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Iron in PDB 8rly: E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+

Enzymatic activity of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+

All present enzymatic activity of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+:
3.1.21.2;

Protein crystallography data

The structure of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+, PDB code: 8rly was solved by M.A.Saper, N.G.Paterson, S.Kirillov, A.Rouvinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.12 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.78, 115.98, 177.7, 90, 90, 90
R / Rfree (%) 15.7 / 20.7

Other elements in 8rly:

The structure of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Zinc (Zn) 10 atoms
Nickel (Ni) 7 atoms

Iron Binding Sites:

The binding sites of Iron atom in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ (pdb code 8rly). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+, PDB code: 8rly:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 8rly

Go back to Iron Binding Sites List in 8rly
Iron binding site 1 out of 5 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:20.4
occ:1.00
OD2 A:ASP179 2.1 15.1 1.0
O2 A:SO4305 2.2 27.0 1.0
OE2 A:GLU145 2.2 17.2 1.0
O A:HOH403 2.2 23.1 1.0
ND1 A:HIS216 2.2 16.2 1.0
OE1 A:GLU261 2.3 15.2 1.0
CD A:GLU145 3.1 16.5 1.0
HB2 A:ASP179 3.1 16.2 1.0
CE1 A:HIS216 3.1 16.1 1.0
CD A:GLU261 3.2 18.3 1.0
CG A:ASP179 3.2 13.4 1.0
CG A:HIS216 3.2 19.4 1.0
HE1 A:HIS216 3.3 19.3 1.0
HE1 A:HIS182 3.3 17.8 1.0
HB2 A:HIS216 3.3 18.0 1.0
HB3 A:HIS216 3.4 18.0 1.0
OE1 A:GLU145 3.4 17.1 1.0
OE2 A:GLU261 3.4 20.5 1.0
ZN A:ZN301 3.5 20.3 1.0
S A:SO4305 3.5 31.1 1.0
CB A:HIS216 3.5 15.0 1.0
HD22 A:ASN218 3.5 19.4 1.0
CE1 A:HIS182 3.6 14.8 1.0
CB A:ASP179 3.7 13.5 1.0
HE1 A:HIS231 3.9 21.9 1.0
HD21 A:ASN218 3.9 19.4 1.0
O4 A:SO4305 4.0 32.0 1.0
ND2 A:ASN218 4.1 16.1 1.0
O3 A:SO4305 4.1 31.9 1.0
NE2 A:HIS182 4.1 16.5 1.0
HB3 A:ASP179 4.1 16.2 1.0
NE2 A:HIS216 4.3 15.5 1.0
CG A:GLU145 4.3 17.1 1.0
HG3 A:GLU145 4.3 20.6 1.0
OD1 A:ASP179 4.3 14.6 1.0
CD2 A:HIS216 4.3 17.5 1.0
ND1 A:HIS182 4.3 14.2 1.0
HD1 A:HIS182 4.5 17.0 1.0
O1 A:SO4305 4.5 23.9 1.0
CE1 A:HIS231 4.5 18.2 1.0
HG2 A:GLU145 4.6 20.6 1.0
CG A:GLU261 4.6 17.9 1.0
HB2 A:GLU261 4.6 19.4 1.0
ZN A:ZN303 4.7 19.2 1.0
HA A:ASP179 4.8 21.6 1.0
HD2 A:HIS69 4.8 17.8 1.0
HG3 A:GLU261 4.8 21.4 1.0
NE2 A:HIS231 4.8 16.6 1.0
HD22 A:ASN107 4.9 18.7 1.0
CA A:ASP179 4.9 18.0 1.0
NE2 A:HIS109 4.9 20.1 1.0

Iron binding site 2 out of 5 in 8rly

Go back to Iron Binding Sites List in 8rly
Iron binding site 2 out of 5 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:21.7
occ:1.00
OD2 B:ASP179 2.2 17.3 1.0
O1 B:SO4304 2.2 22.6 1.0
O B:HOH405 2.2 23.2 1.0
ND1 B:HIS216 2.3 17.9 1.0
OE1 B:GLU261 2.3 14.5 1.0
OE2 B:GLU145 2.3 14.4 1.0
CD B:GLU145 3.1 18.0 1.0
CD B:GLU261 3.1 15.3 1.0
HB2 B:ASP179 3.2 18.7 1.0
CE1 B:HIS216 3.2 18.1 1.0
CG B:ASP179 3.2 18.0 1.0
CG B:HIS216 3.3 14.3 1.0
HE1 B:HIS216 3.3 21.7 1.0
OE1 B:GLU145 3.4 16.6 1.0
HE1 B:HIS182 3.4 21.4 1.0
OE2 B:GLU261 3.4 16.0 1.0
HB3 B:HIS216 3.4 16.5 1.0
HB2 B:HIS216 3.4 16.5 1.0
ZN B:ZN301 3.4 22.0 1.0
HD22 B:ASN218 3.5 19.1 1.0
S B:SO4304 3.6 27.8 1.0
CB B:HIS216 3.6 13.8 1.0
CB B:ASP179 3.7 15.6 1.0
CE1 B:HIS182 3.7 17.8 1.0
HE1 B:HIS231 3.9 19.2 1.0
HD21 B:ASN218 4.0 19.1 1.0
ND2 B:ASN218 4.1 15.9 1.0
O4 B:SO4304 4.1 26.9 1.0
O2 B:SO4304 4.1 27.2 1.0
HB3 B:ASP179 4.2 18.7 1.0
NE2 B:HIS182 4.2 17.7 1.0
CG B:GLU145 4.3 19.5 1.0
NE2 B:HIS216 4.3 19.4 1.0
HG3 B:GLU145 4.3 23.4 1.0
OD1 B:ASP179 4.3 14.7 1.0
CD2 B:HIS216 4.4 16.4 1.0
ND1 B:HIS182 4.4 18.0 1.0
CG B:GLU261 4.5 16.9 1.0
CE1 B:HIS231 4.5 16.0 1.0
HG2 B:GLU145 4.5 23.4 1.0
O3 B:SO4304 4.5 22.0 1.0
HD1 B:HIS182 4.6 21.6 1.0
ZN B:ZN303 4.6 19.8 1.0
HB2 B:GLU261 4.6 20.0 1.0
HD2 B:HIS69 4.7 21.3 1.0
HG3 B:GLU261 4.8 20.3 1.0
HA B:ASP179 4.8 20.8 1.0
NE2 B:HIS231 4.9 17.6 1.0
HD22 B:ASN107 4.9 22.4 1.0
NE2 B:HIS109 4.9 18.8 1.0
CA B:ASP179 4.9 17.3 1.0

Iron binding site 3 out of 5 in 8rly

Go back to Iron Binding Sites List in 8rly
Iron binding site 3 out of 5 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe302

