Fluorine in PDB 7oih: Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase

Enzymatic activity of Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase

All present enzymatic activity of Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase:
1.11.2.2;

Protein crystallography data

The structure of Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase, PDB code: 7oih was solved by L.Krawczyk, S.Semwal, J.Bouckaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.99 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.91, 144.634, 236.454, 90, 91.53, 90
R / Rfree (%) 17.9 / 22

Other elements in 7oih:

The structure of Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Chlorine (Cl) 36 atoms
Calcium (Ca) 8 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase (pdb code 7oih). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase, PDB code: 7oih:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7oih

Go back to Fluorine Binding Sites List in 7oih
Fluorine binding site 1 out of 4 in the Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F807

b:90.6
occ:1.00
 FAA A:8PR807 0.0 90.6 1.0
CAR A:8PR807 1.4 100.7 1.0
CAC A:8PR807 2.3 102.8 1.0
CAB A:8PR807 2.4 93.9 1.0
OG1 A:THR404 3.2 50.5 1.0
O A:HOH1223 3.5 59.3 1.0
CB A:THR404 3.6 52.3 1.0
CAF A:8PR807 3.6 97.2 1.0
CAE A:8PR807 3.6 95.6 1.0
CAT A:8PR807 4.1 93.5 1.0
O A:THR404 4.1 36.5 1.0
C A:THR404 4.5 40.6 1.0
CG2 A:THR404 4.5 52.6 1.0
CZ A:PHE265 4.6 42.8 1.0
CA A:THR404 4.6 48.8 1.0

Fluorine binding site 2 out of 4 in 7oih

Go back to Fluorine Binding Sites List in 7oih
Fluorine binding site 2 out of 4 in the Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F807

b:97.5
occ:0.85
 FAA D:8PR807 0.0 97.5 0.8
CAR D:8PR807 1.4 108.8 0.8
CAC D:8PR807 2.3 111.5 0.8
CAB D:8PR807 2.4 101.0 0.8
OG1 D:THR404 3.1 48.9 1.0
CB D:THR404 3.3 51.0 1.0
CAF D:8PR807 3.6 113.4 0.8
CAE D:8PR807 3.6 107.6 0.8
O D:HOH976 3.7 45.6 1.0
CG2 D:THR404 4.1 47.8 1.0
CAT D:8PR807 4.1 124.1 0.8
O D:THR404 4.3 51.2 1.0
CZ D:PHE265 4.6 60.0 1.0
CA D:THR404 4.6 52.2 1.0
C D:THR404 4.6 51.5 1.0

Fluorine binding site 3 out of 4 in 7oih

Go back to Fluorine Binding Sites List in 7oih
Fluorine binding site 3 out of 4 in the Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F807

b:115.6
occ:0.79
 FAA F:8PR807 0.0 115.6 0.8
CAR F:8PR807 1.4 114.8 0.8
CAC F:8PR807 2.3 108.5 0.8
CAB F:8PR807 2.3 109.3 0.8
OG1 F:THR404 3.2 56.2 1.0
CB F:THR404 3.2 58.1 1.0
O F:THR404 3.3 53.3 1.0
O F:HOH1182 3.4 64.2 1.0
CAF F:8PR807 3.6 109.0 0.8
CAE F:8PR807 3.6 109.7 0.8
C F:THR404 3.8 52.7 1.0
CA F:THR404 4.1 53.2 1.0
CAT F:8PR807 4.1 110.8 0.8
CG2 F:THR404 4.3 62.9 1.0
N F:ARG405 4.8 51.5 1.0

Fluorine binding site 4 out of 4 in 7oih

Go back to Fluorine Binding Sites List in 7oih
Fluorine binding site 4 out of 4 in the Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Glycosylation in the Crystal Structure of Neutrophil Myeloperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F807

b:96.8
occ:0.73
 FAA H:8PR807 0.0 96.8 0.7
CAR H:8PR807 1.4 93.0 0.7
CAC H:8PR807 2.3 88.7 0.7
CAB H:8PR807 2.3 89.7 0.7
O H:HOH1133 2.4 61.8 1.0
O H:THR404 2.7 55.7 1.0
OG1 H:THR404 2.9 48.5 1.0
CB H:THR404 2.9 45.4 1.0
C H:THR404 3.2 49.5 1.0
O H:HOH1168 3.6 57.1 1.0
CAF H:8PR807 3.6 84.2 0.7
CAE H:8PR807 3.6 88.8 0.7
CA H:THR404 3.7 49.7 1.0
N H:ARG405 4.1 51.2 1.0
CAT H:8PR807 4.1 87.4 0.7
CG2 H:THR404 4.2 45.6 1.0
CA H:ARG405 4.4 51.6 1.0
CG H:ARG405 4.7 50.7 1.0
O H:HOH1007 4.8 58.7 1.0
N H:THR404 4.9 49.2 1.0

Reference:

L.Krawczyk, S.Semwal, J.Soubhye, S.Lemri Ouadriri, M.Prevost, P.Van Antwerpen, G.Roos, J.Bouckaert. Native Glycosylation and Binding of the Antidepressant Paroxetine in A Low-Resolution Crystal Structure of Human Myeloperoxidase. Acta Crystallogr D Struct V. 78 1099 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 36048150
DOI: 10.1107/S2059798322007082
Page generated: Wed Apr 5 00:30:39 2023

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