Atomistry » Fluorine » PDB 4zga-4zzi » 4znl
Atomistry »
  Fluorine »
    PDB 4zga-4zzi »
      4znl »

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

Go back to Fluorine Binding Sites List in 4znl
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

Go back to Fluorine Binding Sites List in 4znl
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

Go back to Fluorine Binding Sites List in 4znl
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

Go back to Fluorine Binding Sites List in 4znl
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

Go back to Fluorine Binding Sites List in 4znl
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

Go back to Fluorine Binding Sites List in 4znl
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

Go back to Fluorine Binding Sites List in 4znl
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

Go back to Fluorine Binding Sites List in 4znl
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

Go back to Fluorine Binding Sites List in 4znl
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: Sun Dec 13 12:17:13 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy