Fluorine in PDB 7u1x: 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: 7u1x 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) 46.92 / 2.12
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.3, 117.533, 153.435, 90, 90, 90
R / Rfree (%) 17.6 / 21.6

Other elements in 7u1x:

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

Zinc (Zn) 2 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 7u1x). 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: 7u1x:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7u1x

Go back to Fluorine Binding Sites List in 7u1x
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:27.3
occ:1.00
 F1 A:BFD248 0.0 27.3 1.0
BE A:BFD248 1.5 34.6 1.0
OD1 A:BFD248 2.4 33.6 1.0
F3 A:BFD248 2.5 36.4 1.0
F2 A:BFD248 2.5 35.8 1.0
NZ A:LYS401 2.7 28.0 1.0
N A:ASP363 2.9 28.8 1.0
CB A:ASP363 3.3 22.2 1.0
ND2 A:ASN192 3.3 28.7 1.0
CE A:LYS401 3.4 30.6 1.0
OD1 A:ASN192 3.6 30.5 1.0
CD A:LYS401 3.6 30.4 1.0
CA A:ASP363 3.7 24.1 1.0
OD2 A:ASP195 3.8 49.4 1.0
CA A:GLY362 3.8 24.0 1.0
CG A:ASN192 3.8 29.3 1.0
C A:GLY362 3.8 29.6 1.0
CG A:BFD248 3.9 31.1 1.0
ND2 A:ASN249 4.2 21.8 1.0
O A:HOH712 4.3 38.3 1.0
O A:ASN192 4.4 28.7 1.0
OD2 A:BFD248 4.4 33.1 1.0
N A:LEU364 4.4 21.1 1.0
ZN A:ZN501 4.5 32.1 0.6
O A:HOH684 4.6 27.6 1.0
C A:ASP363 4.6 27.7 1.0
O A:THR399 4.6 23.3 1.0
CG A:LYS401 4.6 26.4 1.0
CG A:ASP195 4.6 42.0 1.0
CG A:ASP363 4.7 35.0 1.0
CB A:ASP195 4.7 31.5 1.0
O A:HOH661 4.9 33.0 1.0

Fluorine binding site 2 out of 6 in 7u1x

Go back to Fluorine Binding Sites List in 7u1x
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:35.8
occ:1.00
 F2 A:BFD248 0.0 35.8 1.0
BE A:BFD248 1.6 34.6 1.0
F1 A:BFD248 2.5 27.3 1.0
OD1 A:BFD248 2.5 33.6 1.0
F3 A:BFD248 2.6 36.4 1.0
O A:HOH661 2.7 33.0 1.0
N A:LEU364 2.9 21.1 1.0
O A:HOH684 2.9 27.6 1.0
OD2 A:BFD248 3.2 33.1 1.0
CG A:BFD248 3.2 31.1 1.0
N A:ASP363 3.3 28.8 1.0
O A:HOH712 3.4 38.3 1.0
ZN A:ZN501 3.4 32.1 0.6
CB A:LEU364 3.5 20.5 1.0
CA A:LEU364 3.8 20.5 1.0
CB A:ASP363 3.8 22.2 1.0
CA A:ASP363 3.8 24.1 1.0
C A:ASP363 3.8 27.7 1.0
C A:GLY362 4.1 29.6 1.0
O A:HOH662 4.3 25.4 1.0
OD2 A:ASP195 4.3 49.4 1.0
CA A:GLY362 4.4 24.0 1.0
O A:HOH702 4.5 32.2 1.0
CB A:BFD248 4.6 31.0 1.0
O A:HOH620 4.7 28.8 1.0
N A:ASN365 4.8 20.2 1.0
C A:LEU364 4.9 24.1 1.0
ND2 A:ASN192 4.9 28.7 1.0
O A:GLY362 4.9 25.0 1.0
OD2 A:ASP286 4.9 36.6 1.0
CG A:LEU364 4.9 28.1 1.0
OD1 A:ASP286 4.9 33.0 1.0
ND2 A:ASN249 5.0 21.8 1.0

Fluorine binding site 3 out of 6 in 7u1x

Go back to Fluorine Binding Sites List in 7u1x
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:36.4
occ:1.00
 F3 A:BFD248 0.0 36.4 1.0
BE A:BFD248 1.6 34.6 1.0
ZN A:ZN501 2.1 32.1 0.6
OD2 A:ASP195 2.4 49.4 1.0
F1 A:BFD248 2.5 27.3 1.0
OD1 A:BFD248 2.5 33.6 1.0
F2 A:BFD248 2.6 35.8 1.0
ND2 A:ASN249 2.9 21.8 1.0
OD2 A:BFD248 3.0 33.1 1.0
OD1 A:ASN249 3.0 30.0 1.0
CG A:ASP195 3.1 42.0 1.0
O A:HOH620 3.1 28.8 1.0
CG A:BFD248 3.2 31.1 1.0
O A:HOH661 3.3 33.0 1.0
CG A:ASN249 3.3 28.9 1.0
O A:HOH712 3.4 38.3 1.0
CB A:ASP195 3.6 31.5 1.0
OD1 A:ASP195 3.9 36.6 1.0
OD1 A:ASP286 4.2 33.0 1.0
ND2 A:ASN192 4.4 28.7 1.0
NZ A:LYS401 4.6 28.0 1.0
CA A:ASP195 4.6 28.8 1.0
CB A:BFD248 4.6 31.0 1.0
CE A:LYS401 4.6 30.6 1.0
CD A:LYS401 4.7 30.4 1.0
CB A:ASN249 4.8 25.7 1.0
O A:HOH684 5.0 27.6 1.0
N A:ASP363 5.0 28.8 1.0

