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Zinc in PDB 1su1: Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli

Protein crystallography data

The structure of Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli, PDB code: 1su1 was solved by D.J.Miller, L.Shuvalova, E.Evdokimova, A.Savchenko, A.Yakunin, W.F.Anderson, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.25
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 71.020, 71.020, 173.680, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli (pdb code 1su1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli, PDB code: 1su1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1su1

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Zinc binding site 1 out of 8 in the Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:22.9
occ:1.00
NE2 A:HIS105 2.2 24.9 1.0
ND1 A:HIS127 2.2 17.8 1.0
OD1 A:ASN73 2.3 24.0 1.0
O2 A:SO4501 2.3 57.0 1.0
OD2 A:ASP37 2.3 22.4 1.0
CE1 A:HIS127 3.0 17.3 1.0
CE1 A:HIS105 3.1 26.4 1.0
CD2 A:HIS105 3.2 22.8 1.0
CG A:ASP37 3.3 27.8 1.0
CG A:ASN73 3.3 22.6 1.0
O1 A:SO4501 3.3 57.5 1.0
S A:SO4501 3.3 58.4 1.0
CG A:HIS127 3.4 17.8 1.0
ZN A:ZN302 3.4 20.5 1.0
OD1 A:ASP9 3.7 6.9 1.0
OD1 A:ASP37 3.7 30.7 1.0
ND2 A:ASN73 3.7 17.3 1.0
CA A:HIS127 3.8 14.3 1.0
CB A:HIS127 3.9 17.5 1.0
O3 A:SO4501 4.0 60.4 1.0
NE2 A:HIS127 4.2 17.9 1.0
O A:HIS127 4.3 15.9 1.0
ND1 A:HIS105 4.3 24.4 1.0
CG A:HIS105 4.4 23.9 1.0
CB A:ASP37 4.4 18.4 1.0
CD2 A:HIS127 4.4 18.8 1.0
N A:ASN73 4.4 10.6 1.0
O4 A:SO4501 4.5 56.4 1.0
CB A:ASN73 4.5 17.8 1.0
C A:HIS127 4.6 15.9 1.0
SG A:CYS74 4.7 22.6 1.0
N A:HIS127 4.7 12.6 1.0
CG A:ASP9 4.9 22.8 1.0
CA A:ASN73 5.0 15.3 1.0

Zinc binding site 2 out of 8 in 1su1

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Zinc binding site 2 out of 8 in the Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:20.5
occ:1.00
OD1 A:ASP9 1.9 6.9 1.0
NE2 A:HIS129 2.2 27.0 1.0
NE2 A:HIS11 2.2 25.0 1.0
O2 A:SO4501 2.6 57.0 1.0
CG A:ASP9 2.9 22.8 1.0
CE1 A:HIS11 3.0 27.5 1.0
CE1 A:HIS129 3.1 29.8 1.0
CD2 A:HIS129 3.3 29.0 1.0
O4 A:SO4501 3.3 56.4 1.0
CD2 A:HIS11 3.3 26.1 1.0
S A:SO4501 3.3 58.4 1.0
OD2 A:ASP37 3.3 22.4 1.0
ZN A:ZN301 3.4 22.9 1.0
CB A:ASP9 3.4 13.8 1.0
O1 A:SO4501 3.7 57.5 1.0
OD2 A:ASP9 4.0 16.9 1.0
CG A:ASP37 4.1 27.8 1.0
CB A:ASP37 4.1 18.4 1.0
O A:HIS127 4.2 15.9 1.0
ND1 A:HIS11 4.2 28.1 1.0
ND1 A:HIS129 4.3 30.1 1.0
CA A:ASP9 4.3 16.4 1.0
CG A:HIS129 4.4 28.8 1.0
CG A:HIS11 4.4 27.0 1.0
CA A:HIS127 4.6 14.3 1.0
CE1 A:HIS105 4.6 26.4 1.0
NE2 A:HIS105 4.7 24.9 1.0
O3 A:SO4501 4.7 60.4 1.0
C A:HIS127 4.7 15.9 1.0
ND1 A:HIS127 4.9 17.8 1.0
O A:HOH544 5.0 54.1 1.0

