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Fluorine in PDB 4jav: Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)

Enzymatic activity of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)

All present enzymatic activity of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V):
2.7.13.3;

Protein crystallography data

The structure of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V), PDB code: 4jav was solved by A.I.Podgornaia, P.Casino, A.Marina, M.T.Laub, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.55 / 3.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 119.319, 143.928, 138.969, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.3

Other elements in 4jav:

The structure of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) (pdb code 4jav). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V), PDB code: 4jav:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4jav

Go back to Fluorine Binding Sites List in 4jav
Fluorine binding site 1 out of 6 in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F53

b:54.0
occ:1.00
 F1 C:BFD53 0.0 54.0 1.0
BE C:BFD53 1.5 53.0 1.0
MG C:MG201 1.8 40.3 1.0
F2 C:BFD53 2.4 54.5 1.0
OD2 C:BFD53 2.5 48.7 1.0
F3 C:BFD53 2.6 51.3 1.0
O C:MET55 2.7 56.2 1.0
OD1 C:BFD53 2.7 49.6 1.0
CG C:BFD53 2.9 49.5 1.0
CB C:MET55 3.2 55.1 1.0
N C:MET55 3.3 54.4 1.0
C C:MET55 3.4 56.3 1.0
CA C:MET55 3.5 54.9 1.0
OD1 C:ASP10 3.9 55.7 1.0
CE C:MET55 4.1 59.0 1.0
NZ C:LYS105 4.2 49.4 1.0
O C:HOH304 4.3 50.3 1.0
CG C:MET55 4.3 56.5 1.0
N C:ILE54 4.4 50.9 1.0
C C:ILE54 4.4 52.8 1.0
CB C:BFD53 4.4 48.4 1.0
OD1 C:ASP9 4.7 53.5 1.0
N C:MET56 4.7 56.6 1.0
CG C:ASP10 4.8 54.1 1.0
SD C:MET55 4.9 59.6 1.0
CA C:ILE54 4.9 50.9 1.0
OG1 C:THR83 5.0 45.7 1.0

Fluorine binding site 2 out of 6 in 4jav

Go back to Fluorine Binding Sites List in 4jav
Fluorine binding site 2 out of 6 in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F53

b:54.5
occ:1.00
 F2 C:BFD53 0.0 54.5 1.0
BE C:BFD53 1.5 53.0 1.0
F1 C:BFD53 2.4 54.0 1.0
F3 C:BFD53 2.4 51.3 1.0
N C:ALA84 2.8 49.6 1.0
OD1 C:BFD53 2.8 49.6 1.0
NZ C:LYS105 3.0 49.4 1.0
CB C:ALA84 3.4 51.5 1.0
OG1 C:THR83 3.6 45.7 1.0
CA C:THR83 3.7 46.7 1.0
C C:THR83 3.7 47.9 1.0
CA C:ALA84 3.7 51.4 1.0
MG C:MG201 3.8 40.3 1.0
CE C:MET55 3.8 59.0 1.0
CG C:BFD53 3.8 49.5 1.0
CE C:LYS105 3.9 48.6 1.0
CD C:LYS105 3.9 47.6 1.0
OD2 C:BFD53 4.1 48.7 1.0
CB C:THR83 4.2 46.1 1.0
O C:LEU82 4.7 48.4 1.0
N C:LYS85 4.7 57.4 1.0
C C:ALA84 4.7 54.2 1.0
N C:MET55 4.8 54.4 1.0
O C:THR83 4.8 47.9 1.0
CB C:MET55 4.8 55.1 1.0
N C:THR83 4.8 46.2 1.0
N C:ILE54 5.0 50.9 1.0

Fluorine binding site 3 out of 6 in 4jav

Go back to Fluorine Binding Sites List in 4jav
Fluorine binding site 3 out of 6 in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F53

b:51.3
occ:1.00
 F3 C:BFD53 0.0 51.3 1.0
BE C:BFD53 1.5 53.0 1.0
F2 C:BFD53 2.4 54.5 1.0
OD1 C:BFD53 2.5 49.6 1.0
OG1 C:THR83 2.6 45.7 1.0
F1 C:BFD53 2.6 54.0 1.0
N C:MET55 2.7 54.4 1.0
N C:ILE54 3.0 50.9 1.0
CB C:ILE54 3.3 49.8 1.0
CA C:ILE54 3.4 50.9 1.0
CG C:BFD53 3.5 49.5 1.0
CB C:THR83 3.5 46.1 1.0
C C:ILE54 3.5 52.8 1.0
CE C:MET55 3.7 59.0 1.0
CB C:MET55 3.7 55.1 1.0
CA C:MET55 3.7 54.9 1.0
CA C:THR83 3.9 46.7 1.0
N C:ALA84 3.9 49.6 1.0
OD2 C:BFD53 3.9 48.7 1.0
CG C:MET55 4.0 56.5 1.0
CG1 C:ILE54 4.1 48.9 1.0
C C:BFD53 4.2 49.7 1.0
MG C:MG201 4.4 40.3 1.0
CG2 C:ILE54 4.4 49.0 1.0
O C:MET55 4.4 56.2 1.0
C C:THR83 4.4 47.9 1.0
C C:MET55 4.5 56.3 1.0
CA C:BFD53 4.6 48.3 1.0
CB C:BFD53 4.6 48.4 1.0
O C:LEU82 4.7 48.4 1.0
SD C:MET55 4.7 59.6 1.0
O C:ILE54 4.7 54.0 1.0
N C:LYS85 4.7 57.4 1.0
CG2 C:THR83 4.8 46.1 1.0
NZ C:LYS105 4.9 49.4 1.0
CA C:ALA84 5.0 51.4 1.0