b:20.9
occ:1.00
O C:HOH407 2.2 22.8 1.0
OD2 C:ASP179 2.2 15.2 1.0
OE1 C:GLU261 2.2 11.8 1.0
O2 C:SO4304 2.2 28.8 1.0
ND1 C:HIS216 2.3 15.3 1.0
OE2 C:GLU145 2.3 14.0 1.0
CD C:GLU261 3.0 17.1 1.0
CD C:GLU145 3.1 18.2 1.0
HB2 C:ASP179 3.1 17.5 1.0
CE1 C:HIS216 3.1 19.4 1.0
OE2 C:GLU261 3.2 15.1 1.0
CG C:ASP179 3.3 13.8 1.0
CG C:HIS216 3.3 14.5 1.0
HE1 C:HIS216 3.3 23.3 1.0
HE1 C:HIS182 3.3 25.8 1.0
HB3 C:HIS216 3.4 17.6 1.0
OE1 C:GLU145 3.4 16.1 1.0
HB2 C:HIS216 3.4 17.6 1.0
ZN C:ZN301 3.4 20.3 1.0
HD22 C:ASN218 3.5 17.5 1.0
S C:SO4304 3.6 28.4 1.0
CB C:HIS216 3.6 14.7 1.0
CE1 C:HIS182 3.7 21.5 1.0
CB C:ASP179 3.7 14.6 1.0
HE1 C:HIS231 3.8 22.4 1.0
O4 C:SO4304 4.0 30.1 1.0
HD21 C:ASN218 4.0 17.5 1.0
ND2 C:ASN218 4.1 14.6 1.0
O1 C:SO4304 4.1 26.9 1.0
NE2 C:HIS182 4.1 13.5 1.0
HB3 C:ASP179 4.2 17.5 1.0
NE2 C:HIS216 4.3 20.2 1.0
CG C:GLU145 4.3 15.6 1.0
OD1 C:ASP179 4.3 15.7 1.0
HG3 C:GLU145 4.3 18.8 1.0
CD2 C:HIS216 4.4 15.9 1.0
ND1 C:HIS182 4.4 15.4 1.0
CG C:GLU261 4.4 23.5 1.0
CE1 C:HIS231 4.5 18.7 1.0
HG2 C:GLU145 4.6 18.8 1.0
HD1 C:HIS182 4.6 18.5 1.0
O3 C:SO4304 4.6 21.5 1.0
HB2 C:GLU261 4.6 22.4 1.0
HG3 C:GLU261 4.6 28.3 1.0
ZN C:ZN303 4.7 19.9 1.0
HD2 C:HIS69 4.7 21.1 1.0
HD22 C:ASN107 4.8 19.3 1.0
HA C:ASP179 4.8 16.2 1.0
NE2 C:HIS231 4.9 18.7 1.0
CA C:ASP179 4.9 13.5 1.0
NE2 C:HIS109 5.0 18.6 1.0

Iron binding site 4 out of 5 in 8rly

Go back to Iron Binding Sites List in 8rly
Iron binding site 4 out of 5 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe302

b:27.5
occ:1.00
OD2 D:ASP179 2.2 18.1 1.0
O2 D:SO4304 2.2 33.0 1.0
OE1 D:GLU261 2.2 23.3 1.0
OE2 D:GLU145 2.3 17.2 1.0
O D:HOH405 2.3 28.0 1.0
ND1 D:HIS216 2.4 18.1 1.0
CD D:GLU261 3.1 23.5 1.0
CD D:GLU145 3.1 21.1 1.0
HB2 D:ASP179 3.2 26.1 1.0
OE2 D:GLU261 3.2 24.8 1.0
CG D:ASP179 3.3 19.7 1.0
CE1 D:HIS216 3.3 18.3 1.0
CG D:HIS216 3.3 17.5 1.0
HB3 D:HIS216 3.3 24.8 1.0
OE1 D:GLU145 3.4 21.9 1.0
HB2 D:HIS216 3.4 24.8 1.0
ZN D:ZN301 3.4 24.2 1.0
HE1 D:HIS216 3.5 22.0 1.0
HE1 D:HIS182 3.5 26.8 1.0
S D:SO4304 3.6 31.0 1.0
HD22 D:ASN218 3.6 22.5 1.0
CB D:HIS216 3.6 20.6 1.0
CB D:ASP179 3.7 21.8 1.0
CE1 D:HIS182 3.8 22.4 1.0
HE1 D:HIS231 3.9 34.3 1.0
HD21 D:ASN218 4.0 22.5 1.0
O3 D:SO4304 4.1 29.6 1.0
O4 D:SO4304 4.1 30.6 1.0
ND2 D:ASN218 4.1 18.8 1.0
NE2 D:HIS182 4.2 20.1 1.0
HB3 D:ASP179 4.2 26.1 1.0
CG D:GLU145 4.3 18.1 1.0
OD1 D:ASP179 4.3 20.6 1.0
HG3 D:GLU145 4.3 21.7 1.0
ND1 D:HIS182 4.4 23.0 1.0
NE2 D:HIS216 4.4 22.4 1.0
CD2 D:HIS216 4.4 20.8 1.0
CG D:GLU261 4.5 23.2 1.0
O1 D:SO4304 4.5 25.8 1.0
CE1 D:HIS231 4.5 28.6 1.0
ZN D:ZN303 4.5 25.1 1.0
HG2 D:GLU145 4.6 21.7 1.0
HD1 D:HIS182 4.6 27.6 1.0
HG3 D:GLU261 4.7 27.9 1.0
HB2 D:GLU261 4.7 28.6 1.0
HD2 D:HIS69 4.8 25.9 1.0
HA D:ASP179 4.8 28.2 1.0
NE2 D:HIS231 4.9 22.0 1.0
CA D:ASP179 4.9 23.5 1.0
HD22 D:ASN107 5.0 27.5 1.0

Iron binding site 5 out of 5 in 8rly

Go back to Iron Binding Sites List in 8rly
Iron binding site 5 out of 5 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe302

b:23.1
occ:1.00
OD2 E:ASP179 2.1 16.5 1.0
O1 E:SO4304 2.2 30.1 1.0
ND1 E:HIS216 2.2 14.4 1.0
OE1 E:GLU261 2.2 17.6 1.0
O E:HOH405 2.2 27.8 1.0
OE2 E:GLU145 2.3 16.9 1.0
CE1 E:HIS216 3.1 14.7 1.0
CD E:GLU261 3.1 22.9 1.0
CD E:GLU145 3.1 18.3 1.0
HB2 E:ASP179 3.2 20.8 1.0
CG E:ASP179 3.2 18.5 1.0
CG E:HIS216 3.2 14.4 1.0
HE1 E:HIS216 3.3 17.6 1.0
OE2 E:GLU261 3.3 20.6 1.0
HE1 E:HIS182 3.4 26.9 1.0
HB3 E:HIS216 3.4 18.8 1.0
HB2 E:HIS216 3.4 18.8 1.0
ZN E:ZN301 3.4 22.9 1.0
OE1 E:GLU145 3.4 16.4 1.0
HD22 E:ASN218 3.5 19.3 1.0
S E:SO4304 3.5 30.7 1.0
CB E:HIS216 3.6 15.6 1.0
CB E:ASP179 3.7 17.3 1.0
CE1 E:HIS182 3.7 22.4 1.0
HE1 E:HIS231 3.9 23.8 1.0
HD21 E:ASN218 4.0 19.3 1.0
O2 E:SO4304 4.0 31.4 1.0
O3 E:SO4304 4.0 27.4 1.0
NE2 E:HIS182 4.1 19.9 1.0
ND2 E:ASN218 4.1 16.1 1.0
HB3 E:ASP179 4.2 20.8 1.0
NE2 E:HIS216 4.3 16.4 1.0
OD1 E:ASP179 4.3 16.9 1.0
CD2 E:HIS216 4.3 17.5 1.0
CG E:GLU145 4.4 15.8 1.0
HG3 E:GLU145 4.4 18.9 1.0
ND1 E:HIS182 4.4 18.2 1.0
O4 E:SO4304 4.5 18.8 1.0
CG E:GLU261 4.5 15.2 1.0
CE1 E:HIS231 4.6 19.8 1.0
HG2 E:GLU145 4.6 18.9 1.0
ZN E:ZN303 4.6 21.0 1.0
HB2 E:GLU261 4.6 21.3 1.0
HD1 E:HIS182 4.6 21.9 1.0
HG3 E:GLU261 4.7 18.3 1.0
HD2 E:HIS69 4.7 24.5 1.0
HA E:ASP179 4.8 20.4 1.0
NE2 E:HIS231 4.9 20.3 1.0
CA E:ASP179 4.9 16.9 1.0
HD22 E:ASN107 4.9 23.6 1.0
CD2 E:HIS182 5.0 23.0 1.0
NE2 E:HIS109 5.0 24.8 1.0

Reference:

S.Kirillov, M.Isupov, N.G.Paterson, R.Wiener, S.Abeldenov, M.A.Saper, A.Rouvinski. Octahedral Iron in Catalytic Sites of Endonuclease IV From Staphylococcus Aureus and Escherichia Coli Biochemistry 2024.
ISSN: ISSN 0006-2960
DOI: 10.1021/ACS.BIOCHEM.4C00447
Page generated: Sun Dec 15 10:43:17 2024

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