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Fluorine in PDB 3n33: Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf)

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf), PDB code: 3n33 was solved by T.Merz, T.Heck, B.Geueke, H.-P.Kohler, M.G.Gruetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.07 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.400, 96.850, 101.300, 90.00, 108.38, 90.00
R / Rfree (%) 16 / 19.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf) (pdb code 3n33). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf), PDB code: 3n33:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3n33

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Fluorine binding site 1 out of 8 in the Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf)


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 the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F376

b:34.6
occ:1.00
 F A:AES376 0.0 34.6 1.0
S A:AES376 1.5 28.3 1.0
O2S A:AES376 2.4 29.6 1.0
O1S A:AES376 2.5 29.8 1.0
C1 A:AES376 2.7 18.8 1.0
O1S B:EPE375 3.0 36.0 0.8
C2 A:AES376 3.2 17.1 1.0
CA B:SER125 3.4 18.7 1.0
O2S B:EPE375 3.4 35.2 0.8
CE2 B:PHE124 3.5 18.9 1.0
CD2 B:PHE124 3.5 17.6 1.0
O B:PHE124 3.6 16.9 1.0
S B:EPE375 3.8 34.5 0.8
C6 A:AES376 3.8 16.3 1.0
N B:SER125 4.0 14.2 1.0
C B:PHE124 4.1 15.6 1.0
CB B:SER125 4.1 16.7 1.0
C B:SER125 4.1 17.0 1.0
O B:SER125 4.2 15.1 1.0
CD2 B:LEU92 4.3 21.7 1.0
O3S B:EPE375 4.4 37.4 0.8
C3 A:AES376 4.6 17.3 1.0
CZ B:PHE124 4.6 19.2 1.0
CG B:PHE124 4.6 17.8 1.0
CG B:LEU92 4.9 22.8 1.0
C5 A:AES376 5.0 19.0 1.0

Fluorine binding site 2 out of 8 in 3n33

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Fluorine binding site 2 out of 8 in the Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf)


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 the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F377

b:35.8
occ:0.77
 F A:AES377 0.0 35.8 0.8
S A:AES377 1.5 24.1 0.8
O1S A:AES377 2.5 26.2 0.8
O2S A:AES377 2.5 24.3 0.8
C1 A:AES377 2.7 26.6 0.8
CE1 B:PHE143 3.2 20.8 1.0
CD1 A:LEU127 3.2 20.6 1.0
CA A:PHE124 3.3 21.5 1.0
N A:PHE124 3.4 17.8 1.0
C2 A:AES377 3.4 24.3 0.8
C A:LEU123 3.5 17.3 1.0
C6 A:AES377 3.5 25.6 0.8
O A:LEU123 3.6 17.0 1.0
CG A:LEU127 3.6 18.1 1.0
CZ B:PHE143 3.9 17.5 1.0
CD2 A:LEU127 3.9 17.6 1.0
CB A:LEU123 4.1 18.8 1.0
CB A:PHE124 4.1 16.6 1.0
CD1 B:PHE143 4.2 18.6 1.0
CA A:LEU123 4.4 16.1 1.0
C A:PHE124 4.5 19.4 1.0
O A:HOH640 4.6 30.1 1.0
C3 A:AES377 4.7 29.0 0.8
O A:PHE124 4.7 18.4 1.0
CD1 A:PHE124 4.8 21.8 1.0
C5 A:AES377 4.8 29.7 0.8
CG A:PHE124 4.8 19.2 1.0
CD1 B:LEU135 4.9 15.4 1.0
CG1 B:VAL142 5.0 18.2 1.0
CD2 B:LEU135 5.0 17.4 1.0

Fluorine binding site 3 out of 8 in 3n33

Go back to Fluorine Binding Sites List in 3n33
Fluorine binding site 3 out of 8 in the Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf)


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 the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F376

b:32.4
occ:1.00
 F B:AES376 0.0 32.4 1.0
S B:AES376 1.5 31.2 1.0
O2S B:AES376 2.5 30.7 1.0
O1S B:AES376 2.5 26.9 1.0
C1 B:AES376 2.7 20.4 1.0
C6 B:AES376 3.2 18.3 1.0
CD2 A:LEU84 3.5 12.8 1.0
C2 B:AES376 3.7 16.2 1.0
CD2 A:LEU92 3.8 23.2 1.0
CD1 A:LEU128 3.8 14.2 1.0
O A:HOH440 4.1 17.2 1.0
O A:SER125 4.1 16.2 1.0
CB A:LEU128 4.1 14.7 1.0
CG A:LEU128 4.2 14.6 1.0
CD1 A:LEU84 4.2 13.3 1.0
O A:HOH424 4.2 16.6 1.0
CA A:SER125 4.5 17.8 1.0
C A:SER125 4.5 15.1 1.0
CG A:LEU84 4.5 13.3 1.0
C5 B:AES376 4.6 17.5 1.0
O A:PHE124 4.6 18.4 1.0
N A:LEU128 4.7 12.2 1.0
CG A:LEU92 4.7 18.6 1.0
C3 B:AES376 5.0 17.4 1.0

Fluorine binding site 4 out of 8 in 3n33

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Fluorine binding site 4 out of 8 in the Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf)


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 the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F377

b:34.1
occ:1.00
 F B:AES377 0.0 34.1 1.0
S B:AES377 1.5 29.1 1.0
O1S B:AES377 2.5 33.5 1.0
O2S B:AES377 2.5 26.8 1.0
C1 B:AES377 2.7 26.9 1.0
C6 B:AES377 3.0 24.9 1.0
CG2 A:VAL142 3.3 16.6 1.0
CB A:VAL142 3.4 18.2 1.0
CB A:ASN137 3.4 18.8 1.0
CG1 A:VAL142 3.8 14.2 1.0
O A:HOH496 3.8 23.8 1.0
C2 B:AES377 3.9 30.2 1.0
CD1 A:LEU135 4.0 11.8 1.0
CE1 A:PHE143 4.0 20.5 1.0
CD1 B:LEU127 4.2 19.2 1.0
CA A:ASN137 4.2 18.9 1.0
O A:HOH902 4.2 35.7 1.0
C5 B:AES377 4.4 26.5 1.0
CD1 A:PHE143 4.4 19.6 1.0
CD2 B:LEU127 4.5 20.0 1.0
CD2 A:LEU135 4.6 15.9 1.0
CG A:ASN137 4.7 20.8 1.0
CG A:LEU135 4.7 17.8 1.0
CA A:VAL142 4.8 16.8 1.0
CG B:LEU127 4.8 17.9 1.0
ND2 A:ASN137 5.0 28.4 1.0

Fluorine binding site 5 out of 8 in 3n33

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Fluorine binding site 5 out of 8 in the Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf)


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 the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F375

b:34.7
occ:1.00
 F C:AES375 0.0 34.7 1.0
S C:AES375 1.5 29.0 1.0
O1S C:AES375 2.5 28.6 1.0
O2S C:AES375 2.5 31.6 1.0
C1 C:AES375 2.7 20.6 1.0
C6 C:AES375 3.1 21.3 1.0
CD1 D:LEU128 3.7 13.8 1.0
C2 C:AES375 3.8 17.6 1.0
CD2 D:LEU84 3.8 14.5 1.0
CD2 D:LEU92 3.9 20.3 1.0
O D:SER125 3.9 15.6 1.0
O D:HOH420 4.0 16.1 1.0
CG D:LEU128 4.1 14.5 1.0
CB D:LEU128 4.1 14.0 1.0
C D:SER125 4.3 14.7 1.0
CA D:SER125 4.3 17.8 1.0
O D:PHE124 4.4 16.8 1.0
O D:HOH427 4.5 16.6 1.0
C5 C:AES375 4.5 21.2 1.0
CD1 D:LEU84 4.6 12.0 1.0
N D:LEU128 4.6 14.4 1.0
CG D:LEU92 4.8 21.8 1.0
CG D:LEU84 4.8 11.9 1.0
CA D:LEU128 5.0 12.8 1.0

Fluorine binding site 6 out of 8 in 3n33

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Fluorine binding site 6 out of 8 in the Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf)


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 the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F376

b:26.8
occ:0.78
 F C:AES376 0.0 26.8 0.8
S C:AES376 1.5 23.2 0.8
O1S C:AES376 2.5 29.2 0.8
O2S C:AES376 2.5 25.0 0.8
C1 C:AES376 2.7 23.5 0.8
C2 C:AES376 2.9 19.4 0.8
CB D:ASN137 3.4 15.6 1.0
CG2 D:VAL142 3.5 14.3 1.0
CB D:VAL142 3.5 14.1 1.0
CG1 D:VAL142 3.8 15.9 1.0
O D:HOH476 3.9 20.6 1.0
C6 C:AES376 3.9 27.9 0.8
CD1 D:LEU135 3.9 11.8 1.0
O D:HOH745 4.0 32.4 1.0
CD1 C:LEU127 4.1 18.8 1.0
CA D:ASN137 4.1 15.1 1.0
CE1 D:PHE143 4.2 18.6 1.0
C3 C:AES376 4.4 23.5 0.8
CD2 D:LEU135 4.5 15.7 1.0
CD1 D:PHE143 4.5 20.9 1.0
CG D:ASN137 4.6 20.0 1.0
CG D:LEU135 4.6 14.4 1.0
CD2 C:LEU127 4.6 14.7 1.0
CG C:LEU127 4.9 15.8 1.0
CA D:VAL142 4.9 15.3 1.0
ND2 D:ASN137 4.9 25.6 1.0

Fluorine binding site 7 out of 8 in 3n33

Go back to Fluorine Binding Sites List in 3n33
Fluorine binding site 7 out of 8 in the Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf)


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 the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F375

b:38.5
occ:1.00
 F D:AES375 0.0 38.5 1.0
S D:AES375 1.5 27.8 1.0
O1S D:AES375 2.5 27.9 1.0
O2S D:AES375 2.5 31.8 1.0
C1 D:AES375 2.7 17.1 1.0
C6 D:AES375 3.2 17.1 1.0
CD2 C:LEU92 3.7 23.6 1.0
CD2 C:LEU84 3.7 14.2 1.0
C2 D:AES375 3.8 15.9 1.0
CD1 C:LEU128 3.8 11.1 1.0
O C:SER125 4.0 14.6 1.0
CB C:LEU128 4.0 9.5 1.0
CG C:LEU128 4.1 11.9 1.0
O C:HOH440 4.1 18.2 1.0
CD1 C:LEU84 4.2 12.6 1.0
O C:HOH410 4.4 15.4 1.0
C C:SER125 4.4 16.6 1.0
CA C:SER125 4.5 17.1 1.0
O C:PHE124 4.5 16.1 1.0
C5 D:AES375 4.6 17.0 1.0
N C:LEU128 4.6 13.9 1.0
CG C:LEU84 4.6 11.3 1.0
CG C:LEU92 4.6 20.6 1.0
CA C:LEU128 4.9 15.1 1.0
C3 D:AES375 5.0 16.1 1.0

Fluorine binding site 8 out of 8 in 3n33

Go back to Fluorine Binding Sites List in 3n33
Fluorine binding site 8 out of 8 in the Crystal Structure of the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf)


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 the N-Terminal Beta-Aminopeptidase Bapa in Complex with Pefabloc Sc (Aebsf) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F376

b:35.1
occ:1.00
 F D:AES376 0.0 35.1 1.0
S D:AES376 1.5 31.1 1.0
O1S D:AES376 2.4 32.3 1.0
O2S D:AES376 2.5 28.1 1.0
C1 D:AES376 2.7 31.4 1.0
CD1 D:LEU127 3.1 23.1 1.0
CA D:PHE124 3.2 21.2 1.0
N D:PHE124 3.3 19.1 1.0
CE1 C:PHE143 3.3 22.4 1.0
C6 D:AES376 3.5 28.9 1.0
C2 D:AES376 3.5 29.2 1.0
C D:LEU123 3.5 19.0 1.0
O D:LEU123 3.6 17.4 1.0
CG D:LEU127 3.7 20.4 1.0
CZ C:PHE143 3.8 21.2 1.0
CB D:PHE124 3.9 20.1 1.0
CD2 D:LEU127 4.1 20.1 1.0
CB D:LEU123 4.1 22.2 1.0
C D:PHE124 4.4 20.3 1.0
CD1 C:PHE143 4.4 21.2 1.0
CA D:LEU123 4.4 21.4 1.0
O D:HOH615 4.5 29.6 1.0
CD1 D:PHE124 4.6 20.6 1.0
O D:PHE124 4.7 16.8 1.0
CG D:PHE124 4.7 21.6 1.0
C5 D:AES376 4.7 36.5 1.0
C3 D:AES376 4.8 32.1 1.0
CD2 C:LEU135 5.0 17.7 1.0

Reference:

T.Merz, T.Heck, B.Geueke, P.R.Mittl, C.Briand, D.Seebach, H.P.Kohler, M.G.Grutter. Autoproteolytic and Catalytic Mechanisms For the Beta-Aminopeptidase Bapa--A Member of the Ntn Hydrolase Family. Structure V. 20 1850 2012.
ISSN: ISSN 0969-2126
PubMed: 22980995
DOI: 10.1016/J.STR.2012.07.017
Page generated: Mon Jul 14 18:00:02 2025

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