Fluorine binding site 4 out of 6 in 4jav

Go back to Fluorine Binding Sites List in 4jav
Fluorine binding site 4 out of 6 in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F53

b:64.2
occ:1.00
 F1 D:BFD53 0.0 64.2 1.0
BE D:BFD53 1.5 64.3 1.0
MG D:MG201 1.8 45.5 1.0
F2 D:BFD53 2.4 65.5 1.0
F3 D:BFD53 2.6 63.9 1.0
OD2 D:BFD53 2.7 55.8 1.0
OD1 D:BFD53 2.9 56.9 1.0
O D:MET55 3.0 71.2 1.0
CG D:BFD53 3.2 57.2 1.0
CB D:MET55 3.4 70.7 1.0
N D:MET55 3.6 66.4 1.0
CE D:MET55 3.7 74.4 1.0
CA D:MET55 3.7 68.5 1.0
C D:MET55 3.7 69.2 1.0
OD1 D:ASP10 3.9 57.9 1.0
NZ D:LYS105 4.2 57.6 1.0
CG D:MET55 4.3 72.4 1.0
SD D:MET55 4.6 75.9 1.0
C D:ILE54 4.6 63.3 1.0
N D:ILE54 4.6 60.2 1.0
CB D:BFD53 4.7 57.1 1.0
CG D:ASP10 4.8 56.1 1.0
OD1 D:ASP9 5.0 57.5 1.0
OD2 D:ASP10 5.0 55.4 1.0

Fluorine binding site 5 out of 6 in 4jav

Go back to Fluorine Binding Sites List in 4jav
Fluorine binding site 5 out of 6 in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F53

b:65.5
occ:1.00
 F2 D:BFD53 0.0 65.5 1.0
BE D:BFD53 1.5 64.3 1.0
F1 D:BFD53 2.4 64.2 1.0
F3 D:BFD53 2.4 63.9 1.0
OD1 D:BFD53 2.6 56.9 1.0
N D:ALA84 2.9 72.1 1.0
NZ D:LYS105 2.9 57.6 1.0
CB D:ALA84 3.3 75.6 1.0
CE D:LYS105 3.6 57.2 1.0
CG D:BFD53 3.6 57.2 1.0
CA D:ALA84 3.7 76.9 1.0
CA D:THR83 3.7 66.3 1.0
CD D:LYS105 3.7 57.9 1.0
C D:THR83 3.7 68.6 1.0
OG1 D:THR83 3.7 65.9 1.0
OD2 D:BFD53 3.9 55.8 1.0
MG D:MG201 3.9 45.5 1.0
CE D:MET55 3.9 74.4 1.0
CB D:THR83 4.3 66.6 1.0
O D:LEU82 4.4 66.0 1.0
C D:ALA84 4.6 83.0 1.0
O D:THR83 4.9 67.4 1.0
N D:ILE54 4.9 60.2 1.0
N D:THR83 4.9 64.1 1.0
CG D:LYS105 4.9 58.0 1.0
CB D:BFD53 4.9 57.1 1.0
OD2 D:ASP9 5.0 60.2 1.0
N D:MET55 5.0 66.4 1.0
N D:LYS85 5.0 88.8 1.0

Fluorine binding site 6 out of 6 in 4jav

Go back to Fluorine Binding Sites List in 4jav
Fluorine binding site 6 out of 6 in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F53

b:63.9
occ:1.00
 F3 D:BFD53 0.0 63.9 1.0
BE D:BFD53 1.5 64.3 1.0
F2 D:BFD53 2.4 65.5 1.0
OD1 D:BFD53 2.6 56.9 1.0
F1 D:BFD53 2.6 64.2 1.0
OG1 D:THR83 2.7 65.9 1.0
N D:MET55 2.9 66.4 1.0
N D:ILE54 3.0 60.2 1.0
CB D:ILE54 3.3 61.0 1.0
CE D:MET55 3.4 74.4 1.0
CG D:BFD53 3.4 57.2 1.0
CA D:ILE54 3.4 61.2 1.0
CB D:THR83 3.6 66.6 1.0
C D:ILE54 3.6 63.3 1.0
OD2 D:BFD53 3.8 55.8 1.0
CB D:MET55 3.9 70.7 1.0
CA D:MET55 3.9 68.5 1.0
N D:ALA84 3.9 72.1 1.0
CA D:THR83 3.9 66.3 1.0
CG D:MET55 4.1 72.4 1.0
C D:BFD53 4.2 59.2 1.0
CG1 D:ILE54 4.2 61.1 1.0
MG D:MG201 4.2 45.5 1.0
CG2 D:ILE54 4.4 59.3 1.0
C D:THR83 4.5 68.6 1.0
O D:MET55 4.5 71.2 1.0
CA D:BFD53 4.5 57.9 1.0
CB D:BFD53 4.5 57.1 1.0
SD D:MET55 4.6 75.9 1.0
CG D:LYS85 4.6 92.6 1.0
C D:MET55 4.6 69.2 1.0
O D:ILE54 4.8 64.2 1.0
O D:LEU82 4.9 66.0 1.0
CA D:ALA84 4.9 76.9 1.0
CG2 D:THR83 5.0 67.5 1.0
NZ D:LYS105 5.0 57.6 1.0

Reference:

A.I.Podgornaia, P.Casino, A.Marina, M.T.Laub. Structural Basis of A Rationally Rewired Protein-Protein Interface Critical to Bacterial Signaling Structure V. 21 1636 2013.
ISSN: ISSN 0969-2126
PubMed: 23954504
DOI: 10.1016/J.STR.2013.07.005
Page generated: Thu Aug 1 02:49:31 2024

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