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Fluorine in PDB 3gpt: Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand

Enzymatic activity of Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand

All present enzymatic activity of Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand:
3.4.25.1;

Protein crystallography data

The structure of Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand, PDB code: 3gpt was solved by M.Groll, V.R.Macherla, R.R.Manam, K.A.M.Arthur, C.B.Potts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.41
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.000, 301.260, 143.810, 90.00, 112.56, 90.00
R / Rfree (%) 22.6 / 24.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand (pdb code 3gpt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand, PDB code: 3gpt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3gpt

Go back to Fluorine Binding Sites List in 3gpt
Fluorine binding site 1 out of 6 in the Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand


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 Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F224

b:53.5
occ:1.00
F21 H:GPT224 0.0 53.5 1.0
C1 H:GPT224 1.3 47.9 1.0
C2 H:GPT224 2.4 45.9 1.0
OH Z:TYR24 3.1 56.1 1.0
CZ Z:TYR24 3.4 55.0 1.0
CE1 Z:TYR24 3.7 53.9 1.0
C3 H:GPT224 3.8 45.0 1.0
O H:HOH822 4.0 41.1 1.0
O5 H:GPT224 4.0 41.4 1.0
CE2 Z:TYR24 4.1 53.1 1.0
O20 H:GPT224 4.4 44.1 1.0
C19 H:GPT224 4.4 44.3 1.0
C4 H:GPT224 4.6 43.7 1.0
CD1 Z:TYR24 4.6 52.6 1.0
CB H:SER129 4.8 31.1 1.0
OG H:SER129 4.9 33.7 1.0
CD2 Z:TYR24 5.0 51.1 1.0

Fluorine binding site 2 out of 6 in 3gpt

Go back to Fluorine Binding Sites List in 3gpt
Fluorine binding site 2 out of 6 in the Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand


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 Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F224

b:44.4
occ:1.00
F21 K:GPT224 0.0 44.4 1.0
C1 K:GPT224 1.4 37.4 1.0
C2 K:GPT224 2.4 36.0 1.0
O K:HOH1348 3.1 29.1 1.0
CD2 K:TYR168 3.6 37.9 1.0
CE2 K:TYR168 3.8 37.4 1.0
C3 K:GPT224 3.8 35.0 1.0
O K:HOH1345 4.0 35.1 1.0
O K:HOH1347 4.2 26.5 1.0
O5 K:GPT224 4.2 32.6 1.0
O20 K:GPT224 4.4 36.1 1.0
C19 K:GPT224 4.4 36.0 1.0
CG K:TYR168 4.4 36.9 1.0
O K:HOH1344 4.5 31.7 1.0
C4 K:GPT224 4.7 34.0 1.0
CZ K:TYR168 4.8 39.8 1.0

Fluorine binding site 3 out of 6 in 3gpt

Go back to Fluorine Binding Sites List in 3gpt
Fluorine binding site 3 out of 6 in the Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand


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 Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
N:F224

b:53.3
occ:1.00
F21 N:GPT224 0.0 53.3 1.0
C1 N:GPT224 1.4 46.9 1.0
C2 N:GPT224 2.4 41.0 1.0
O N:HOH871 3.5 38.4 1.0
OG N:SER168 3.7 36.9 1.0
C3 N:GPT224 3.8 36.8 1.0
O5 N:GPT224 4.1 34.7 1.0
O20 N:GPT224 4.4 39.6 1.0
C19 N:GPT224 4.4 37.4 1.0
CB N:SER168 4.5 36.1 1.0
C4 N:GPT224 4.6 35.1 1.0
OG1 N:THR21 5.0 47.1 1.0

Fluorine binding site 4 out of 6 in 3gpt

Go back to Fluorine Binding Sites List in 3gpt
Fluorine binding site 4 out of 6 in the Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand


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 Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
V:F224

b:54.2
occ:1.00
F21 V:GPT224 0.0 54.2 1.0
C1 V:GPT224 1.4 49.3 1.0
C2 V:GPT224 2.4 46.5 1.0
OH L:TYR24 3.1 53.2 1.0
CZ L:TYR24 3.4 51.9 1.0
CE1 L:TYR24 3.7 52.2 1.0
C3 V:GPT224 3.8 44.8 1.0
O5 V:GPT224 4.1 41.0 1.0
CE2 L:TYR24 4.1 50.8 1.0
O20 V:GPT224 4.3 48.2 1.0
C19 V:GPT224 4.3 45.5 1.0
O V:HOH1327 4.6 44.6 1.0
C4 V:GPT224 4.6 44.6 1.0
CD1 L:TYR24 4.6 48.9 1.0
CB V:SER129 4.9 34.4 1.0
OG V:SER129 5.0 35.0 1.0
CD2 L:TYR24 5.0 48.5 1.0

Fluorine binding site 5 out of 6 in 3gpt

Go back to Fluorine Binding Sites List in 3gpt
Fluorine binding site 5 out of 6 in the Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand


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 Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:F224

b:49.3
occ:1.00
F21 Y:GPT224 0.0 49.3 1.0
C1 Y:GPT224 1.4 43.0 1.0
C2 Y:GPT224 2.4 39.0 1.0
CD2 Y:TYR168 3.6 42.0 1.0
CE2 Y:TYR168 3.8 45.6 1.0
C3 Y:GPT224 3.8 38.0 1.0
O5 Y:GPT224 4.2 37.9 1.0
C19 Y:GPT224 4.4 37.5 1.0
O20 Y:GPT224 4.4 37.8 1.0
CG Y:TYR168 4.4 40.9 1.0
C4 Y:GPT224 4.6 36.8 1.0
CZ Y:TYR168 4.7 47.1 1.0
O Y:HOH248 4.9 46.7 1.0
CB Y:TYR168 5.0 38.4 1.0

Fluorine binding site 6 out of 6 in 3gpt

Go back to Fluorine Binding Sites List in 3gpt
Fluorine binding site 6 out of 6 in the Crystal Structure of the Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand


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 Yeast 20S Proteasome in Complex with Salinosporamide Derivatives: Slow Substrate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
2:F224

b:54.9
occ:1.00
F21 2:GPT224 0.0 54.9 1.0
C1 2:GPT224 1.4 48.1 1.0
C2 2:GPT224 2.4 44.2 1.0
O 2:HOH316 3.0 38.0 1.0
OG 2:SER168 3.7 32.9 1.0
C3 2:GPT224 3.8 40.6 1.0
O5 2:GPT224 4.2 39.1 1.0
O20 2:GPT224 4.3 42.0 1.0
C19 2:GPT224 4.4 40.3 1.0
CB 2:SER168 4.5 36.0 1.0
C4 2:GPT224 4.6 38.5 1.0

Reference:

M.Groll, K.A.Mcarthur, V.R.Macherla, R.R.Manam, B.C.Potts. Snapshots of the Fluorosalinosporamide/20S Complex Offer Mechanistic Insights For Fine Tuning Proteasome Inhibition J.Med.Chem. V. 52 5420 2009.
ISSN: ISSN 0022-2623
PubMed: 19678642
DOI: 10.1021/JM900559X
Page generated: Wed Jul 31 18:58:13 2024

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