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Zinc 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:

Fluorine (F) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3, PDB code: 7u1x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7u1x

Go back to Zinc Binding Sites List in 7u1x
Zinc binding site 1 out of 2 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn501

b:32.1
occ:0.63
O A:HOH620 2.1 28.8 1.0
F3 A:BFD248 2.1 36.4 1.0
OD1 A:ASP286 2.1 33.0 1.0
OD1 A:ASN249 2.1 30.0 1.0
OD2 A:BFD248 2.2 33.1 1.0
O A:HOH661 2.3 33.0 1.0
CG A:ASN249 3.0 28.9 1.0
BE A:BFD248 3.1 34.6 1.0
CG A:ASP286 3.1 31.4 1.0
CG A:BFD248 3.2 31.1 1.0
F2 A:BFD248 3.4 35.8 1.0
ND2 A:ASN249 3.5 21.8 1.0
OD1 A:BFD248 3.5 33.6 1.0
OD2 A:ASP286 3.5 36.6 1.0
OD2 A:ASP195 3.6 49.4 1.0
CG A:ASP195 4.0 42.0 1.0
O A:HOH712 4.0 38.3 1.0
OD1 A:ASP195 4.1 36.6 1.0
O A:PHE283 4.2 27.4 1.0
CB A:ASN249 4.3 25.7 1.0
OG A:SER285 4.3 29.1 1.0
N A:ASN249 4.4 27.1 1.0
CB A:ASP286 4.4 25.6 1.0
F1 A:BFD248 4.5 27.3 1.0
CB A:PHE283 4.5 24.2 1.0
C A:BFD248 4.5 30.8 1.0
CB A:BFD248 4.5 31.0 1.0
CA A:ASN249 4.5 29.4 1.0
N A:ASP286 4.5 27.3 1.0
CA A:ASP286 4.6 29.1 1.0
O A:HOH662 4.7 25.4 1.0
CA A:BFD248 4.8 30.4 1.0
CB A:ASP195 4.9 31.5 1.0
O A:BFD248 4.9 29.3 1.0
C A:SER285 5.0 25.4 1.0

Zinc binding site 2 out of 2 in 7u1x

Go back to Zinc Binding Sites List in 7u1x
Zinc binding site 2 out of 2 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn501

b:28.9
occ:0.61
OD1 B:ASP286 2.0 32.0 1.0
O B:HOH606 2.0 30.0 1.0
F2 B:BFD248 2.1 30.5 1.0
OD1 B:ASN249 2.1 27.8 1.0
OD2 B:BFD248 2.2 28.6 1.0
O B:HOH689 2.4 29.9 1.0
CG B:ASN249 2.9 28.0 1.0
CG B:ASP286 3.1 29.0 1.0
BE B:BFD248 3.1 34.1 1.0
ND2 B:ASN249 3.2 25.9 1.0
CG B:BFD248 3.2 29.4 1.0
OD2 B:ASP286 3.5 32.5 1.0
F3 B:BFD248 3.5 31.3 1.0
OD1 B:BFD248 3.6 31.8 1.0
OD1 B:ASP195 3.8 44.2 1.0
O B:HOH722 3.9 41.6 1.0
CG B:ASP195 4.0 42.8 1.0
OD2 B:ASP195 4.0 47.8 1.0
O B:PHE283 4.0 26.1 1.0
OG B:SER285 4.1 30.0 1.0
CB B:ASN249 4.3 25.5 1.0
CB B:ASP286 4.4 20.6 1.0
CB B:PHE283 4.4 28.0 1.0
F1 B:BFD248 4.5 27.2 1.0
N B:ASN249 4.5 22.4 1.0
CA B:ASN249 4.5 29.1 1.0
N B:ASP286 4.5 24.1 1.0
C B:BFD248 4.6 30.4 1.0
CB B:BFD248 4.6 27.6 1.0
CA B:ASP286 4.6 28.6 1.0
CA B:BFD248 4.9 32.1 1.0
O B:BFD248 4.9 26.7 1.0
C B:SER285 4.9 28.3 1.0
CB B:ASP195 4.9 35.9 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: Sat Apr 8 03:53:12 2023

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