Fluorine in PDB 7u1v: Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3

Protein crystallography data

The structure of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3, PDB code: 7u1v was solved by A.Jacewicz, A.M.Sanchez, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.49 / 2.10
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.495, 115.864, 161.674, 90, 90, 90
R / Rfree (%) 17.9 / 20.9

Other elements in 7u1v:

The structure of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 also contains other interesting chemical elements:

Potassium (K) 1 atom
Nickel (Ni) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 (pdb code 7u1v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3, PDB code: 7u1v:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7u1v

Go back to Fluorine Binding Sites List in 7u1v
Fluorine binding site 1 out of 6 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F248

b:30.1
occ:1.00
 F1 A:BFD248 0.0 30.1 1.0
BE A:BFD248 1.5 36.0 1.0
OD1 A:BFD248 2.4 32.7 1.0
F2 A:BFD248 2.5 34.5 1.0
F3 A:BFD248 2.6 32.4 1.0
N A:ASP363 2.7 34.6 1.0
NZ A:LYS401 2.8 33.4 1.0
ND2 A:ASN192 3.2 42.5 1.0
CB A:ASP363 3.3 32.8 1.0
OD1 A:ASN192 3.4 41.4 1.0
CA A:GLY362 3.5 31.3 1.0
CE A:LYS401 3.6 38.2 1.0
CA A:ASP363 3.6 36.6 1.0
C A:GLY362 3.6 35.5 1.0
CG A:ASN192 3.7 40.4 1.0
CG A:BFD248 3.8 28.5 1.0
CD A:LYS401 3.8 32.2 1.0
ND2 A:ASN249 4.1 32.4 1.0
OD2 A:ASP195 4.2 39.6 1.0
O A:ASN192 4.2 38.7 1.0
OD2 A:BFD248 4.3 31.3 1.0
N A:LEU364 4.3 34.8 1.0
O A:HOH694 4.4 32.2 1.0
NI A:NI501 4.4 31.9 0.5
CG A:LYS401 4.4 40.6 1.0
C A:ASP363 4.5 34.1 1.0
O A:HOH739 4.6 36.7 1.0
O A:THR399 4.6 36.8 1.0
CG A:ASP195 4.7 34.6 1.0
CG A:ASP363 4.7 39.9 1.0
CB A:ASP195 4.8 34.1 1.0
O A:HOH650 4.8 28.9 1.0
O A:GLY362 4.8 33.8 1.0
N A:GLY362 4.9 31.6 1.0
CB A:BFD248 4.9 31.1 1.0

Fluorine binding site 2 out of 6 in 7u1v

Go back to Fluorine Binding Sites List in 7u1v
Fluorine binding site 2 out of 6 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F248

b:34.5
occ:1.00
 F2 A:BFD248 0.0 34.5 1.0
BE A:BFD248 1.6 36.0 1.0
NI A:NI501 2.1 31.9 0.5
OD1 A:BFD248 2.5 32.7 1.0
F1 A:BFD248 2.5 30.1 1.0
F3 A:BFD248 2.6 32.4 1.0
OD2 A:BFD248 2.8 31.3 1.0
ND2 A:ASN249 2.9 32.4 1.0
O A:HOH667 2.9 31.3 1.0
OD1 A:ASN249 3.0 32.7 1.0
O A:HOH650 3.1 28.9 1.0
CG A:BFD248 3.1 28.5 1.0
OD2 A:ASP195 3.1 39.6 1.0
CG A:ASP195 3.3 34.6 1.0
CG A:ASN249 3.3 32.2 1.0
O A:HOH739 3.5 36.7 1.0
OD1 A:ASP195 3.7 33.7 1.0
CB A:ASP195 3.8 34.1 1.0
OD1 A:ASP286 4.0 31.0 1.0
ND2 A:ASN192 4.4 42.5 1.0
CB A:BFD248 4.5 31.1 1.0
NZ A:LYS401 4.5 33.4 1.0
CA A:ASP195 4.7 33.9 1.0
CE A:LYS401 4.7 38.2 1.0
O A:HOH694 4.8 32.2 1.0
CD A:LYS401 4.8 32.2 1.0
CB A:ASN249 4.8 29.3 1.0
N A:ASP363 4.8 34.6 1.0
CG A:ASP286 5.0 32.5 1.0

Fluorine binding site 3 out of 6 in 7u1v

Go back to Fluorine Binding Sites List in 7u1v
Fluorine binding site 3 out of 6 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F248

b:32.4
occ:1.00
 F3 A:BFD248 0.0 32.4 1.0
BE A:BFD248 1.6 36.0 1.0
OD1 A:BFD248 2.5 32.7 1.0
F1 A:BFD248 2.6 30.1 1.0
F2 A:BFD248 2.6 34.5 1.0
O A:HOH694 2.7 32.2 1.0
O A:HOH650 2.7 28.9 1.0
N A:LEU364 2.8 34.8 1.0
N A:ASP363 3.2 34.6 1.0
CG A:BFD248 3.2 28.5 1.0
OD2 A:BFD248 3.2 31.3 1.0
O A:HOH739 3.4 36.7 1.0
NI A:NI501 3.4 31.9 0.5
CB A:LEU364 3.4 32.8 1.0
CA A:LEU364 3.7 30.8 1.0
C A:ASP363 3.7 34.1 1.0
CA A:ASP363 3.8 36.6 1.0
CB A:ASP363 3.9 32.8 1.0
C A:GLY362 3.9 35.5 1.0
CA A:GLY362 4.2 31.3 1.0
O A:HOH689 4.3 29.5 1.0
CB A:BFD248 4.5 31.1 1.0
O A:HOH667 4.5 31.3 1.0
O A:HOH630 4.5 34.0 1.0
N A:ASN365 4.6 30.3 1.0
C A:LEU364 4.7 34.9 1.0
O A:GLY362 4.8 33.8 1.0
OD2 A:ASP286 4.8 32.2 1.0
ND2 A:ASN192 4.8 42.5 1.0
OD1 A:ASP286 4.9 31.0 1.0
CG A:LEU364 4.9 37.5 1.0
O A:ASP363 4.9 37.6 1.0
ND2 A:ASN249 5.0 32.4 1.0
OD2 A:ASP195 5.0 39.6 1.0
O A:LYS361 5.0 33.4 1.0

Fluorine binding site 4 out of 6 in 7u1v

Go back to Fluorine Binding Sites List in 7u1v
Fluorine binding site 4 out of 6 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F248

b:32.0
occ:1.00
 F1 B:BFD248 0.0 32.0 1.0
BE B:BFD248 1.6 33.9 1.0
NI B:NI501 2.1 49.1 1.0
F3 B:BFD248 2.5 30.7 1.0
F2 B:BFD248 2.6 29.0 1.0
OD1 B:BFD248 2.6 28.2 1.0
OD2 B:ASP195 2.8 42.5 1.0
ND2 B:ASN249 2.9 30.8 1.0
OD2 B:BFD248 3.0 34.8 1.0
O B:HOH654 3.0 30.7 1.0
O B:HOH661 3.0 31.4 1.0
CG B:BFD248 3.2 31.1 1.0
CG B:ASP195 3.3 40.5 1.0
OD1 B:ASN249 3.3 35.4 1.0
O B:HOH801 3.5 35.6 1.0
CG B:ASN249 3.5 33.8 1.0
NZ B:LYS401 3.5 36.3 1.0
OD1 B:ASP195 3.7 39.6 1.0
O B:HOH604 3.9 44.7 1.0
OD1 B:ASP286 4.1 32.4 1.0
CB B:ASP195 4.2 38.6 1.0
ND2 B:ASN192 4.4 32.6 1.0
CB B:BFD248 4.6 29.8 1.0
CE B:LYS401 4.7 38.6 1.0
CD B:LYS401 4.7 40.5 1.0
N B:ASP363 4.8 31.4 1.0
O B:HOH694 4.8 27.4 1.0
CB B:ASN249 5.0 34.0 1.0

Fluorine binding site 5 out of 6 in 7u1v

Go back to Fluorine Binding Sites List in 7u1v
Fluorine binding site 5 out of 6 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F248

b:29.0
occ:1.00
 F2 B:BFD248 0.0 29.0 1.0
BE B:BFD248 1.5 33.9 1.0
OD1 B:BFD248 2.5 28.2 1.0
F3 B:BFD248 2.5 30.7 1.0
F1 B:BFD248 2.6 32.0 1.0
O B:HOH661 2.7 31.4 1.0
N B:LEU364 2.7 28.5 1.0
O B:HOH694 2.8 27.4 1.0
N B:ASP363 3.1 31.4 1.0
O B:HOH801 3.2 35.6 1.0
CG B:BFD248 3.3 31.1 1.0
CB B:LEU364 3.4 29.8 1.0
OD2 B:BFD248 3.5 34.8 1.0
NI B:NI501 3.5 49.1 1.0
CA B:LEU364 3.6 31.8 1.0
C B:ASP363 3.7 30.2 1.0
CA B:ASP363 3.7 32.5 1.0
CB B:ASP363 3.8 31.1 1.0
C B:GLY362 3.9 32.4 1.0
CA B:GLY362 4.3 31.9 1.0
O B:HOH735 4.4 30.4 1.0
O B:HOH672 4.5 33.3 1.0
N B:ASN365 4.5 29.7 1.0
CB B:BFD248 4.6 29.8 1.0
C B:LEU364 4.7 32.5 1.0
O B:GLY362 4.7 28.7 1.0
O B:HOH654 4.7 30.7 1.0
OD2 B:ASP195 4.8 42.5 1.0
CG B:LEU364 4.8 30.8 1.0
NZ B:LYS401 4.8 36.3 1.0
O B:ASP363 4.8 30.2 1.0
OD2 B:ASP286 4.9 32.0 1.0
O B:HOH604 4.9 44.7 1.0
ND2 B:ASN192 5.0 32.6 1.0
CG B:ASP363 5.0 34.3 1.0

Fluorine binding site 6 out of 6 in 7u1v

Go back to Fluorine Binding Sites List in 7u1v
Fluorine binding site 6 out of 6 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F248

b:30.7
occ:1.00
 F3 B:BFD248 0.0 30.7 1.0
BE B:BFD248 1.5 33.9 1.0
OD1 B:BFD248 2.4 28.2 1.0
F1 B:BFD248 2.5 32.0 1.0
NZ B:LYS401 2.5 36.3 1.0
F2 B:BFD248 2.5 29.0 1.0
N B:ASP363 2.6 31.4 1.0
ND2 B:ASN192 3.2 32.6 1.0
OD1 B:ASN192 3.3 37.6 1.0
CB B:ASP363 3.3 31.1 1.0
CA B:GLY362 3.5 31.9 1.0
C B:GLY362 3.5 32.4 1.0
CA B:ASP363 3.5 32.5 1.0
CD B:LYS401 3.6 40.5 1.0
CE B:LYS401 3.6 38.6 1.0
CG B:ASN192 3.6 35.2 1.0
OD2 B:ASP195 3.8 42.5 1.0
CG B:BFD248 3.9 31.1 1.0
ND2 B:ASN249 4.2 30.8 1.0
N B:LEU364 4.3 28.5 1.0
OD2 B:BFD248 4.4 34.8 1.0
O B:HOH694 4.4 27.4 1.0
C B:ASP363 4.5 30.2 1.0
NI B:NI501 4.5 49.1 1.0
O B:ASN192 4.5 35.2 1.0
O B:HOH801 4.6 35.6 1.0
CG B:ASP195 4.7 40.5 1.0
O B:GLY362 4.7 28.7 1.0
O B:THR399 4.7 36.3 1.0
CG B:ASP363 4.8 34.3 1.0
O B:HOH661 4.8 31.4 1.0
O B:HOH604 4.8 44.7 1.0
N B:GLY362 4.9 31.0 1.0
CG B:LYS401 4.9 40.7 1.0
OG1 B:THR399 4.9 36.0 1.0
CB B:BFD248 5.0 29.8 1.0

Reference:

A.M.Sanchez, A.Jacewicz, S.Shuman. Fission Yeast DUF89 and DUF8901 Are Cobalt/Nickel-Dependent Phosphatase-Pyrophosphatases That Act Via A Covalent Aspartyl-Phosphate Intermediate. J.Biol.Chem. V. 298 01851 2022.
ISSN: ESSN 1083-351X
PubMed: 35314193
DOI: 10.1016/J.JBC.2022.101851
Page generated: Fri Aug 2 13:47:57 2024

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