Fluorine binding site 4 out of 6 in 7u1x

Go back to Fluorine Binding Sites List in 7u1x
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:27.2
occ:1.00
 F1 B:BFD248 0.0 27.2 1.0
BE B:BFD248 1.5 34.1 1.0
OD1 B:BFD248 2.4 31.8 1.0
F2 B:BFD248 2.5 30.5 1.0
NZ B:LYS401 2.5 31.7 1.0
F3 B:BFD248 2.6 31.3 1.0
N B:ASP363 2.9 24.2 1.0
ND2 B:ASN192 3.2 28.4 1.0
CB B:ASP363 3.3 28.6 1.0
CE B:LYS401 3.5 37.1 1.0
OD1 B:ASN192 3.5 30.3 1.0
CD B:LYS401 3.6 29.5 1.0
CA B:ASP363 3.7 22.3 1.0
CA B:GLY362 3.7 24.1 1.0
CG B:ASN192 3.8 30.7 1.0
C B:GLY362 3.8 29.1 1.0
OD2 B:ASP195 3.8 47.8 1.0
CG B:BFD248 3.8 29.4 1.0
ND2 B:ASN249 4.0 25.9 1.0
O B:HOH722 4.3 41.6 1.0
OD2 B:BFD248 4.3 28.6 1.0
O B:ASN192 4.3 34.7 1.0
N B:LEU364 4.4 21.9 1.0
ZN B:ZN501 4.5 28.9 0.6
O B:HOH682 4.5 21.9 1.0
CG B:ASP195 4.5 42.8 1.0
C B:ASP363 4.6 23.6 1.0
O B:THR399 4.6 28.1 1.0
CB B:ASP195 4.7 35.9 1.0
CG B:ASP363 4.7 34.3 1.0
CG B:LYS401 4.8 33.2 1.0
O B:HOH689 4.8 29.9 1.0
CB B:BFD248 5.0 27.6 1.0
O B:GLY362 5.0 23.7 1.0

Fluorine binding site 5 out of 6 in 7u1x

Go back to Fluorine Binding Sites List in 7u1x
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:30.5
occ:1.00
 F2 B:BFD248 0.0 30.5 1.0
BE B:BFD248 1.6 34.1 1.0
ZN B:ZN501 2.1 28.9 0.6
F1 B:BFD248 2.5 27.2 1.0
F3 B:BFD248 2.6 31.3 1.0
OD1 B:BFD248 2.6 31.8 1.0
ND2 B:ASN249 2.7 25.9 1.0
OD2 B:ASP195 2.8 47.8 1.0
OD2 B:BFD248 2.9 28.6 1.0
CG B:ASP195 3.1 42.8 1.0
O B:HOH606 3.1 30.0 1.0
CG B:BFD248 3.1 29.4 1.0
OD1 B:ASN249 3.2 27.8 1.0
O B:HOH689 3.2 29.9 1.0
CG B:ASN249 3.3 28.0 1.0
O B:HOH722 3.4 41.6 1.0
OD1 B:ASP195 3.6 44.2 1.0
CB B:ASP195 3.8 35.9 1.0
OD1 B:ASP286 4.1 32.0 1.0
NZ B:LYS401 4.3 31.7 1.0
ND2 B:ASN192 4.4 28.4 1.0
CB B:BFD248 4.6 27.6 1.0
CE B:LYS401 4.6 37.1 1.0
CD B:LYS401 4.6 29.5 1.0
CA B:ASP195 4.7 32.9 1.0
CB B:ASN249 4.8 25.5 1.0
N B:ASP363 4.9 24.2 1.0
O B:HOH682 4.9 21.9 1.0

Fluorine binding site 6 out of 6 in 7u1x

Go back to Fluorine Binding Sites List in 7u1x
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:31.3
occ:1.00
 F3 B:BFD248 0.0 31.3 1.0
BE B:BFD248 1.6 34.1 1.0
OD1 B:BFD248 2.5 31.8 1.0
F2 B:BFD248 2.6 30.5 1.0
F1 B:BFD248 2.6 27.2 1.0
O B:HOH689 2.7 29.9 1.0
N B:LEU364 2.8 21.9 1.0
O B:HOH682 2.9 21.9 1.0
O B:HOH722 3.1 41.6 1.0
N B:ASP363 3.2 24.2 1.0
CG B:BFD248 3.3 29.4 1.0
OD2 B:BFD248 3.3 28.6 1.0
CB B:LEU364 3.5 21.3 1.0
ZN B:ZN501 3.5 28.9 0.6
C B:ASP363 3.7 23.6 1.0
CA B:LEU364 3.7 23.9 1.0
CA B:ASP363 3.7 22.3 1.0
CB B:ASP363 3.8 28.6 1.0
C B:GLY362 4.0 29.1 1.0
O B:HOH671 4.4 32.4 1.0
CA B:GLY362 4.4 24.1 1.0
O B:HOH697 4.4 21.9 1.0
OD2 B:ASP195 4.5 47.8 1.0
CB B:BFD248 4.6 27.6 1.0
N B:ASN365 4.6 20.4 1.0
C B:LEU364 4.7 23.4 1.0
O B:HOH606 4.8 30.0 1.0
OD2 B:ASP286 4.8 32.5 1.0
ND2 B:ASN249 4.8 25.9 1.0
O B:GLY362 4.9 23.7 1.0
O B:ASP363 4.9 23.5 1.0
OD1 B:ASP286 4.9 32.0 1.0
CG B:LEU364 4.9 30.2 1.0
ND2 B:ASN192 5.0 28.4 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 13:48:30 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy