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Fluorine in PDB 3u61: Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp

Protein crystallography data

The structure of Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp, PDB code: 3u61 was solved by B.A.Kelch, D.L.Makino, M.O'donnell, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.65 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.303, 137.272, 222.779, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 30.5

Other elements in 3u61:

The structure of Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp (pdb code 3u61). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp, PDB code: 3u61:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3u61

Go back to Fluorine Binding Sites List in 3u61
Fluorine binding site 1 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F700

b:83.6
occ:1.00
 F1 C:08T700 0.0 83.6 1.0
BE C:08T700 1.4 83.6 1.0
F3 C:08T700 2.2 83.6 1.0
F2 C:08T700 2.3 83.6 1.0
O3B C:08T700 2.4 83.6 1.0
MG C:MG800 2.4 83.6 1.0
OE2 C:GLU108 2.6 61.1 1.0
O1B C:08T700 2.8 83.6 1.0
PB C:08T700 3.1 83.6 1.0
CD C:GLU108 3.5 61.4 1.0
NH2 D:ARG151 3.6 62.8 1.0
OE1 C:GLU108 3.7 62.6 1.0
CE C:LYS56 3.7 61.0 1.0
NZ C:LYS56 3.7 61.4 1.0
O2B C:08T700 3.9 83.6 1.0
ND2 C:ASN139 3.9 76.4 1.0
CG2 C:THR57 4.1 75.8 1.0
CG2 C:THR137 4.3 57.5 1.0
OD1 C:ASN139 4.3 76.2 1.0
O3A C:08T700 4.4 83.6 1.0
CG C:ASN139 4.5 76.9 1.0
NH1 D:ARG151 4.5 61.4 1.0
CZ D:ARG151 4.5 61.4 1.0
OG1 C:THR57 4.6 75.7 1.0
NH2 C:ARG205 4.7 71.4 1.0
CG C:GLU108 4.8 60.8 1.0
CB C:LYS56 4.9 59.2 1.0

Fluorine binding site 2 out of 6 in 3u61

Go back to Fluorine Binding Sites List in 3u61
Fluorine binding site 2 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F700

b:83.6
occ:1.00
 F2 C:08T700 0.0 83.6 1.0
BE C:08T700 1.4 83.6 1.0
F3 C:08T700 2.2 83.6 1.0
F1 C:08T700 2.3 83.6 1.0
O3B C:08T700 2.3 83.6 1.0
NH1 D:ARG151 2.8 61.4 1.0
NH2 D:ARG151 3.1 62.8 1.0
OE2 C:GLU108 3.4 61.1 1.0
CZ D:ARG151 3.4 61.4 1.0
MG C:MG800 3.8 83.6 1.0
OD1 C:ASN139 3.8 76.2 1.0
PB C:08T700 3.9 83.6 1.0
NH2 C:ARG205 3.9 71.4 1.0
NH1 C:ARG205 3.9 72.3 1.0
ND2 C:ASN139 3.9 76.4 1.0
CB C:PRO52 3.9 64.9 1.0
CA C:PRO52 4.1 64.7 1.0
CB D:PRO147 4.2 62.4 1.0
O1B C:08T700 4.2 83.6 1.0
CG C:ASN139 4.3 76.9 1.0
CZ C:ARG205 4.4 71.7 1.0
CD C:GLU108 4.4 61.4 1.0
N C:GLY53 4.5 63.1 1.0
OE1 C:GLU108 4.5 62.6 1.0
NZ C:LYS56 4.6 61.4 1.0
CA D:PRO147 4.6 62.1 1.0
NE D:ARG151 4.7 60.5 1.0
O3A C:08T700 4.7 83.6 1.0
O2B C:08T700 4.8 83.6 1.0
O D:PRO147 4.8 59.9 1.0
CG D:PRO147 4.9 64.4 1.0
C C:PRO52 4.9 64.8 1.0

Fluorine binding site 3 out of 6 in 3u61

Go back to Fluorine Binding Sites List in 3u61
Fluorine binding site 3 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F700

b:83.6
occ:1.00
 F3 C:08T700 0.0 83.6 1.0
BE C:08T700 1.4 83.6 1.0
F1 C:08T700 2.2 83.6 1.0
F2 C:08T700 2.2 83.6 1.0
O3B C:08T700 2.4 83.6 1.0
ND2 C:ASN139 2.5 76.4 1.0
NZ C:LYS56 2.5 61.4 1.0
CE C:LYS56 2.9 61.0 1.0
PB C:08T700 3.4 83.6 1.0
CG C:ASN139 3.5 76.9 1.0
CA C:PRO52 3.5 64.7 1.0
O2B C:08T700 3.6 83.6 1.0
OD1 C:ASN139 3.7 76.2 1.0
O1B C:08T700 3.9 83.6 1.0
N C:GLY53 4.0 63.1 1.0
CB C:PRO52 4.2 64.9 1.0
C C:PRO52 4.3 64.8 1.0
OE2 C:GLU108 4.3 61.1 1.0
CB C:SER49 4.3 78.0 1.0
O C:PRO50 4.4 99.5 1.0
N C:PRO52 4.4 67.0 1.0
CD C:LYS56 4.4 61.7 1.0
MG C:MG800 4.4 83.6 1.0
OG C:SER49 4.5 77.6 1.0
OE1 C:GLU108 4.6 62.6 1.0
O C:SER51 4.7 72.3 1.0
O3A C:08T700 4.7 83.6 1.0
CB C:ASN139 4.8 78.8 1.0
C C:SER51 4.8 73.1 1.0
CD C:GLU108 4.9 61.4 1.0

Fluorine binding site 4 out of 6 in 3u61

Go back to Fluorine Binding Sites List in 3u61
Fluorine binding site 4 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F700

b:83.6
occ:1.00
 F1 D:08T700 0.0 83.6 1.0
BE D:08T700 1.4 83.6 1.0
MG D:MG800 2.2 83.6 1.0
F3 D:08T700 2.3 83.6 1.0
F2 D:08T700 2.3 83.6 1.0
O3B D:08T700 2.3 83.6 1.0
O1B D:08T700 2.4 83.6 1.0
PB D:08T700 2.8 83.6 1.0
OE2 D:GLU108 2.9 74.0 1.0
NZ D:LYS56 3.7 61.1 1.0
O2B D:08T700 3.8 83.6 1.0
NH2 E:ARG151 3.8 69.5 1.0
CE D:LYS56 3.8 59.6 1.0
CD D:GLU108 3.8 73.7 1.0
O3A D:08T700 4.1 83.6 1.0
OE1 D:GLU108 4.1 74.0 1.0
CG2 D:THR57 4.1 65.2 1.0
NH2 D:ARG205 4.2 71.5 1.0
ND2 D:ASN139 4.2 63.5 1.0
OG1 D:THR57 4.3 66.9 1.0
CG2 D:THR137 4.6 55.9 1.0
O2A D:08T700 4.7 83.6 1.0
CZ E:ARG151 4.7 69.1 1.0
OD1 D:ASN139 4.7 64.8 1.0
NH1 E:ARG151 4.8 69.4 1.0
CB D:THR57 4.9 65.8 1.0
OE1 E:GLU126 4.9 70.0 1.0
CB D:LYS56 4.9 57.7 1.0
CG D:ASN139 4.9 64.3 1.0
N D:THR57 4.9 65.2 1.0

Fluorine binding site 5 out of 6 in 3u61

Go back to Fluorine Binding Sites List in 3u61
Fluorine binding site 5 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F700

b:83.6
occ:1.00
 F2 D:08T700 0.0 83.6 1.0
BE D:08T700 1.4 83.6 1.0
F3 D:08T700 2.2 83.6 1.0
O3B D:08T700 2.3 83.6 1.0
F1 D:08T700 2.3 83.6 1.0
NH2 E:ARG151 2.7 69.5 1.0
NH2 D:ARG205 3.0 71.5 1.0
NH1 D:ARG205 3.0 72.6 1.0
CZ E:ARG151 3.3 69.1 1.0
CZ D:ARG205 3.4 72.4 1.0
NH1 E:ARG151 3.5 69.4 1.0
PB D:08T700 3.6 83.6 1.0
MG D:MG800 3.7 83.6 1.0
O1B D:08T700 3.8 83.6 1.0
OE2 D:GLU108 3.8 74.0 1.0
CB D:PRO52 4.0 69.7 1.0
N D:GLY53 4.1 66.3 1.0
CA D:PRO52 4.2 68.0 1.0
O3A D:08T700 4.2 83.6 1.0
NE E:ARG151 4.3 68.9 1.0
CB E:PRO147 4.5 70.5 1.0
ND2 D:ASN139 4.6 63.5 1.0
C D:PRO52 4.7 68.0 1.0
OD1 D:ASN139 4.7 64.8 1.0
O2B D:08T700 4.8 83.6 1.0
NE D:ARG205 4.8 73.4 1.0
NZ D:LYS56 4.8 61.1 1.0
O E:PRO147 4.9 68.9 1.0
CD D:GLU108 4.9 73.7 1.0
OE1 E:GLU126 4.9 70.0 1.0
O2A D:08T700 5.0 83.6 1.0

Fluorine binding site 6 out of 6 in 3u61

Go back to Fluorine Binding Sites List in 3u61
Fluorine binding site 6 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of T4 Bacteriophage Clamp Loader Bound to Closed Clamp, Dna and Atp Analog and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F700

b:83.6
occ:1.00
 F3 D:08T700 0.0 83.6 1.0
BE D:08T700 1.4 83.6 1.0
F2 D:08T700 2.2 83.6 1.0
F1 D:08T700 2.3 83.6 1.0
O3B D:08T700 2.3 83.6 1.0
ND2 D:ASN139 2.6 63.5 1.0
NZ D:LYS56 3.0 61.1 1.0
CA D:PRO52 3.3 68.0 1.0
CG D:ASN139 3.5 64.3 1.0
CE D:LYS56 3.5 59.6 1.0
OD1 D:ASN139 3.6 64.8 1.0
PB D:08T700 3.6 83.6 1.0
CB D:PRO52 3.8 69.7 1.0
N D:GLY53 3.9 66.3 1.0
O1B D:08T700 4.1 83.6 1.0
C D:PRO52 4.1 68.0 1.0
O2B D:08T700 4.1 83.6 1.0
N D:PRO52 4.2 70.0 1.0
OE2 D:GLU108 4.3 74.0 1.0
NH2 E:ARG151 4.4 69.5 1.0
MG D:MG800 4.5 83.6 1.0
O D:PRO50 4.5 0.8 1.0
CB E:PRO147 4.7 70.5 1.0
OE1 D:GLU108 4.7 74.0 1.0
NH1 D:ARG205 4.7 72.6 1.0
O D:SER51 4.8 70.2 1.0
CB D:SER49 4.8 85.1 1.0
C D:SER51 4.8 71.8 1.0
O3A D:08T700 4.8 83.6 1.0
CB D:ASN139 4.9 65.1 1.0
CD D:GLU108 4.9 73.7 1.0
OG D:SER49 4.9 85.4 1.0
CG E:PRO147 4.9 72.0 1.0
NH2 D:ARG205 5.0 71.5 1.0

Reference:

B.A.Kelch, D.L.Makino, M.O'donnell, J.Kuriyan. How A Dna Polymerase Clamp Loader Opens A Sliding Clamp. Science V. 334 1675 2011.
ISSN: ISSN 0036-8075
PubMed: 22194570
DOI: 10.1126/SCIENCE.1211884
Page generated: Wed Jul 31 23:00:29 2024

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