Zinc binding site 3 out of 8 in 1su1

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Zinc binding site 3 out of 8 in the Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:26.6
occ:1.00
NE2 B:HIS105 2.2 25.3 1.0
ND1 B:HIS127 2.2 16.1 1.0
OD2 B:ASP37 2.2 15.8 1.0
OD1 B:ASN73 2.3 26.9 1.0
O1 B:SO4502 2.3 58.6 1.0
CE1 B:HIS127 3.0 15.0 1.0
CE1 B:HIS105 3.1 26.5 1.0
CG B:ASN73 3.2 24.2 1.0
CG B:ASP37 3.3 24.4 1.0
CD2 B:HIS105 3.3 23.5 1.0
CG B:HIS127 3.4 16.0 1.0
ZN B:ZN304 3.5 21.0 1.0
S B:SO4502 3.5 60.4 1.0
ND2 B:ASN73 3.7 21.4 1.0
OD1 B:ASP9 3.7 5.1 1.0
OD1 B:ASP37 3.7 20.2 1.0
O3 B:SO4502 3.8 58.4 1.0
CA B:HIS127 3.8 16.1 1.0
CB B:HIS127 3.8 19.1 1.0
O2 B:SO4502 3.9 62.0 1.0
O B:HIS127 4.2 17.1 1.0
NE2 B:HIS127 4.2 18.9 1.0
ND1 B:HIS105 4.3 24.5 1.0
CG B:HIS105 4.4 24.9 1.0
CD2 B:HIS127 4.4 17.7 1.0
N B:ASN73 4.4 12.3 1.0
CB B:ASN73 4.4 21.6 1.0
CB B:ASP37 4.4 16.0 1.0
C B:HIS127 4.5 17.2 1.0
O4 B:SO4502 4.7 58.7 1.0
N B:HIS127 4.7 14.9 1.0
SG B:CYS74 4.7 23.5 1.0
CG B:ASP9 4.9 20.7 1.0
CA B:ASN73 5.0 18.3 1.0

Zinc binding site 4 out of 8 in 1su1

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Zinc binding site 4 out of 8 in the Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:21.0
occ:1.00
OD1 B:ASP9 1.9 5.1 1.0
NE2 B:HIS129 2.2 25.4 1.0
NE2 B:HIS11 2.2 22.6 1.0
O1 B:SO4502 2.6 58.6 1.0
CE1 B:HIS11 2.9 26.1 1.0
CG B:ASP9 2.9 20.7 1.0
OD2 B:ASP37 3.0 15.8 1.0
CE1 B:HIS129 3.1 26.9 1.0
O3 B:SO4502 3.3 58.4 1.0
CD2 B:HIS129 3.3 27.8 1.0
S B:SO4502 3.3 60.4 1.0
CD2 B:HIS11 3.4 22.1 1.0
ZN B:ZN303 3.5 26.6 1.0
CB B:ASP9 3.5 14.7 1.0
O4 B:SO4502 3.5 58.7 1.0
CG B:ASP37 4.0 24.4 1.0
OD2 B:ASP9 4.0 15.9 1.0
CB B:ASP37 4.1 16.0 1.0
ND1 B:HIS11 4.1 27.3 1.0
O B:HIS127 4.1 17.1 1.0
ND1 B:HIS129 4.2 26.9 1.0
CA B:ASP9 4.3 17.5 1.0
CG B:HIS129 4.4 26.3 1.0
CG B:HIS11 4.4 24.9 1.0
CA B:HIS127 4.5 16.1 1.0
CE1 B:HIS105 4.7 26.5 1.0
O2 B:SO4502 4.7 62.0 1.0
C B:HIS127 4.7 17.2 1.0
NE2 B:HIS105 4.7 25.3 1.0
O B:HOH537 4.8 50.4 1.0
ND1 B:HIS127 4.9 16.1 1.0
ND2 B:ASN45 5.0 37.6 1.0

Zinc binding site 5 out of 8 in 1su1

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Zinc binding site 5 out of 8 in the Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn305

b:24.1
occ:1.00
OD1 C:ASN73 2.1 22.8 1.0
ND1 C:HIS127 2.1 18.7 1.0
OD2 C:ASP37 2.2 16.2 1.0
NE2 C:HIS105 2.3 29.3 1.0
O3 C:SO4503 2.4 45.5 1.0
CE1 C:HIS127 2.9 23.0 1.0
CD2 C:HIS105 3.0 19.5 1.0
O2 C:SO4503 3.0 47.9 1.0
CG C:ASN73 3.1 25.3 1.0
CG C:ASP37 3.2 20.0 1.0
S C:SO4503 3.3 51.5 1.0
CG C:HIS127 3.3 21.9 1.0
CE1 C:HIS105 3.4 25.2 1.0
ZN C:ZN306 3.5 29.0 1.0
ND2 C:ASN73 3.6 24.5 1.0
OD1 C:ASP37 3.7 15.4 1.0
CB C:HIS127 3.7 22.0 1.0
CA C:HIS127 3.7 25.8 1.0
OD1 C:ASP9 4.0 25.5 1.0
O4 C:SO4503 4.1 54.9 1.0
NE2 C:HIS127 4.1 20.8 1.0
O C:HIS127 4.2 25.0 1.0
CG C:HIS105 4.2 30.9 1.0
CD2 C:HIS127 4.3 19.2 1.0
CB C:ASN73 4.3 18.3 1.0
N C:ASN73 4.4 15.1 1.0
ND1 C:HIS105 4.4 27.2 1.0
O1 C:SO4503 4.4 54.3 1.0
CB C:ASP37 4.5 14.6 1.0
C C:HIS127 4.5 25.9 1.0
SG C:CYS74 4.7 23.2 1.0
N C:HIS127 4.7 26.2 1.0
CA C:ASN73 4.9 18.1 1.0

Zinc binding site 6 out of 8 in 1su1

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Zinc binding site 6 out of 8 in the Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn306

b:29.0
occ:1.00
O3 C:SO4503 2.2 45.5 1.0
NE2 C:HIS129 2.3 33.1 1.0
NE2 C:HIS11 2.3 14.1 1.0
OD1 C:ASP9 2.6 25.5 1.0
OD2 C:ASP37 2.8 16.2 1.0
CE1 C:HIS11 3.0 13.0 1.0
CE1 C:HIS129 3.2 32.1 1.0
CG C:ASP9 3.2 25.4 1.0
S C:SO4503 3.3 51.5 1.0
O1 C:SO4503 3.3 54.3 1.0
CD2 C:HIS129 3.4 34.5 1.0
CB C:ASP9 3.4 22.3 1.0
CD2 C:HIS11 3.5 15.9 1.0
ZN C:ZN305 3.5 24.1 1.0
CG C:ASP37 3.8 20.0 1.0
CB C:ASP37 4.0 14.6 1.0
OD2 C:ASP9 4.1 28.6 1.0
O2 C:SO4503 4.2 47.9 1.0
ND1 C:HIS11 4.2 16.2 1.0
CA C:ASP9 4.2 22.3 1.0
O C:HIS127 4.2 25.0 1.0
O4 C:SO4503 4.3 54.9 1.0
ND1 C:HIS129 4.3 32.9 1.0
NE2 C:HIS105 4.4 29.3 1.0
CG C:HIS129 4.4 33.5 1.0
CG C:HIS11 4.5 17.9 1.0
CA C:HIS127 4.6 25.8 1.0
CE1 C:HIS105 4.7 25.2 1.0
C C:HIS127 4.8 25.9 1.0
ND1 C:HIS127 4.9 18.7 1.0
OD1 C:ASP37 5.0 15.4 1.0

Zinc binding site 7 out of 8 in 1su1

Go back to Zinc Binding Sites List in 1su1
Zinc binding site 7 out of 8 in the Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn307

b:28.4
occ:1.00
O1 D:SO4505 2.2 45.9 1.0
NE2 D:HIS11 2.3 12.7 1.0
NE2 D:HIS129 2.3 33.0 1.0
OD1 D:ASP9 2.5 28.6 1.0
OD2 D:ASP37 2.8 14.8 1.0
CE1 D:HIS11 3.0 10.3 1.0
CE1 D:HIS129 3.1 34.0 1.0
CG D:ASP9 3.1 27.0 1.0
O2 D:SO4505 3.3 54.7 1.0
S D:SO4505 3.3 52.1 1.0
CD2 D:HIS129 3.4 35.0 1.0
CD2 D:HIS11 3.4 14.8 1.0
CB D:ASP9 3.4 25.0 1.0
ZN D:ZN308 3.5 26.2 1.0
CG D:ASP37 3.7 19.4 1.0
CB D:ASP37 3.9 13.3 1.0
OD2 D:ASP9 4.0 31.9 1.0
ND1 D:HIS11 4.2 13.8 1.0
CA D:ASP9 4.2 23.7 1.0
O4 D:SO4505 4.3 57.1 1.0
ND1 D:HIS129 4.3 33.4 1.0
O D:HIS127 4.3 25.1 1.0
O3 D:SO4505 4.3 46.8 1.0
NE2 D:HIS105 4.4 29.3 1.0
CG D:HIS129 4.4 32.4 1.0
CG D:HIS11 4.4 14.9 1.0
CA D:HIS127 4.5 23.6 1.0
CE1 D:HIS105 4.6 26.0 1.0
C D:HIS127 4.8 24.7 1.0
ND1 D:HIS127 4.9 19.0 1.0
OD1 D:ASP37 4.9 16.1 1.0

Zinc binding site 8 out of 8 in 1su1

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Zinc binding site 8 out of 8 in the Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural and Biochemical Characterization of Yfce, A Phosphoesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn308

b:26.2
occ:1.00
OD1 D:ASN73 2.1 24.8 1.0
OD2 D:ASP37 2.1 14.8 1.0
ND1 D:HIS127 2.2 19.0 1.0
NE2 D:HIS105 2.3 29.3 1.0
O1 D:SO4505 2.4 45.9 1.0
O3 D:SO4505 3.0 46.8 1.0
CD2 D:HIS105 3.0 18.9 1.0
CE1 D:HIS127 3.0 21.1 1.0
CG D:ASN73 3.1 26.1 1.0
CG D:ASP37 3.2 19.4 1.0
S D:SO4505 3.2 52.1 1.0
CG D:HIS127 3.3 21.5 1.0
CE1 D:HIS105 3.4 26.0 1.0
ZN D:ZN307 3.5 28.4 1.0
ND2 D:ASN73 3.6 26.1 1.0
OD1 D:ASP37 3.7 16.1 1.0
CB D:HIS127 3.7 19.4 1.0
CA D:HIS127 3.7 23.6 1.0
OD1 D:ASP9 4.0 28.6 1.0
O D:HIS127 4.2 25.1 1.0
O2 D:SO4505 4.2 54.7 1.0
NE2 D:HIS127 4.2 21.7 1.0
CG D:HIS105 4.3 29.7 1.0
O4 D:SO4505 4.3 57.1 1.0
CD2 D:HIS127 4.4 19.2 1.0
CB D:ASN73 4.4 19.5 1.0
ND1 D:HIS105 4.4 25.3 1.0
N D:ASN73 4.4 14.9 1.0
CB D:ASP37 4.4 13.3 1.0
C D:HIS127 4.5 24.7 1.0
SG D:CYS74 4.6 22.2 1.0
N D:HIS127 4.7 24.4 1.0
CA D:ASN73 4.9 18.1 1.0

Reference:

D.J.Miller, L.Shuvalova, E.Evdokimova, A.Savchenko, A.F.Yakunin, W.F.Anderson. Structural and Biochemical Characterization of A Novel MN2+-Dependent Phosphodiesterase Encoded By the Yfce Gene. Protein Sci. V. 16 1338 2007.
ISSN: ISSN 0961-8368
PubMed: 17586769
DOI: 10.1110/PS.072764907
Page generated: Mon Jan 25 16:13:30 2021

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