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Iron in PDB 3icf: Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5

Enzymatic activity of Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5

All present enzymatic activity of Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5:
3.1.3.16;

Protein crystallography data

The structure of Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5, PDB code: 3icf was solved by A.U.Singer, X.Xu, C.Chang, H.Cui, O.Kagan, A.M.Edwards, A.Joachimiak, A.F.Yakunin, A.Savchenko, 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) 40.29 / 2.30
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 47.194, 47.194, 237.096, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 24

Other elements in 3icf:

The structure of Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5 (pdb code 3icf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5, PDB code: 3icf:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3icf

Go back to Iron Binding Sites List in 3icf
Iron binding site 1 out of 4 in the Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:50.6
occ:1.00
 NE2 A:HIS359 1.9 47.1 1.0
ND1 A:HIS434 1.9 51.0 1.0
O4 A:PO41 2.0 46.4 1.0
OD2 A:ASP278 2.1 53.0 1.0
OD1 A:ASN310 2.1 50.4 1.0
CE1 A:HIS434 2.6 50.1 1.0
CE1 A:HIS359 2.8 46.0 1.0
CD2 A:HIS359 3.0 46.9 1.0
CG A:ASP278 3.0 50.0 1.0
CG A:HIS434 3.1 50.2 1.0
CG A:ASN310 3.2 50.3 1.0
P A:PO41 3.2 47.8 1.0
FE A:FE602 3.3 52.2 1.0
OD1 A:ASP278 3.4 52.3 1.0
O1 A:PO41 3.6 49.5 1.0
CA A:HIS434 3.6 48.6 1.0
CB A:HIS434 3.7 48.5 1.0
ND2 A:ASN310 3.7 47.4 1.0
O2 A:PO41 3.7 51.2 1.0
NE2 A:HIS434 3.8 49.5 1.0
ND1 A:HIS359 3.9 42.5 1.0
OD2 A:ASP249 4.0 52.8 1.0
CD2 A:HIS434 4.0 50.5 1.0
CG A:HIS359 4.1 47.3 1.0
O A:HIS434 4.1 50.3 1.0
CB A:ASP278 4.3 48.9 1.0
C A:HIS434 4.4 49.0 1.0
CB A:ASN310 4.5 51.8 1.0
O3 A:PO41 4.5 49.2 1.0
N A:ASN310 4.6 51.9 1.0
O A:LEU392 4.6 50.4 1.0
N A:HIS434 4.7 48.2 1.0
CD2 A:HIS311 4.7 50.1 1.0
NE2 A:HIS251 4.9 52.9 1.0
NH1 A:ARG407 5.0 53.8 1.0
O A:HOH517 5.0 36.4 1.0
CG A:ASP249 5.0 50.5 1.0

Iron binding site 2 out of 4 in 3icf

Go back to Iron Binding Sites List in 3icf
Iron binding site 2 out of 4 in the Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:52.2
occ:1.00
 NE2 A:HIS251 2.0 52.9 1.0
O1 A:PO41 2.0 49.5 1.0
OD2 A:ASP249 2.1 52.8 1.0
OD2 A:ASP278 2.1 53.0 1.0
CE1 A:HIS251 2.8 52.1 1.0
O A:HOH517 2.9 36.4 1.0
CG A:ASP278 3.1 50.0 1.0
P A:PO41 3.1 47.8 1.0
CD2 A:HIS251 3.1 52.5 1.0
FE A:FE601 3.3 50.6 1.0
CG A:ASP249 3.3 50.5 1.0
O4 A:PO41 3.4 46.4 1.0
CB A:ASP278 3.5 48.9 1.0
O2 A:PO41 3.7 51.2 1.0
ND1 A:HIS251 4.0 50.6 1.0
CE1 A:HIS359 4.1 46.0 1.0
CB A:ASP249 4.1 51.1 1.0
NH2 A:ARG282 4.1 48.1 1.0
CD2 A:HIS311 4.2 50.1 1.0
OD1 A:ASP249 4.2 51.3 1.0
CG A:HIS251 4.2 51.3 1.0
OD1 A:ASP278 4.2 52.3 1.0
NE2 A:HIS359 4.2 47.1 1.0
O3 A:PO41 4.3 49.2 1.0
O A:HIS434 4.4 50.3 1.0
CA A:HIS434 4.5 48.6 1.0
ND1 A:HIS434 4.5 51.0 1.0
OH A:TYR458 4.5 58.9 1.0
C A:HIS434 4.7 49.0 1.0
NE2 A:HIS311 4.7 50.1 1.0
CE1 A:PHE453 4.8 44.0 1.0
OD1 A:ASN310 4.9 50.4 1.0
CA A:ASP278 4.9 49.2 1.0

Iron binding site 3 out of 4 in 3icf

Go back to Iron Binding Sites List in 3icf
Iron binding site 3 out of 4 in the Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:51.0
occ:1.00
 ND1 B:HIS434 1.9 50.8 1.0
NE2 B:HIS359 1.9 47.1 1.0
O1 B:PO42 2.0 46.3 1.0
OD1 B:ASN310 2.1 49.9 1.0
OD2 B:ASP278 2.1 52.5 1.0
CE1 B:HIS434 2.6 50.2 1.0
CE1 B:HIS359 2.9 45.6 1.0
CD2 B:HIS359 2.9 46.7 1.0
CG B:ASP278 3.0 49.8 1.0
CG B:HIS434 3.1 50.2 1.0
CG B:ASN310 3.2 50.8 1.0
FE B:FE602 3.3 51.1 1.0
P B:PO42 3.3 47.8 1.0
OD1 B:ASP278 3.4 52.4 1.0
CA B:HIS434 3.6 48.7 1.0
CB B:HIS434 3.7 48.6 1.0
O2 B:PO42 3.7 47.8 1.0
ND2 B:ASN310 3.7 46.7 1.0
O4 B:PO42 3.8 51.9 1.0
NE2 B:HIS434 3.8 49.5 1.0
ND1 B:HIS359 4.0 42.3 1.0
OD2 B:ASP249 4.0 53.2 1.0
CD2 B:HIS434 4.0 50.1 1.0
CG B:HIS359 4.1 47.5 1.0
O B:HIS434 4.1 50.2 1.0
CB B:ASP278 4.3 48.7 1.0
C B:HIS434 4.3 49.2 1.0
CB B:ASN310 4.5 52.0 1.0
N B:ASN310 4.5 52.0 1.0
O3 B:PO42 4.5 46.7 1.0
O B:LEU392 4.6 49.9 1.0
N B:HIS434 4.7 48.5 1.0
ND1 B:HIS311 4.7 51.0 1.0
NE2 B:HIS251 4.9 52.7 1.0
CG B:ASP249 5.0 50.5 1.0
NH1 B:ARG407 5.0 54.0 1.0

Iron binding site 4 out of 4 in 3icf

Go back to Iron Binding Sites List in 3icf
Iron binding site 4 out of 4 in the Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:51.1
occ:1.00
 NE2 B:HIS251 2.0 52.7 1.0
O2 B:PO42 2.1 47.8 1.0
OD2 B:ASP249 2.1 53.2 1.0
OD2 B:ASP278 2.1 52.5 1.0
CE1 B:HIS251 2.8 52.3 1.0
O B:HOH518 2.8 39.8 1.0
CG B:ASP278 3.1 49.8 1.0
CD2 B:HIS251 3.1 52.9 1.0
P B:PO42 3.1 47.8 1.0
O1 B:PO42 3.3 46.3 1.0
FE B:FE601 3.3 51.0 1.0
CG B:ASP249 3.3 50.5 1.0
CB B:ASP278 3.5 48.7 1.0
O4 B:PO42 3.8 51.9 1.0
ND1 B:HIS251 4.0 50.4 1.0
CE1 B:HIS359 4.1 45.6 1.0
CB B:ASP249 4.1 51.3 1.0
NH2 B:ARG282 4.1 48.0 1.0
OD1 B:ASP249 4.2 51.9 1.0
CG B:HIS251 4.2 51.8 1.0
NE2 B:HIS359 4.2 47.1 1.0
OD1 B:ASP278 4.2 52.4 1.0
O3 B:PO42 4.4 46.7 1.0
O B:HIS434 4.5 50.2 1.0
ND1 B:HIS434 4.5 50.8 1.0
CA B:HIS434 4.5 48.7 1.0
OH B:TYR458 4.6 58.8 1.0
C B:HIS434 4.7 49.2 1.0
CE1 B:PHE453 4.9 43.8 1.0
OD1 B:ASN310 4.9 49.9 1.0
CA B:ASP278 4.9 49.1 1.0

Reference:

A.U.Singer, X.Xu, C.Chang, H.Cui, A.M.Edwards, A.Joachimiak, A.Savchenko, A.F.Yakunin. Structure of Protein Serine/Threonine Phosphatase From Saccharomyces Cerevisiae with Similarity to Human Phosphatase PP5 To Be Published.
Page generated: Sun Dec 13 15:08:50 2020

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