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Fluorine in PDB 4dle: Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant

Enzymatic activity of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant

All present enzymatic activity of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant:
2.7.7.7;

Protein crystallography data

The structure of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant, PDB code: 4dle was solved by B.Holzberger, S.Obeid, W.Welte, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.09 / 2.44
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.619, 109.619, 91.011, 90.00, 90.00, 120.00
R / Rfree (%) 23.3 / 28.2

Other elements in 4dle:

The structure of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Manganese (Mn) 1 atom

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Fluorine atom in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant (pdb code 4dle). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 34 binding sites of Fluorine where determined in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant, PDB code: 4dle:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 34 in 4dle

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Fluorine binding site 1 out of 34 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F298

b:93.2
occ:1.00
 FD A:FP9298 0.0 93.2 1.0
CG A:FP9298 1.4 90.1 1.0
CB A:FP9298 2.3 88.6 1.0
CD A:FP9298 2.4 88.8 1.0
N A:FP9298 2.9 87.2 1.0
CA A:FP9298 3.0 88.4 1.0
C A:ALA297 3.8 81.7 1.0
C A:FP9298 4.5 88.7 1.0
CA A:ALA297 4.5 76.9 1.0
O A:ALA297 4.5 78.8 1.0

Fluorine binding site 2 out of 34 in 4dle

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Fluorine binding site 2 out of 34 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:82.0
occ:0.50
 FD A:FP9300 0.0 82.0 0.5
CG A:FP9300 1.2 83.3 0.5
FD A:FP9300 1.3 81.1 0.5
CG A:FP9300 1.4 83.8 0.5
CD A:FP9300 2.3 84.5 0.5
CB A:FP9300 2.3 83.5 0.5
CB A:FP9300 2.4 83.5 0.5
CD A:FP9300 2.5 84.9 0.5
N A:FP9300 3.5 84.4 0.5
N A:FP9300 3.5 84.4 0.5
CA A:FP9300 3.5 84.2 0.5
CA A:FP9300 3.5 84.3 0.5
CG A:ASP344 3.6 67.6 1.0
OD2 A:ASP344 3.7 69.7 1.0
CB A:ASP344 3.8 65.0 1.0
OD1 A:ASP344 4.0 66.9 1.0
CD1 A:TRP299 4.4 73.5 1.0
C A:TRP299 4.5 84.6 1.0
NE1 A:TRP299 4.6 71.9 1.0
C A:FP9300 4.7 83.9 0.5
C A:FP9300 4.7 83.9 0.5
CA A:ASP344 5.0 62.9 1.0
O A:TRP299 5.0 85.5 1.0

Fluorine binding site 3 out of 34 in 4dle

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Fluorine binding site 3 out of 34 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:81.1
occ:0.50
 FD A:FP9300 0.0 81.1 0.5
FD A:FP9300 1.3 82.0 0.5
CG A:FP9300 1.4 83.3 0.5
CG A:FP9300 1.8 83.8 0.5
CD A:FP9300 2.0 84.5 0.5
CB A:FP9300 2.3 83.5 0.5
CB A:FP9300 2.3 83.5 0.5
CD A:FP9300 2.4 84.9 0.5
OD2 A:ASP344 2.9 69.7 1.0
N A:FP9300 3.0 84.4 0.5
N A:FP9300 3.0 84.4 0.5
CA A:FP9300 3.0 84.2 0.5
CA A:FP9300 3.0 84.3 0.5
CD1 A:TRP299 3.1 73.5 1.0
CG A:ASP344 3.2 67.6 1.0
NE1 A:TRP299 3.4 71.9 1.0
CB A:ASP344 3.5 65.0 1.0
C A:TRP299 3.8 84.6 1.0
OD1 A:ASP344 3.8 66.9 1.0
CG A:TRP299 4.0 74.4 1.0
O A:TRP299 4.4 85.5 1.0
CE2 A:TRP299 4.4 69.9 1.0
C A:FP9300 4.5 83.9 0.5
C A:FP9300 4.5 83.9 0.5
CB A:TRP299 4.8 77.8 1.0
CA A:TRP299 4.8 82.1 1.0
CD2 A:TRP299 4.8 71.0 1.0
CA A:ASP344 4.9 62.9 1.0

Fluorine binding site 4 out of 34 in 4dle

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Fluorine binding site 4 out of 34 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:78.7
occ:1.00
 FD A:FP9301 0.0 78.7 1.0
CG A:FP9301 1.4 77.3 1.0
CD A:FP9301 2.4 78.0 1.0
CB A:FP9301 2.4 78.8 1.0
CB A:ALA326 2.8 73.3 1.0
CZ3 A:TRP299 3.2 66.6 1.0
CH2 A:TRP299 3.4 65.8 1.0
N A:FP9301 3.5 82.0 1.0
CA A:FP9301 3.6 80.4 1.0
CE3 A:TRP299 3.8 69.1 1.0
CD2 A:LEU345 3.9 56.8 1.0
CA A:ALA326 3.9 71.3 1.0
N A:ALA326 4.1 63.7 1.0
CB A:HIS333 4.2 85.4 1.0
CZ2 A:TRP299 4.2 66.8 1.0
O A:HIS333 4.4 89.8 1.0
O A:ALA326 4.5 78.6 1.0
CB A:ALA305 4.5 50.2 1.0
CD2 A:TRP299 4.5 71.0 1.0
C A:ALA326 4.6 76.1 1.0
C A:FP9301 4.6 79.2 1.0
C A:FP9300 4.7 83.9 0.5
C A:FP9300 4.7 83.9 0.5
CE2 A:TRP299 4.7 69.9 1.0
CG A:HIS333 4.9 89.7 1.0
C A:ALA325 4.9 57.9 1.0

Fluorine binding site 5 out of 34 in 4dle

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Fluorine binding site 5 out of 34 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:80.1
occ:1.00
 FD A:FP9302 0.0 80.1 1.0
CG A:FP9302 1.4 80.8 1.0
CB A:FP9302 2.3 80.6 1.0
CD A:FP9302 2.4 81.3 1.0
N A:FP9302 3.0 80.2 1.0
CA A:FP9302 3.0 79.6 1.0
C A:FP9301 3.9 79.2 1.0
CE1 A:HIS333 4.1 95.8 1.0
NE2 A:HIS333 4.2 96.1 1.0
C A:FP9302 4.4 75.6 1.0
O A:FP9301 4.6 76.6 1.0
CA A:FP9301 4.7 80.4 1.0
CG A:ARG328 4.8 84.8 1.0

Fluorine binding site 6 out of 34 in 4dle

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Fluorine binding site 6 out of 34 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F316

b:27.5
occ:1.00
 FD A:FP9316 0.0 27.5 1.0
CG A:FP9316 1.4 28.8 1.0
CB A:FP9316 2.3 26.1 1.0
CD A:FP9316 2.4 30.0 1.0
N A:FP9316 2.9 27.9 1.0
CA A:FP9316 3.0 27.6 1.0
CB A:ASP355 3.1 33.6 1.0
CG A:ASP355 3.2 38.6 1.0
OD1 A:ASP355 3.3 36.3 1.0
O A:LYS314 3.5 34.7 1.0
CA A:ASP355 3.6 36.4 1.0
CD1 A:LEU311 3.6 31.8 1.0
O A:ASP355 3.8 42.8 1.0
C A:ASP355 4.0 41.1 1.0
C A:GLU315 4.0 25.4 1.0
OD2 A:ASP355 4.0 44.0 1.0
O A:HOH1078 4.3 13.4 1.0
C A:FP9316 4.4 28.7 1.0
NH2 A:ARG563 4.5 39.9 1.0
C A:LYS314 4.5 33.0 1.0
CA A:GLU315 4.6 31.4 1.0
NE A:ARG563 4.7 36.4 1.0
CZ A:ARG563 4.7 41.5 1.0
O A:GLU315 4.8 25.6 1.0
N A:ASP355 5.0 37.5 1.0

Fluorine binding site 7 out of 34 in 4dle

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Fluorine binding site 7 out of 34 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F336

b:76.1
occ:1.00
 FD A:FP9336 0.0 76.1 1.0
CG A:FP9336 1.4 74.3 1.0
CB A:FP9336 2.3 69.8 1.0
CD A:FP9336 2.4 76.6 1.0
CA A:FP9336 3.0 68.1 1.0
N A:FP9336 3.0 74.0 1.0
C A:ALA335 3.9 75.3 1.0
C A:FP9336 4.5 62.7 1.0
O A:ALA335 4.6 74.0 1.0
CA A:ALA335 4.7 76.8 1.0
O A:ARG334 4.9 83.4 1.0
O A:HOH1087 5.0 40.4 1.0

