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Fluorine in PDB 3agv: Crystal Structure of A Human Igg-Aptamer Complex

Protein crystallography data

The structure of Crystal Structure of A Human Igg-Aptamer Complex, PDB code: 3agv was solved by Y.Nomura, S.Sugiyama, T.Sakamoto, S.Miyakawa, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori, Y.Nakamura, H.Matsumura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.37 / 2.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.587, 107.238, 79.458, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 27.7

Other elements in 3agv:

The structure of Crystal Structure of A Human Igg-Aptamer Complex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of A Human Igg-Aptamer Complex (pdb code 3agv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Crystal Structure of A Human Igg-Aptamer Complex, PDB code: 3agv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 3agv

Go back to Fluorine Binding Sites List in 3agv
Fluorine binding site 1 out of 18 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:F6

b:63.4
occ:1.00
 F2' S:UFT6 0.0 63.4 1.0
C2' S:UFT6 1.4 63.5 1.0
C3' S:UFT6 2.4 63.3 1.0
C1' S:UFT6 2.4 64.8 1.0
O3' S:UFT6 2.6 62.8 1.0
O S:HOH158 2.9 42.5 1.0
C8 S:G7 3.0 42.7 1.0
C4' S:UFT6 3.1 63.8 1.0
O4' S:UFT6 3.3 64.4 1.0
N7 S:G7 3.3 41.6 1.0
O S:HOH248 3.5 65.4 1.0
P S:G7 3.6 63.0 1.0
OP2 S:G7 3.6 61.9 1.0
N1 S:UFT6 3.6 66.2 1.0
C5' S:G7 3.7 56.4 1.0
O2 S:UFT6 3.8 68.5 1.0
O S:HOH252 3.9 43.0 1.0
O5' S:G7 4.0 59.9 1.0
N9 S:G7 4.0 44.3 1.0
C2 S:UFT6 4.1 67.1 1.0
O4' S:G7 4.1 51.2 1.0
C5 S:G7 4.4 39.9 1.0
C4' S:G7 4.4 53.7 1.0
C5' S:UFT6 4.6 65.4 1.0
CA S:CA25 4.6 79.5 1.0
C6 S:UFT6 4.6 65.9 1.0
N1 S:A19 4.7 54.5 1.0
C1' S:G7 4.7 47.9 1.0
C4 S:G7 4.8 41.8 1.0
C3' S:G7 4.8 52.4 1.0
N6 S:A18 4.9 61.0 1.0
O S:HOH235 4.9 66.1 1.0
OP1 S:G7 4.9 63.9 1.0
O4 S:UFT9 5.0 44.8 1.0

Fluorine binding site 2 out of 18 in 3agv

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Fluorine binding site 2 out of 18 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:F8

b:42.0
occ:1.00
 F2' S:CFZ8 0.0 42.0 1.0
C2' S:CFZ8 1.4 43.2 1.0
C3' S:CFZ8 2.4 44.3 1.0
C1' S:CFZ8 2.4 41.1 1.0
O3' S:CFZ8 2.7 47.5 1.0
C4' S:CFZ8 3.0 45.6 1.0
CD2 A:LEU398 3.1 32.1 1.0
O4' S:CFZ8 3.2 43.1 1.0
O2 S:CFZ8 3.6 38.9 1.0
N1 S:CFZ8 3.7 39.6 1.0
C5' S:UFT9 3.7 48.3 1.0
O5' S:UFT9 4.0 46.5 1.0
P S:UFT9 4.0 48.0 1.0
C2 S:CFZ8 4.1 40.8 1.0
O4' S:UFT9 4.1 50.9 1.0
O S:HOH57 4.4 45.3 1.0
C5' S:CFZ8 4.5 47.2 1.0
C4' S:UFT9 4.5 50.2 1.0
CG A:LEU398 4.6 31.5 1.0
OP1 S:UFT9 4.6 51.2 1.0
C6 S:CFZ8 4.8 37.5 1.0
C6 S:UFT9 5.0 46.6 1.0
O S:HOH152 5.0 40.2 1.0

Fluorine binding site 3 out of 18 in 3agv

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Fluorine binding site 3 out of 18 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:F9

b:53.7
occ:1.00
 F2' S:UFT9 0.0 53.7 1.0
C2' S:UFT9 1.4 51.6 1.0
C3' S:UFT9 2.4 51.9 1.0
C1' S:UFT9 2.4 49.9 1.0
O3' S:UFT9 2.6 56.6 1.0
C4' S:UFT9 3.0 50.2 1.0
O4' S:UFT9 3.1 50.9 1.0
O4' S:CFZ10 3.4 62.6 1.0
C5' S:CFZ10 3.6 59.4 1.0
N1 S:UFT9 3.7 45.9 1.0
O5' S:CFZ10 3.7 57.6 1.0
P S:CFZ10 3.8 58.6 1.0
O2 S:UFT9 3.8 45.3 1.0
C4' S:CFZ10 4.0 61.8 1.0
C2 S:UFT9 4.2 45.9 1.0
C5' S:UFT9 4.4 48.3 1.0
C6 S:CFZ10 4.5 56.1 1.0
C1' S:CFZ10 4.6 60.5 1.0
O1P S:CFZ10 4.6 58.8 1.0
C6 S:UFT9 4.7 46.6 1.0
O2P S:CFZ10 4.8 57.6 1.0
O S:HOH57 4.8 45.3 1.0
N1 S:CFZ10 4.9 56.7 1.0

Fluorine binding site 4 out of 18 in 3agv

Go back to Fluorine Binding Sites List in 3agv
Fluorine binding site 4 out of 18 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:F10

b:62.8
occ:1.00
 F2' S:CFZ10 0.0 62.8 1.0
C2' S:CFZ10 1.4 62.8 1.0
C3' S:CFZ10 2.4 63.8 1.0
C1' S:CFZ10 2.4 60.5 1.0
O3' S:CFZ10 2.8 68.2 1.0
C4' S:CFZ10 2.9 61.8 1.0
O4' S:CFZ10 3.1 62.6 1.0
N1 S:CFZ10 3.7 56.7 1.0
O2 S:CFZ10 3.8 53.8 1.0
O5' S:CFZ11 4.1 72.2 1.0
P S:CFZ11 4.1 70.4 1.0
C2 S:CFZ10 4.2 55.1 1.0
C5' S:CFZ10 4.4 59.4 1.0
C6 S:CFZ10 4.7 56.1 1.0
O4' S:CFZ11 4.8 81.5 1.0
O2P S:CFZ11 4.9 68.9 1.0

Fluorine binding site 5 out of 18 in 3agv

Go back to Fluorine Binding Sites List in 3agv
Fluorine binding site 5 out of 18 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:F11

b:83.2
occ:1.00
 F2' S:CFZ11 0.0 83.2 1.0
C2' S:CFZ11 1.4 81.8 1.0
C3' S:CFZ11 2.4 81.0 1.0
C1' S:CFZ11 2.5 82.2 1.0
O3' S:CFZ11 2.8 79.7 1.0
C4' S:CFZ11 3.0 80.0 1.0
O4' S:CFZ11 3.2 81.5 1.0
N1 S:CFZ11 3.7 81.9 1.0
O2 S:CFZ11 4.1 83.1 1.0
C2 S:CFZ11 4.3 82.3 1.0
C5' S:CFZ11 4.5 77.3 1.0
C6 S:CFZ11 4.6 81.4 1.0

Fluorine binding site 6 out of 18 in 3agv

Go back to Fluorine Binding Sites List in 3agv
Fluorine binding site 6 out of 18 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:F20

b:51.4
occ:1.00
 F2' S:CFZ20 0.0 51.4 1.0
C2' S:CFZ20 1.4 52.6 1.0
C3' S:CFZ20 2.4 51.7 1.0
C1' S:CFZ20 2.4 53.1 1.0
O3' S:CFZ20 2.7 52.4 1.0
C4' S:CFZ20 3.0 52.5 1.0
O4' S:CFZ20 3.1 52.4 1.0
CG A:GLN342 3.3 42.4 1.0
O A:HOH51 3.3 30.2 1.0
CG A:ARG344 3.3 33.7 1.0
C5' S:UFT21 3.5 57.6 1.0
CD A:ARG344 3.5 34.3 1.0
NE A:ARG344 3.5 33.8 1.0
N1 S:CFZ20 3.7 54.0 1.0
CB A:GLN342 3.7 39.7 1.0
O5' S:UFT21 3.7 54.6 1.0
O2 S:CFZ20 3.8 53.4 1.0
O4' S:UFT21 3.8 60.9 1.0
P S:UFT21 3.9 54.9 1.0
O A:GLN342 3.9 38.5 1.0
C2 S:CFZ20 4.2 54.1 1.0
C4' S:UFT21 4.2 60.3 1.0
CZ A:ARG344 4.3 34.3 1.0
C A:GLN342 4.4 39.9 1.0
O A:PRO343 4.4 38.1 1.0
C5' S:CFZ20 4.5 51.9 1.0
CB A:ARG344 4.5 33.6 1.0
CA A:GLN342 4.7 40.0 1.0
C6 S:CFZ20 4.7 53.6 1.0
C6 S:UFT21 4.7 68.5 1.0
OP2 S:UFT21 4.7 57.2 1.0
CD A:GLN342 4.7 42.7 1.0
OP1 S:UFT21 4.8 55.5 1.0
C A:PRO343 4.9 38.4 1.0
NH1 A:ARG344 4.9 33.4 1.0
NH2 A:ARG344 4.9 32.0 1.0

Fluorine binding site 7 out of 18 in 3agv

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Fluorine binding site 7 out of 18 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:F21

b:62.4
occ:1.00
 F2' S:UFT21 0.0 62.4 1.0
C2' S:UFT21 1.4 61.4 1.0
C3' S:UFT21 2.4 61.4 1.0
C1' S:UFT21 2.4 63.0 1.0
O3' S:UFT21 2.7 63.7 1.0
C4' S:UFT21 3.0 60.3 1.0
O4' S:UFT21 3.2 60.9 1.0
O4' S:CFZ22 3.3 83.3 1.0
O2 S:UFT21 3.5 67.5 1.0
N1 S:UFT21 3.6 66.2 1.0
O5' S:CFZ22 3.7 70.3 1.0
NE2 A:GLN342 3.8 37.6 1.0
C5' S:CFZ22 3.9 77.4 1.0
P S:CFZ22 3.9 65.8 1.0
C2 S:UFT21 4.0 67.5 1.0
C4' S:CFZ22 4.2 82.2 1.0
C6 S:CFZ22 4.2 86.6 1.0
CD A:GLN342 4.3 42.7 1.0
C5' S:UFT21 4.4 57.6 1.0
C1' S:CFZ22 4.4 84.7 1.0
OE1 A:GLN342 4.7 43.4 1.0
N1 S:CFZ22 4.7 85.7 1.0
O2P S:CFZ22 4.8 65.9 1.0
C6 S:UFT21 4.8 68.5 1.0
O1P S:CFZ22 4.8 65.3 1.0

Fluorine binding site 8 out of 18 in 3agv

Go back to Fluorine Binding Sites List in 3agv
Fluorine binding site 8 out of 18 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:F22

b:84.5
occ:1.00
 F2' S:CFZ22 0.0 84.5 1.0
C2' S:CFZ22 1.4 84.6 1.0
C3' S:CFZ22 2.4 84.7 1.0
C1' S:CFZ22 2.4 84.7 1.0
O3' S:CFZ22 2.7 88.0 1.0
C4' S:CFZ22 3.0 82.2 1.0
O4' S:CFZ22 3.2 83.3 1.0
C5' S:CFZ23 3.3 90.3 1.0
O5' S:CFZ23 3.4 89.5 1.0
O2 S:CFZ22 3.6 88.4 1.0
N1 S:CFZ22 3.7 85.7 1.0
P S:CFZ23 3.7 89.4 1.0
C4' S:CFZ23 3.9 91.1 1.0
C2 S:CFZ22 4.1 86.6 1.0
O4' S:CFZ23 4.3 91.3 1.0
C5' S:CFZ22 4.5 77.4 1.0
O2P S:CFZ23 4.6 89.6 1.0
O1P S:CFZ23 4.7 89.7 1.0
C6 S:CFZ22 4.7 86.6 1.0

Fluorine binding site 9 out of 18 in 3agv

Go back to Fluorine Binding Sites List in 3agv
Fluorine binding site 9 out of 18 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:F23

b:91.8
occ:1.00
 F2' S:CFZ23 0.0 91.8 1.0
C2' S:CFZ23 1.4 92.0 1.0
C3' S:CFZ23 2.4 92.0 1.0
C1' S:CFZ23 2.5 92.7 1.0
O3' S:CFZ23 2.7 91.9 1.0
C4' S:CFZ23 3.1 91.1 1.0
O4' S:CFZ23 3.1 91.3 1.0
N1 S:CFZ23 3.7 94.0 1.0
O2 S:CFZ23 4.0 95.9 1.0
C2 S:CFZ23 4.3 95.2 1.0
C5' S:CFZ23 4.5 90.3 1.0
C6 S:CFZ23 4.7 94.1 1.0

Fluorine binding site 10 out of 18 in 3agv

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Fluorine binding site 10 out of 18 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
U:F6

b:51.2
occ:1.00
 F2' U:UFT6 0.0 51.2 1.0
C2' U:UFT6 1.4 50.2 1.0
C3' U:UFT6 2.4 49.8 1.0
C1' U:UFT6 2.5 52.5 1.0
O3' U:UFT6 2.6 48.1 1.0
O U:HOH54 2.9 31.8 1.0
C8 U:G7 3.2 35.2 1.0
C4' U:UFT6 3.2 51.6 1.0
N7 U:G7 3.3 35.7 1.0
O2 U:UFT6 3.3 52.7 1.0
O4' U:UFT6 3.3 49.6 1.0
OP2 U:G7 3.4 46.8 1.0
O U:HOH246 3.4 0.2 1.0
O U:HOH82 3.5 39.6 1.0
N1 U:UFT6 3.6 52.9 1.0
P U:G7 3.6 46.2 1.0
C2 U:UFT6 3.8 52.9 1.0
C5' U:G7 3.8 43.1 1.0
O U:HOH253 4.0 35.1 1.0
O5' U:G7 4.0 45.0 1.0
N9 U:G7 4.3 37.0 1.0
O U:HOH134 4.4 39.2 1.0
C5 U:G7 4.5 34.0 1.0
O4' U:G7 4.5 40.1 1.0
C5' U:UFT6 4.6 53.5 1.0
C4' U:G7 4.7 41.1 1.0
C6 U:UFT6 4.7 53.1 1.0
OP1 U:G7 4.9 48.7 1.0
N6 U:A18 4.9 44.5 1.0
CA U:CA25 5.0 56.6 1.0
CA B:GLY341 5.0 33.7 1.0
C4 U:G7 5.0 34.0 1.0

Reference:

Y.Nomura, S.Sugiyama, T.Sakamoto, S.Miyakawa, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori, Y.Nakamura, H.Matsumura. Conformational Plasticity of Rna For Target Recognition As Revealed By the 2.15 A Crystal Structure of A Human Igg-Aptamer Complex Nucleic Acids Res. V. 38 7822 2010.
ISSN: ISSN 0305-1048
PubMed: 20675355
DOI: 10.1093/NAR/GKQ615
Page generated: Wed Jul 31 17:07:42 2024

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