Fluorine in PDB 6rti: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G, PDB code: 6rti was solved by L.Motlova, P.Kolenko, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.66 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.096, 121.096, 216.271, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.7

Other elements in 6rti:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Fluorine atom in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G (pdb code 6rti). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 22 binding sites of Fluorine where determined in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G, PDB code: 6rti:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 22 in 6rti

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Fluorine binding site 1 out of 22 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F5

b:58.8
occ:1.00
F2' X:CFZ5 0.0 58.8 1.0
C2' X:CFZ5 1.4 61.3 1.0
C1' X:CFZ5 2.4 59.3 1.0
C3' X:CFZ5 2.4 60.0 1.0
O3' X:CFZ5 2.8 62.0 1.0
C4' X:CFZ5 2.9 59.2 1.0
O4' X:CFZ5 3.1 58.1 1.0
O4' X:CFZ6 3.3 60.7 1.0
C5' X:CFZ6 3.4 59.6 1.0
CB A:ASP316 3.5 58.4 1.0
N1 X:CFZ5 3.6 57.2 1.0
O5' X:CFZ6 3.8 59.1 1.0
O2 X:CFZ5 3.8 60.2 1.0
C4' X:CFZ6 3.8 60.0 1.0
O A:HOH1015 3.8 47.8 1.0
P X:CFZ6 4.0 64.2 1.0
C2 X:CFZ5 4.2 57.9 1.0
O A:PRO315 4.2 55.5 1.0
CG A:ASP316 4.4 59.7 1.0
OD2 A:ASP316 4.4 59.1 1.0
C5' X:CFZ5 4.4 56.5 1.0
O2P X:CFZ6 4.6 67.4 1.0
CA A:ASP316 4.6 52.1 1.0
C1' X:CFZ6 4.6 59.5 1.0
C6 X:CFZ5 4.7 57.4 1.0
C6 X:CFZ6 4.8 56.8 1.0

Fluorine binding site 2 out of 22 in 6rti

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Fluorine binding site 2 out of 22 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F6

b:59.5
occ:1.00
F2' X:CFZ6 0.0 59.5 1.0
C2' X:CFZ6 1.4 59.5 1.0
C3' X:CFZ6 2.4 62.7 1.0
C1' X:CFZ6 2.4 59.5 1.0
O5' X:G7 2.7 67.8 0.5
O3' X:CFZ6 2.7 61.9 1.0
C4' X:CFZ6 2.9 60.0 1.0
OG A:SER318 3.0 47.3 1.0
OD1 A:ASP316 3.1 57.6 1.0
O4' X:CFZ6 3.1 60.7 1.0
C5' X:G7 3.1 69.2 0.5
O4' X:G7 3.3 71.0 0.5
O4' X:G7 3.3 71.3 0.5
P X:G7 3.3 64.4 0.5
O5' X:G7 3.3 65.9 0.5
CB A:SER318 3.4 47.5 1.0
N1 X:CFZ6 3.6 56.2 1.0
CG A:ASP316 3.6 59.7 1.0
P X:G7 3.7 63.3 0.5
OD2 A:ASP316 3.8 59.1 1.0
C4' X:G7 3.8 73.3 0.5
O2 X:CFZ6 3.8 50.4 1.0
C5' X:G7 3.9 72.7 0.5
OP2 X:G7 4.1 57.5 0.5
C2 X:CFZ6 4.1 54.3 1.0
C4' X:G7 4.2 75.2 0.5
C8 X:G7 4.2 68.8 0.5
C1' X:G7 4.3 71.8 0.5
C8 X:G7 4.4 69.2 0.5
C5' X:CFZ6 4.4 59.6 1.0
OP1 X:G7 4.4 66.8 0.5
N9 X:G7 4.4 69.9 0.5
C1' X:G7 4.5 73.2 0.5
N9 X:G7 4.5 70.1 0.5
C6 X:CFZ6 4.6 56.8 1.0
OP2 X:G7 4.6 56.9 0.5
OP1 X:G7 4.6 68.1 0.5
CA A:SER318 4.7 46.9 1.0
CB A:ASP316 4.8 58.4 1.0
N A:SER318 4.8 51.2 1.0
O5' X:CFZ6 4.9 59.1 1.0
C3' X:G7 5.0 75.8 0.5

Fluorine binding site 3 out of 22 in 6rti

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Fluorine binding site 3 out of 22 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F15

b:41.9
occ:1.00
F2' X:CFZ15 0.0 41.9 1.0
C2' X:CFZ15 1.4 41.7 1.0
C1' X:CFZ15 2.3 41.2 1.0
C3' X:CFZ15 2.4 41.0 1.0
O3' X:CFZ15 2.7 36.4 1.0
C4' X:CFZ15 2.9 43.5 1.0
O4' X:CFZ15 3.1 40.3 1.0
C5' X:CFZ16 3.2 41.1 1.0
O5' X:CFZ16 3.4 42.4 1.0
O4' X:CFZ16 3.5 40.0 1.0
N1 X:CFZ15 3.5 43.5 1.0
O2 X:CFZ15 3.6 42.4 1.0
P X:CFZ16 3.7 40.5 1.0
C4' X:CFZ16 3.8 39.5 1.0
C2 X:CFZ15 4.0 43.1 1.0
C5' X:CFZ15 4.4 45.1 1.0
O1P X:CFZ16 4.4 40.3 1.0
C6 X:CFZ15 4.6 44.6 1.0
C6 X:CFZ16 4.8 45.1 1.0
O2P X:CFZ16 4.8 43.8 1.0
C1' X:CFZ16 4.8 41.5 1.0
O X:HOH223 5.0 47.4 1.0

Fluorine binding site 4 out of 22 in 6rti

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Fluorine binding site 4 out of 22 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F16

b:39.1
occ:1.00
F2' X:CFZ16 0.0 39.1 1.0
C2' X:CFZ16 1.4 39.7 1.0
C1' X:CFZ16 2.3 41.5 1.0
C3' X:CFZ16 2.4 39.5 1.0
O3' X:CFZ16 2.7 38.5 1.0
C4' X:CFZ16 2.9 39.5 1.0
O4' X:UFT17 3.0 39.1 1.0
O4' X:CFZ16 3.1 40.0 1.0
C5' X:UFT17 3.3 37.7 1.0
O X:HOH249 3.3 43.5 1.0
O5' X:UFT17 3.4 37.6 1.0
N1 X:CFZ16 3.6 44.8 1.0
C4' X:UFT17 3.6 37.8 1.0
P X:UFT17 3.7 39.0 1.0
O2 X:CFZ16 3.9 41.4 1.0
C2 X:CFZ16 4.2 42.9 1.0
C1' X:UFT17 4.2 39.0 1.0
C5' X:CFZ16 4.4 41.1 1.0
C6 X:CFZ16 4.6 45.1 1.0
N1 X:UFT17 4.6 37.4 1.0
OP2 X:UFT17 4.6 42.7 1.0
C6 X:UFT17 4.6 35.2 1.0
OP1 X:UFT17 4.7 38.2 1.0
C3' X:UFT17 5.0 40.7 1.0

Fluorine binding site 5 out of 22 in 6rti

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Fluorine binding site 5 out of 22 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F17

b:40.0
occ:1.00
F2' X:UFT17 0.0 40.0 1.0
C2' X:UFT17 1.4 39.3 1.0
C1' X:UFT17 2.3 39.0 1.0
C3' X:UFT17 2.3 40.7 1.0
O3' X:UFT17 2.6 38.6 1.0
C4' X:UFT17 2.9 37.8 1.0
O4' X:UFT17 3.1 39.1 1.0
O X:HOH255 3.3 44.4 1.0
C5' X:G18 3.3 44.4 1.0
O4' X:G18 3.4 42.9 1.0
N1 X:UFT17 3.5 37.4 1.0
O5' X:G18 3.6 41.0 1.0
O4 X:UFT29 3.7 48.8 1.0
P X:G18 3.8 40.5 1.0
C4' X:G18 3.9 44.2 1.0
O2 X:UFT17 4.1 37.8 1.0
C2 X:UFT17 4.2 36.1 1.0
N6 X:A30 4.3 42.7 1.0
C5' X:UFT17 4.4 37.7 1.0
C6 X:UFT17 4.4 35.2 1.0
O X:HOH249 4.4 43.5 1.0
OP2 X:G18 4.6 40.8 1.0
OP1 X:G18 4.7 43.1 1.0
C1' X:G18 4.7 42.3 1.0
C8 X:G18 4.9 39.2 1.0
C4 X:UFT29 4.9 46.8 1.0
O5' X:UFT17 5.0 37.6 1.0

Fluorine binding site 6 out of 22 in 6rti

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Fluorine binding site 6 out of 22 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F20

b:67.5
occ:1.00
F2' X:CFZ20 0.0 67.5 1.0
C2' X:CFZ20 1.4 70.3 1.0
C3' X:CFZ20 2.4 67.6 1.0
C1' X:CFZ20 2.4 74.8 1.0
C4' X:CFZ20 2.7 66.1 1.0
O3' X:CFZ20 2.8 53.8 1.0
O4' X:CFZ20 2.9 75.7 1.0
OP2 X:UFT21 3.6 56.4 1.0
N1 X:CFZ20 3.7 75.0 1.0
P X:UFT21 3.7 54.1 1.0
O2 X:CFZ20 4.1 76.9 1.0
C5' X:CFZ20 4.2 58.2 1.0
O X:HOH247 4.2 43.3 1.0
OP1 X:UFT21 4.3 58.0 1.0
C2 X:CFZ20 4.4 75.3 1.0
C6 X:CFZ20 4.7 71.9 1.0
O5' X:CFZ20 4.9 50.1 1.0

Fluorine binding site 7 out of 22 in 6rti

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Fluorine binding site 7 out of 22 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F21

b:46.3
occ:1.00
F2' X:UFT21 0.0 46.3 1.0
C2' X:UFT21 1.4 48.9 1.0
C1' X:UFT21 2.3 49.9 1.0
C3' X:UFT21 2.4 44.6 1.0
O3' X:UFT21 2.7 40.9 1.0
C4' X:UFT21 2.9 49.9 1.0
O4' X:UFT21 3.0 50.4 1.0
O X:HOH246 3.3 33.2 1.0
C5 X:UFT22 3.5 38.4 1.0
N1 X:UFT21 3.5 53.5 1.0
C6 X:UFT22 3.6 39.5 1.0
O5' X:UFT22 3.6 43.1 1.0
C5 X:CFZ23 3.7 41.8 1.0
O2' X:G18 3.7 41.0 1.0
P X:UFT22 3.9 44.1 1.0
O2 X:UFT21 3.9 49.5 1.0
C2 X:UFT21 4.1 52.9 1.0
O1P X:CFZ23 4.1 41.3 1.0
C5' X:UFT21 4.3 53.7 1.0
C4 X:UFT22 4.4 40.4 1.0
N4 X:CFZ23 4.4 45.2 1.0
N1 X:UFT22 4.4 42.3 1.0
CM X:MPD102 4.5 52.4 1.0
C6 X:UFT21 4.5 52.2 1.0
C6 X:CFZ23 4.5 42.0 1.0
C4 X:CFZ23 4.5 46.4 1.0
C3' X:UFT22 4.6 43.1 1.0
OP1 X:UFT22 4.7 46.4 1.0
OP2 X:UFT22 4.8 43.1 1.0
C5 X:UFT24 4.8 45.9 1.0
O5' X:UFT21 4.8 56.7 1.0
O4 X:UFT22 4.9 37.9 1.0
C5' X:UFT22 4.9 40.9 1.0
O4' X:A19 4.9 48.2 1.0

Fluorine binding site 8 out of 22 in 6rti

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Fluorine binding site 8 out of 22 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F22

b:42.8
occ:1.00
F2' X:UFT22 0.0 42.8 1.0
C2' X:UFT22 1.4 43.9 1.0
C1' X:UFT22 2.3 42.4 1.0
C3' X:UFT22 2.4 43.1 1.0
O3' X:UFT22 2.7 41.2 1.0
C4' X:UFT22 2.9 42.6 1.0
O4' X:UFT22 2.9 43.1 1.0
NE2 A:GLN620 3.0 65.7 1.0
CG A:PRO619 3.1 38.7 1.0
CB A:PRO619 3.2 40.0 1.0
CD A:GLN620 3.4 60.5 1.0
C5' X:CFZ23 3.5 43.3 1.0
N1 X:UFT22 3.7 42.3 1.0
N A:GLN620 3.8 43.1 1.0
C A:PRO619 3.9 41.0 1.0
O5' X:CFZ23 3.9 45.0 1.0
OE1 A:GLN620 3.9 62.7 1.0
O2 X:UFT22 3.9 38.8 1.0
P X:CFZ23 4.0 41.8 1.0
CG A:GLN620 4.1 54.5 1.0
O4' X:CFZ23 4.1 42.0 1.0
CA A:PRO619 4.1 39.2 1.0
C2 X:UFT22 4.3 40.5 1.0
O A:PRO619 4.3 41.5 1.0
C4' X:CFZ23 4.3 44.1 1.0
C5' X:UFT22 4.4 40.9 1.0
CD A:PRO619 4.4 37.8 1.0
CA A:GLN620 4.5 46.8 1.0
O X:HOH214 4.6 47.1 1.0
C6 X:UFT22 4.7 39.5 1.0
O2P X:CFZ23 4.7 43.1 1.0
O X:HOH257 4.7 44.9 1.0
N A:PRO619 4.8 39.3 1.0
CB A:GLN620 4.8 50.1 1.0
O5' X:UFT22 5.0 43.1 1.0

Fluorine binding site 9 out of 22 in 6rti

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Fluorine binding site 9 out of 22 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F23

b:42.2
occ:1.00
F2' X:CFZ23 0.0 42.2 1.0
C2' X:CFZ23 1.4 41.6 1.0
C1' X:CFZ23 2.3 41.0 1.0
C3' X:CFZ23 2.4 43.9 1.0
O3' X:CFZ23 2.8 40.8 1.0
O X:HOH256 3.0 42.4 1.0
C4' X:CFZ23 3.0 44.1 1.0
O4' X:CFZ23 3.0 42.0 1.0
O5' X:UFT24 3.1 42.2 1.0
O A:HOH1275 3.1 41.9 1.0
O A:HOH1108 3.4 60.0 1.0
N1 X:CFZ23 3.5 40.2 1.0
P X:UFT24 3.6 43.2 1.0
O4' X:UFT24 3.7 48.7 1.0
O2 X:CFZ23 3.8 43.7 1.0
CE A:MET622 4.0 37.0 1.0
C2 X:CFZ23 4.1 44.0 1.0
C4' X:UFT24 4.2 48.2 1.0
C5' X:UFT24 4.3 45.3 1.0
CB A:MET622 4.4 39.9 1.0
OP1 X:UFT24 4.5 44.5 1.0
C5' X:CFZ23 4.5 43.3 1.0
SD A:MET616 4.5 39.6 1.0
C6 X:CFZ23 4.6 42.0 1.0
O A:PRO619 4.7 41.5 1.0
OP2 X:UFT24 4.7 41.5 1.0
C1' X:UFT24 4.8 47.2 1.0

Fluorine binding site 10 out of 22 in 6rti

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Fluorine binding site 10 out of 22 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F24

b:47.2
occ:1.00
F2' X:UFT24 0.0 47.2 1.0
C2' X:UFT24 1.4 47.2 1.0
C3' X:UFT24 2.4 48.4 1.0
C1' X:UFT24 2.4 47.2 1.0
O3' X:UFT24 2.5 55.0 1.0
C4' X:UFT24 3.1 48.2 1.0
O2 X:UFT24 3.1 43.6 1.0
O X:HOH254 3.2 39.2 1.0
O4' X:UFT24 3.3 48.7 1.0
O A:HOH1087 3.3 34.1 1.0
N4 X:CFZ28 3.3 40.0 1.0
N1 X:UFT24 3.4 46.4 1.0
C2 X:UFT24 3.6 45.6 1.0
O5' X:A25 3.8 57.6 1.0
P X:A25 3.8 58.6 1.0
C1' X:UFT26 4.0 52.3 1.0
O X:HOH256 4.0 42.4 1.0
O2 X:UFT26 4.0 47.9 1.0
O4' X:UFT26 4.1 56.5 1.0
F2' X:UFT26 4.1 49.4 1.0
C1 A:MPD927 4.3 46.0 1.0
OP1 X:A25 4.4 56.6 1.0
C5' X:UFT24 4.5 45.3 1.0
C6 X:UFT24 4.6 44.3 1.0
C4 X:CFZ28 4.6 42.5 1.0
C2' X:UFT26 4.7 50.2 1.0
C4' X:UFT26 4.8 58.5 1.0
OP2 X:A25 4.8 61.5 1.0
N3 X:UFT24 4.9 48.3 1.0
C2 X:UFT26 4.9 52.5 1.0
N1 X:UFT26 5.0 53.1 1.0

Reference:

L.Motlova, P.Kolenko, C.Barinka. X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Aptamer A9G To Be Published.
Page generated: Sun Dec 13 13:10:25 2020

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