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Iron in PDB 2yz5: Histidinol Phosphate Phosphatase Complexed with Phosphate

Enzymatic activity of Histidinol Phosphate Phosphatase Complexed with Phosphate

All present enzymatic activity of Histidinol Phosphate Phosphatase Complexed with Phosphate:
3.1.3.15;

Protein crystallography data

The structure of Histidinol Phosphate Phosphatase Complexed with Phosphate, PDB code: 2yz5 was solved by R.Omi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.04 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.490, 96.929, 74.153, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.2

Other elements in 2yz5:

The structure of Histidinol Phosphate Phosphatase Complexed with Phosphate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Histidinol Phosphate Phosphatase Complexed with Phosphate (pdb code 2yz5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Histidinol Phosphate Phosphatase Complexed with Phosphate, PDB code: 2yz5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2yz5

Go back to Iron Binding Sites List in 2yz5
Iron binding site 1 out of 4 in the Histidinol Phosphate Phosphatase Complexed with Phosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Histidinol Phosphate Phosphatase Complexed with Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:35.2
occ:1.00
O A:HOH2146 2.0 24.4 1.0
O4 A:PO42001 2.2 35.5 1.0
OE2 A:GLU80 2.3 25.6 1.0
NE2 A:HIS108 2.3 23.2 1.0
NE2 A:HIS154 2.3 26.1 1.0
CD2 A:HIS154 3.1 25.4 1.0
CE1 A:HIS108 3.2 22.8 1.0
CD A:GLU80 3.3 24.2 1.0
P A:PO42001 3.3 35.1 1.0
CD2 A:HIS108 3.4 24.4 1.0
FE A:FE503 3.5 31.9 1.0
CE1 A:HIS154 3.5 25.0 1.0
OE1 A:GLU80 3.6 25.1 1.0
O1 A:PO42001 3.7 32.6 1.0
O2 A:PO42001 3.7 33.2 1.0
CE1 A:HIS38 4.2 24.6 1.0
OG A:SER106 4.2 24.1 1.0
CG A:HIS154 4.3 24.4 1.0
CB A:SER106 4.3 24.7 1.0
O A:HOH2118 4.3 36.7 1.0
ND1 A:HIS108 4.3 23.4 1.0
OD2 A:ASP224 4.4 28.2 1.0
ND1 A:HIS154 4.5 24.7 1.0
CG A:HIS108 4.5 22.7 1.0
O A:HOH2139 4.6 32.2 1.0
O3 A:PO42001 4.6 33.4 1.0
CG A:GLU80 4.6 22.8 1.0
CE1 A:HIS5 4.7 26.9 1.0
OD2 A:ASP116 4.9 28.9 1.0
NE2 A:HIS5 5.0 27.2 1.0

Iron binding site 2 out of 4 in 2yz5

Go back to Iron Binding Sites List in 2yz5
Iron binding site 2 out of 4 in the Histidinol Phosphate Phosphatase Complexed with Phosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Histidinol Phosphate Phosphatase Complexed with Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:31.9
occ:1.00
O A:HOH2146 2.1 24.4 1.0
NE2 A:HIS5 2.2 27.2 1.0
O1 A:PO42001 2.3 32.6 1.0
NE2 A:HIS7 2.3 23.2 1.0
OE1 A:GLU80 2.4 25.1 1.0
OD1 A:ASP224 2.5 26.5 1.0
CE1 A:HIS5 2.9 26.9 1.0
CE1 A:HIS7 3.1 23.0 1.0
CG A:ASP224 3.1 27.0 1.0
CD A:GLU80 3.1 24.2 1.0
OD2 A:ASP224 3.2 28.2 1.0
OE2 A:GLU80 3.4 25.6 1.0
CD2 A:HIS5 3.4 23.8 1.0
CD2 A:HIS7 3.5 22.6 1.0
P A:PO42001 3.5 35.1 1.0
FE A:FE502 3.5 35.2 1.0
O4 A:PO42001 3.7 35.5 1.0
CE1 A:HIS38 4.0 24.6 1.0
O2 A:PO42001 4.1 33.2 1.0
ND1 A:HIS5 4.1 25.4 1.0
NE2 A:HIS38 4.2 24.3 1.0
ND1 A:HIS7 4.3 22.6 1.0
CG A:HIS5 4.3 26.1 1.0
CG A:GLU80 4.4 22.8 1.0
CG A:HIS7 4.5 24.1 1.0
CB A:ASP224 4.5 24.5 1.0
CE1 A:HIS226 4.5 26.0 1.0
O3 A:PO42001 4.7 33.4 1.0
ZN A:ZN501 4.7 35.7 1.0
CB A:GLU80 4.8 21.7 1.0
CA A:ASP224 4.8 21.9 1.0
NE2 A:HIS226 4.9 25.1 1.0
ND1 A:HIS38 4.9 24.9 1.0

Iron binding site 3 out of 4 in 2yz5

Go back to Iron Binding Sites List in 2yz5
Iron binding site 3 out of 4 in the Histidinol Phosphate Phosphatase Complexed with Phosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Histidinol Phosphate Phosphatase Complexed with Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1502

b:33.7
occ:1.00
O2 B:PO42002 2.1 31.6 1.0
O B:HOH2151 2.1 27.7 1.0
OE2 B:GLU80 2.3 21.5 1.0
NE2 B:HIS108 2.3 24.2 1.0
NE2 B:HIS154 2.4 24.3 1.0
CE1 B:HIS108 3.1 22.1 1.0
CD2 B:HIS154 3.1 23.1 1.0
P B:PO42002 3.2 31.5 1.0
CD B:GLU80 3.3 23.1 1.0
CD2 B:HIS108 3.4 22.6 1.0
O1 B:PO42002 3.4 29.6 1.0
FE B:FE1503 3.4 29.1 1.0
CE1 B:HIS154 3.5 24.7 1.0
OE1 B:GLU80 3.6 23.9 1.0
O3 B:PO42002 3.7 29.0 1.0
O B:HOH2090 4.0 31.3 1.0
ND1 B:HIS108 4.3 22.2 1.0
OD2 B:ASP224 4.3 23.1 1.0
CG B:HIS154 4.4 25.1 1.0
O4 B:PO42002 4.4 28.3 1.0
OG B:SER106 4.4 23.9 1.0
CG B:HIS108 4.5 23.1 1.0
O B:HOH2102 4.5 34.0 1.0
CB B:SER106 4.5 22.9 1.0
CE1 B:HIS38 4.5 20.8 1.0
ND1 B:HIS154 4.5 22.8 1.0
CG B:GLU80 4.6 20.8 1.0
CE1 B:HIS5 4.7 20.8 1.0
OD2 B:ASP116 4.7 28.9 1.0
NE2 B:HIS5 4.9 20.5 1.0
OD1 B:ASP224 5.0 25.5 1.0

Iron binding site 4 out of 4 in 2yz5

Go back to Iron Binding Sites List in 2yz5
Iron binding site 4 out of 4 in the Histidinol Phosphate Phosphatase Complexed with Phosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Histidinol Phosphate Phosphatase Complexed with Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1503

b:29.1
occ:1.00
O B:HOH2151 2.1 27.7 1.0
NE2 B:HIS5 2.2 20.5 1.0
O1 B:PO42002 2.2 29.6 1.0
NE2 B:HIS7 2.3 22.2 1.0
OD1 B:ASP224 2.3 25.5 1.0
OE1 B:GLU80 2.4 23.9 1.0
CE1 B:HIS5 2.9 20.8 1.0
CG B:ASP224 3.1 25.7 1.0
CD B:GLU80 3.1 23.1 1.0
CE1 B:HIS7 3.1 19.2 1.0
OD2 B:ASP224 3.2 23.1 1.0
OE2 B:GLU80 3.2 21.5 1.0
CD2 B:HIS5 3.3 19.2 1.0
CD2 B:HIS7 3.3 20.1 1.0
FE B:FE1502 3.4 33.7 1.0
P B:PO42002 3.5 31.5 1.0
O2 B:PO42002 3.8 31.6 1.0
O3 B:PO42002 4.0 29.0 1.0
ND1 B:HIS5 4.1 19.2 1.0
CE1 B:HIS38 4.1 20.8 1.0
ND1 B:HIS7 4.3 22.3 1.0
CG B:HIS5 4.3 21.6 1.0
CE1 B:HIS226 4.3 22.2 1.0
CG B:HIS7 4.4 22.2 1.0
CG B:GLU80 4.4 20.8 1.0
CB B:ASP224 4.4 23.3 1.0
NE2 B:HIS38 4.5 20.4 1.0
O4 B:PO42002 4.6 28.3 1.0
ZN B:ZN1501 4.7 31.4 1.0
NE2 B:HIS226 4.7 21.8 1.0
CA B:ASP224 4.8 22.1 1.0
CB B:GLU80 4.8 20.2 1.0
ND1 B:HIS38 5.0 22.1 1.0

Reference:

R.Omi, M.Goto, I.Miyahara, M.Manzoku, A.Ebihara, K.Hirotsu. Crystal Structure of Monofunctional Histidinol Phosphate Phosphatase From Thermus Thermophilus HB8. Biochemistry V. 46 12618 2007.
ISSN: ISSN 0006-2960
PubMed: 17929834
DOI: 10.1021/BI701204R
Page generated: Sun Dec 13 14:58:33 2020

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