Atomistry » Iron » PDB 8rk1-8smu » 8rly
Atomistry »
  Iron »
    PDB 8rk1-8smu »
      8rly »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy