Atomistry » Zinc » PDB 1sdz-1sxb » 1su1
Atomistry »
  Zinc »
    PDB 1sdz-1sxb »
      1su1 »

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

Go back to Zinc Binding Sites List in 1su1
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

Go back to Zinc Binding Sites List in 1su1
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

Go back to Zinc Binding Sites List in 1su1
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

Go back to Zinc Binding Sites List in 1su1
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

Go back to Zinc Binding Sites List in 1su1
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

Go back to Zinc Binding Sites List in 1su1
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

Go back to Zinc Binding Sites List in 1su1
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: Wed Oct 16 18:55:17 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy