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Fluorine in PDB 4znl: Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride

Protein crystallography data

The structure of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride, PDB code: 4znl was solved by B.J.Hilbert, J.A.Hayes, N.P.Stone, C.M.Duffy, B.A.Kelch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.46 / 2.07
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 76.920, 76.920, 131.120, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 23.8

Other elements in 4znl:

The structure of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride (pdb code 4znl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride, PDB code: 4znl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 4znl

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Fluorine binding site 1 out of 9 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:40.4
occ:1.00
 F1 A:BEF302 0.0 40.4 1.0
BE A:BEF302 1.5 40.8 1.0
O A:HOH554 2.0 45.2 1.0
F3 A:BEF302 2.5 22.4 1.0
F2 A:BEF302 2.6 30.0 1.0
O1B A:ADP303 2.6 15.6 1.0
O A:HOH583 2.9 40.6 1.0
NZ A:LYS43 3.4 30.0 1.0
OE2 A:GLU150 3.6 28.5 1.0
PB A:ADP303 3.9 19.9 1.0
CA A:ARG39 4.0 19.3 1.0
N A:GLN40 4.0 19.2 1.0
CG A:ARG39 4.1 36.2 1.0
O3B A:ADP303 4.2 15.8 1.0
MG A:MG301 4.2 15.1 1.0
O A:HOH411 4.2 12.0 1.0
O A:HOH542 4.2 30.6 1.0
CE A:LYS43 4.3 28.5 1.0
CD A:GLU150 4.4 26.2 1.0
CB A:ARG39 4.4 27.1 1.0
O2B A:ADP303 4.6 16.9 1.0
C A:ARG39 4.6 16.1 1.0
NE A:ARG39 4.6 52.2 1.0
OG1 A:THR179 4.7 24.2 1.0
O A:HOH549 4.8 20.6 1.0
OE1 A:GLU150 4.9 25.5 1.0
O A:HOH496 4.9 33.0 1.0

Fluorine binding site 2 out of 9 in 4znl

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Fluorine binding site 2 out of 9 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:30.0
occ:1.00
 F2 A:BEF302 0.0 30.0 1.0
BE A:BEF302 1.6 40.8 1.0
O A:HOH542 2.0 30.6 1.0
F1 A:BEF302 2.6 40.4 1.0
O1B A:ADP303 2.7 15.6 1.0
F3 A:BEF302 2.7 22.4 1.0
OE1 A:GLN40 3.0 25.4 1.0
O A:HOH583 3.0 40.6 1.0
CD A:GLN40 3.9 24.9 1.0
NH2 A:ARG39 3.9 60.1 1.0
PB A:ADP303 4.0 19.9 1.0
O A:HOH554 4.1 45.2 1.0
N A:GLN40 4.1 19.2 1.0
CG A:GLN40 4.1 24.8 1.0
O A:HOH509 4.1 16.5 1.0
O3A A:ADP303 4.3 20.8 1.0
CZ A:ARG39 4.3 58.8 1.0
MG A:MG301 4.4 15.1 1.0
O3B A:ADP303 4.4 15.8 1.0
NE A:ARG39 4.5 52.2 1.0
CA A:GLN40 4.6 23.5 1.0
NH1 A:ARG39 4.9 61.9 1.0
O A:HOH549 4.9 20.6 1.0
CB A:GLN40 5.0 24.9 1.0

Fluorine binding site 3 out of 9 in 4znl

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Fluorine binding site 3 out of 9 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:22.4
occ:1.00
 F3 A:BEF302 0.0 22.4 1.0
BE A:BEF302 1.6 40.8 1.0
MG A:MG301 1.9 15.1 1.0
O A:HOH583 2.0 40.6 1.0
F1 A:BEF302 2.5 40.4 1.0
O A:HOH509 2.6 16.5 1.0
O3B A:ADP303 2.7 15.8 1.0
F2 A:BEF302 2.7 30.0 1.0
O A:HOH549 2.7 20.6 1.0
O1B A:ADP303 2.7 15.6 1.0
O A:HOH411 2.9 12.0 1.0
PB A:ADP303 3.2 19.9 1.0
O A:HOH496 3.7 33.0 1.0
OE2 A:GLU150 3.8 28.5 1.0
O A:HOH554 3.9 45.2 1.0
OG A:SER44 3.9 17.7 1.0
O3A A:ADP303 4.1 20.8 1.0
O A:HOH542 4.2 30.6 1.0
O2B A:ADP303 4.4 16.9 1.0
NZ A:LYS43 4.5 30.0 1.0
CD A:GLU150 4.7 26.2 1.0
O1A A:ADP303 4.8 20.1 1.0
CB A:SER44 4.8 17.5 1.0
PA A:ADP303 5.0 19.4 1.0
CE A:LYS43 5.0 28.5 1.0

Fluorine binding site 4 out of 9 in 4znl

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Fluorine binding site 4 out of 9 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:60.7
occ:1.00
 F1 B:BEF302 0.0 60.7 1.0
BE B:BEF302 1.7 46.5 1.0
O B:HOH525 2.0 48.9 1.0
O B:HOH535 2.6 72.7 1.0
F2 B:BEF302 2.7 43.0 1.0
O3B B:ADP303 2.7 29.0 1.0
F3 B:BEF302 2.8 61.3 1.0
NE2 B:GLN40 3.4 35.7 1.0
PB B:ADP303 4.0 27.6 1.0
O B:HOH520 4.0 80.6 1.0
O B:HOH452 4.0 29.6 1.0
NE B:ARG39 4.1 47.5 1.0
NH2 B:ARG39 4.2 51.6 1.0
CG B:GLN40 4.2 33.7 1.0
CG B:ARG39 4.2 41.5 1.0
CD B:GLN40 4.2 35.4 1.0
CZ B:ARG39 4.3 50.3 1.0
O1B B:ADP303 4.4 25.6 1.0
N B:GLN40 4.4 30.8 1.0
MG B:MG301 4.4 30.9 1.0
O3A B:ADP303 4.4 29.8 1.0
O B:HOH415 4.7 51.4 1.0
CA B:GLN40 4.7 33.3 1.0
O B:HOH509 4.7 36.6 1.0
CD B:ARG39 4.8 44.6 1.0
O B:HOH507 4.8 32.2 1.0
O B:HOH530 4.9 46.6 1.0

Fluorine binding site 5 out of 9 in 4znl

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Fluorine binding site 5 out of 9 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:43.0
occ:1.00
 F2 B:BEF302 0.0 43.0 1.0
BE B:BEF302 1.6 46.5 1.0
MG B:MG301 2.0 30.9 1.0
O B:HOH535 2.1 72.7 1.0
O B:HOH509 2.6 36.6 1.0
O1B B:ADP303 2.6 25.6 1.0
F3 B:BEF302 2.7 61.3 1.0
F1 B:BEF302 2.7 60.7 1.0
O3B B:ADP303 2.7 29.0 1.0
O B:HOH414 2.8 39.3 1.0
O B:HOH452 2.9 29.6 1.0
PB B:ADP303 3.2 27.6 1.0
O B:HOH507 3.7 32.2 1.0
O B:HOH520 3.7 80.6 1.0
OE2 B:GLU150 3.7 36.6 1.0
OG B:SER44 4.0 24.1 1.0
O B:HOH525 4.1 48.9 1.0
O3A B:ADP303 4.2 29.8 1.0
NZ B:LYS43 4.2 39.1 1.0
O2B B:ADP303 4.4 26.1 1.0
O2A B:ADP303 4.7 26.1 1.0
CD B:GLU150 4.7 35.2 1.0
CB B:SER44 4.9 26.1 1.0
CE B:LYS43 4.9 38.4 1.0
PA B:ADP303 5.0 26.7 1.0

Fluorine binding site 6 out of 9 in 4znl

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Fluorine binding site 6 out of 9 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:61.3
occ:1.00
 F3 B:BEF302 0.0 61.3 1.0
BE B:BEF302 1.7 46.5 1.0
O B:HOH520 2.0 80.6 1.0
F2 B:BEF302 2.7 43.0 1.0
F1 B:BEF302 2.8 60.7 1.0
O3B B:ADP303 2.8 29.0 1.0
O B:HOH535 3.1 72.7 1.0
CG B:ARG39 3.1 41.5 1.0
NZ B:LYS43 3.2 39.1 1.0
OE2 B:GLU150 3.6 36.6 1.0
N B:GLN40 4.0 30.8 1.0
CA B:ARG39 4.0 32.9 1.0
PB B:ADP303 4.0 27.6 1.0
CB B:ARG39 4.1 37.6 1.0
CD B:ARG39 4.2 44.6 1.0
O B:HOH414 4.2 39.3 1.0
NE B:ARG39 4.2 47.5 1.0
O1B B:ADP303 4.3 25.6 1.0
CE B:LYS43 4.3 38.4 1.0
CD B:GLU150 4.4 35.2 1.0
O B:HOH525 4.4 48.9 1.0
MG B:MG301 4.5 30.9 1.0
C B:ARG39 4.6 31.1 1.0
O2B B:ADP303 4.6 26.1 1.0
OG1 B:THR179 4.6 32.6 1.0
O B:HOH509 4.9 36.6 1.0
OE1 B:GLU150 4.9 35.9 1.0

Fluorine binding site 7 out of 9 in 4znl

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Fluorine binding site 7 out of 9 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F302

b:27.4
occ:1.00
 F1 C:BEF302 0.0 27.4 1.0
BE C:BEF302 1.6 25.7 1.0
O C:HOH525 1.9 22.5 1.0
O C:HOH526 2.4 44.6 1.0
O3B C:ADP303 2.5 16.3 1.0
F2 C:BEF302 2.5 24.9 1.0
F3 C:BEF302 2.7 22.1 1.0
NZ C:LYS43 3.2 30.3 1.0
CA C:ARG39 3.5 24.9 1.0
CG C:ARG39 3.6 36.1 1.0
O C:HOH538 3.8 32.8 1.0
N C:GLN40 3.8 24.5 1.0
PB C:ADP303 3.9 40.9 1.0
OE2 C:GLU150 3.9 30.4 1.0
CB C:ARG39 3.9 30.1 1.0
CG2 C:THR179 4.0 28.0 1.0
O C:HOH524 4.0 17.1 1.0
CE C:LYS43 4.1 29.0 1.0
NH1 C:ARG39 4.1 46.3 1.0
O1B C:ADP303 4.2 19.7 1.0
C C:ARG39 4.3 22.7 1.0
O C:HOH414 4.3 20.1 1.0
O2B C:ADP303 4.3 20.2 1.0
MG C:MG301 4.4 17.5 1.0
N C:ARG39 4.5 23.9 1.0
CD C:ARG39 4.6 41.7 1.0
CD C:GLU150 4.6 30.1 1.0
CZ C:ARG39 4.8 48.2 1.0
O C:GLY38 4.9 26.3 1.0
NE C:ARG39 5.0 46.0 1.0

Fluorine binding site 8 out of 9 in 4znl

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Fluorine binding site 8 out of 9 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F302

b:24.9
occ:1.00
 F2 C:BEF302 0.0 24.9 1.0
BE C:BEF302 1.6 25.7 1.0
O C:HOH524 2.0 17.1 1.0
O3B C:ADP303 2.5 16.3 1.0
F1 C:BEF302 2.5 27.4 1.0
F3 C:BEF302 2.7 22.1 1.0
O C:HOH538 2.8 32.8 1.0
O C:HOH526 3.2 44.6 1.0
O B:HOH470 3.4 38.1 1.0
OE1 C:GLN40 3.5 37.9 1.0
PB C:ADP303 3.9 40.9 1.0
N C:GLN40 3.9 24.5 1.0
NH1 C:ARG39 3.9 46.3 1.0
O C:HOH525 4.0 22.5 1.0
O C:HOH418 4.2 21.3 1.0
CG C:GLN40 4.3 31.9 1.0
CD C:GLN40 4.3 36.0 1.0
O3A C:ADP303 4.3 80.3 1.0
O1B C:ADP303 4.4 19.7 1.0
MG C:MG301 4.5 17.5 1.0
CA C:GLN40 4.5 26.5 1.0
CG C:ARG39 4.6 36.1 1.0
CB C:ARG39 4.6 30.1 1.0
CA C:ARG39 4.6 24.9 1.0
O C:HOH481 4.6 29.3 1.0
C C:ARG39 4.7 22.7 1.0
CD C:ARG39 5.0 41.7 1.0
O C:HOH523 5.0 29.8 1.0
O2B C:ADP303 5.0 20.2 1.0

Fluorine binding site 9 out of 9 in 4znl

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Fluorine binding site 9 out of 9 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F302

b:22.1
occ:1.00
 F3 C:BEF302 0.0 22.1 1.0
BE C:BEF302 1.6 25.7 1.0
MG C:MG301 2.0 17.5 1.0
O C:HOH526 2.3 44.6 1.0
O C:HOH538 2.5 32.8 1.0
O C:HOH523 2.7 29.8 1.0
F1 C:BEF302 2.7 27.4 1.0
F2 C:BEF302 2.7 24.9 1.0
O3B C:ADP303 2.7 16.3 1.0
O C:HOH418 2.7 21.3 1.0
O1B C:ADP303 2.8 19.7 1.0
O C:HOH414 2.9 20.1 1.0
PB C:ADP303 3.3 40.9 1.0
O C:HOH524 3.8 17.1 1.0
O C:HOH525 3.8 22.5 1.0
OE2 C:GLU150 3.9 30.4 1.0
OG C:SER44 4.1 18.2 1.0
O3A C:ADP303 4.3 80.3 1.0
O2B C:ADP303 4.4 20.2 1.0
NZ C:LYS43 4.5 30.3 1.0
O2A C:ADP303 4.6 21.1 1.0
CD C:GLU150 4.7 30.1 1.0
CE C:LYS43 4.8 29.0 1.0
CG C:GLU150 4.9 27.7 1.0

Reference:

B.J.Hilbert, J.A.Hayes, N.P.Stone, C.M.Duffy, B.Sankaran, B.A.Kelch. Structure and Mechanism of the Atpase That Powers Viral Genome Packaging. Proc.Natl.Acad.Sci.Usa V. 112 E3792 2015.
ISSN: ESSN 1091-6490
PubMed: 26150523
DOI: 10.1073/PNAS.1506951112
Page generated: Thu Aug 1 07:22:38 2024

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