 1.0
N A:THR75 4.8 34.9 1.0
N A:GLY100 4.8 34.0 1.0
CA A:HIS74 4.8 34.2 1.0
O2B A:GDP402 4.8 39.8 1.0
NZ A:LYS51 4.9 34.0 1.0
O A:GLN72 4.9 33.0 1.0

Fluorine binding site 4 out of 6 in 7ckf

Go back to Fluorine Binding Sites List in 7ckf
Fluorine binding site 4 out of 6 in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:46.8
occ:1.00
 F1 B:AF3403 0.0 46.8 1.0
AL B:AF3403 1.6 49.9 1.0
MG B:MG401 2.1 37.8 1.0
O3B B:GDP402 2.3 38.6 1.0
F3 B:AF3403 2.6 42.3 1.0
F2 B:AF3403 2.7 37.5 1.0
O2B B:GDP402 2.9 39.8 1.0
PB B:GDP402 3.1 32.8 1.0
OG1 B:THR75 3.3 38.4 1.0
N B:THR75 3.3 36.9 1.0
CB B:THR75 3.4 38.9 1.0
NH2 B:ARG48 3.8 31.2 1.0
CA B:THR75 3.9 41.6 1.0
O1B B:GDP402 4.1 36.3 1.0
N B:HIS74 4.1 38.3 1.0
O2A B:GDP402 4.2 36.3 1.0
CB B:HIS74 4.3 41.2 1.0
C B:HIS74 4.3 42.6 1.0
O3A B:GDP402 4.3 40.1 1.0
CA B:HIS74 4.4 40.6 1.0
OG B:SER52 4.5 38.6 1.0
O B:THR75 4.6 38.5 1.0
NZ B:LYS51 4.6 32.1 1.0
O B:HOH578 4.6 38.4 1.0
NE B:ARG48 4.7 33.1 1.0
CZ B:ARG48 4.7 37.1 1.0
C B:THR75 4.8 43.0 1.0
CG2 B:THR75 4.8 38.3 1.0
PA B:GDP402 4.8 38.2 1.0
N B:GLY100 4.8 34.6 1.0
N B:ARG48 4.9 36.2 1.0
O B:THR98 4.9 43.9 1.0

Fluorine binding site 5 out of 6 in 7ckf

Go back to Fluorine Binding Sites List in 7ckf
Fluorine binding site 5 out of 6 in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:37.5
occ:1.00
 F2 B:AF3403 0.0 37.5 1.0
AL B:AF3403 1.6 49.9 1.0
NZ B:LYS51 2.5 32.1 1.0
F3 B:AF3403 2.6 42.3 1.0
F1 B:AF3403 2.7 46.8 1.0
O3B B:GDP402 2.7 38.6 1.0
N B:GLY100 3.0 34.6 1.0
CA B:GLY100 3.2 37.0 1.0
CA B:TYR47 3.2 40.4 1.0
O1B B:GDP402 3.3 36.3 1.0
PB B:GDP402 3.4 32.8 1.0
CB B:TYR47 3.5 36.9 1.0
CE B:LYS51 3.5 34.2 1.0
O B:HOH578 3.5 38.4 1.0
N B:ARG48 3.5 36.2 1.0
MG B:MG401 3.7 37.8 1.0
O2B B:GDP402 3.9 39.8 1.0
C B:TYR47 3.9 36.0 1.0
O B:LEU46 4.2 33.8 1.0
C B:GLU99 4.3 37.2 1.0
N B:TYR47 4.3 39.5 1.0
C B:GLY100 4.4 35.4 1.0
O B:THR98 4.5 43.9 1.0
C B:LEU46 4.7 35.9 1.0
CA B:ARG48 4.8 36.9 1.0
CA B:GLU99 4.8 41.7 1.0
O B:GLY100 4.8 32.5 1.0
O3A B:GDP402 4.9 40.1 1.0
CG B:TYR47 4.9 35.1 1.0
CD B:LYS51 4.9 32.3 1.0

Fluorine binding site 6 out of 6 in 7ckf

Go back to Fluorine Binding Sites List in 7ckf
Fluorine binding site 6 out of 6 in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:42.3
occ:1.00
 F3 B:AF3403 0.0 42.3 1.0
AL B:AF3403 1.5 49.9 1.0
O3B B:GDP402 2.5 38.6 1.0
F2 B:AF3403 2.6 37.5 1.0
F1 B:AF3403 2.6 46.8 1.0
NE B:ARG48 2.8 33.1 1.0
N B:ARG48 3.2 36.2 1.0
NH2 B:ARG48 3.4 31.2 1.0
CB B:TYR47 3.5 36.9 1.0
CZ B:ARG48 3.5 37.1 1.0
O B:HOH578 3.5 38.4 1.0
CA B:SER73 3.5 38.1 1.0
N B:HIS74 3.5 38.3 1.0
CD B:ARG48 3.8 34.7 1.0
CA B:TYR47 3.9 40.4 1.0
CA B:ARG48 4.0 36.9 1.0
PB B:GDP402 4.0 32.8 1.0
C B:TYR47 4.0 36.0 1.0
CB B:SER73 4.0 37.2 1.0
CG B:ARG48 4.0 35.3 1.0
C B:SER73 4.1 36.9 1.0
CD2 B:TYR47 4.2 38.2 1.0
CG B:TYR47 4.3 35.1 1.0
O1B B:GDP402 4.5 36.3 1.0
CB B:ARG48 4.6 32.9 1.0
N B:SER73 4.6 32.9 1.0
MG B:MG401 4.6 37.8 1.0
N B:THR75 4.7 36.9 1.0
CA B:HIS74 4.7 40.6 1.0
O2B B:GDP402 4.7 39.8 1.0
O B:GLN72 4.8 34.7 1.0
CB B:HIS74 4.8 41.2 1.0
NH1 B:ARG48 4.8 36.4 1.0
NZ B:LYS51 4.9 32.1 1.0
O3A B:GDP402 4.9 40.1 1.0
N B:GLY100 5.0 34.6 1.0

Reference:

W.Cui, E.Braun, W.Wang, J.Tang, Y.Zheng, B.Slater, N.Li, C.Chen, Q.Liu, B.Wang, X.Li, Y.Duan, Y.Xiao, R.Ti, D.Hotter, X.Ji, L.Zhang, J.Cui, Y.Xiong, D.Sauter, Z.Wang, F.Kirchhoff, H.Yang. Structural Basis For Gtp-Induced Dimerization and Antiviral Function of Guanylate-Binding Proteins. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33876762
DOI: 10.1073/PNAS.2022269118
Page generated: Fri Aug 2 06:10:26 2024

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