Fluorine binding site 8 out of 34 in 4dle

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Fluorine binding site 8 out of 34 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F338

b:53.3
occ:1.00
 FD A:FP9338 0.0 53.3 1.0
CG A:FP9338 1.4 53.6 1.0
CB A:FP9338 2.3 53.3 1.0
CD A:FP9338 2.4 54.1 1.0
CA A:FP9338 3.0 51.7 1.0
N A:FP9338 3.0 53.5 1.0
O A:LEU322 3.2 47.1 1.0
CA A:ALA323 3.3 41.6 1.0
N A:LEU324 3.4 42.7 1.0
C A:ALA323 3.6 44.5 1.0
C A:LEU322 3.7 44.4 1.0
N A:ALA323 3.8 41.0 1.0
C A:GLU337 4.1 53.5 1.0
CB A:LEU324 4.2 38.0 1.0
O A:LEU321 4.2 41.4 1.0
CA A:LEU324 4.4 43.2 1.0
O A:FP9336 4.4 63.7 1.0
C A:FP9338 4.4 42.4 1.0
O A:ALA323 4.5 49.4 1.0
CB A:ALA323 4.5 36.9 1.0
O A:ALA335 4.5 74.0 1.0
CA A:GLU337 4.7 56.6 1.0
O A:GLU337 4.9 50.8 1.0
C A:FP9336 4.9 62.7 1.0
O A:LEU324 5.0 52.4 1.0

Fluorine binding site 9 out of 34 in 4dle

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Fluorine binding site 9 out of 34 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F368

b:43.0
occ:1.00
 FD A:FP9368 0.0 43.0 1.0
CG A:FP9368 1.4 40.9 1.0
CB A:FP9368 2.3 38.2 1.0
CD A:FP9368 2.4 39.0 1.0
N A:FP9368 3.0 39.9 1.0
CA A:FP9368 3.0 38.7 1.0
O A:HOH1047 3.8 23.8 1.0
C A:LEU367 4.0 40.5 1.0
O A:GLY366 4.4 55.3 1.0
C A:GLY366 4.4 49.6 1.0
C A:FP9368 4.5 42.9 1.0
N A:LEU367 4.5 46.6 1.0
CA A:LEU367 4.6 42.9 1.0
O A:LEU367 4.8 40.2 1.0
CA A:GLY366 5.0 47.6 1.0

Fluorine binding site 10 out of 34 in 4dle

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Fluorine binding site 10 out of 34 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Ternary Structure of the Large Fragment of Taq Dna Polymerase: 4- Fluoroproline Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F369

b:59.7
occ:1.00
 FD A:FP9369 0.0 59.7 1.0
CG A:FP9369 1.4 52.9 1.0
CB A:FP9369 2.3 50.0 1.0
CD A:FP9369 2.4 51.1 1.0
CB A:SER357 2.9 28.9 1.0
OG A:SER357 2.9 29.0 1.0
N A:FP9369 3.0 48.3 1.0
CA A:FP9369 3.1 47.1 1.0
CA A:LYS354 3.4 35.3 1.0
O A:SER438 3.5 25.9 1.0
CB A:ALA442 3.8 30.5 1.0
O A:ALA353 3.9 29.6 1.0
C A:FP9368 3.9 42.9 1.0
N A:LYS354 4.0 33.8 1.0
CB A:LYS354 4.1 31.9 1.0
C A:SER438 4.1 28.0 1.0
O A:LYS354 4.2 35.4 1.0
C A:ALA353 4.2 29.7 1.0
C A:LYS354 4.3 36.3 1.0
CG A:LYS354 4.3 31.8 1.0
CA A:SER357 4.4 28.6 1.0
CA A:ALA439 4.4 28.8 1.0
C A:FP9369 4.5 44.3 1.0
O A:LEU367 4.5 40.2 1.0
N A:ALA439 4.5 30.5 1.0
O A:FP9368 4.6 39.8 1.0
CA A:FP9368 4.7 38.7 1.0
CB A:SER438 4.8 15.9 1.0
OG A:SER438 4.9 19.2 1.0
N A:SER357 4.9 29.9 1.0
O A:FP9369 5.0 45.8 1.0

Reference:

B.Holzberger, S.Obeid, W.Welte, K.Diederichs, A.Marx. Structural Insights Into the Potential of 4-Fluoroproline to Modulate Biophysical Properties of Protein Chem Sci V. 3 2924 2012.
ISSN: ISSN 2041-6520
DOI: 10.1039/C2SC20545A
Page generated: Thu Aug 1 01:02:41 2024

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