Chlorine 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:

Iron (Fe) 5 atoms
Zinc (Zn) 10 atoms
Nickel (Ni) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+, PDB code: 8rly:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8rly

Go back to Chlorine Binding Sites List in 8rly
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl307

b:18.8
occ:1.00
H A:GLN150 2.5 17.8 1.0
HD21 A:ASN153 2.5 25.0 1.0
H A:GLY149 2.8 19.4 1.0
HB2 A:GLN150 3.0 20.4 1.0
HB A:THR147 3.0 20.7 1.0
O A:HOH556 3.1 16.7 1.0
O A:HOH538 3.2 27.8 1.0
N A:GLN150 3.3 14.8 1.0
HB2 A:ASN153 3.3 25.9 1.0
ND2 A:ASN153 3.3 20.8 1.0
N A:GLY149 3.4 16.1 1.0
H A:ALA148 3.5 22.3 1.0
HB3 A:ALA148 3.5 19.4 1.0
HG3 A:GLN150 3.6 20.4 1.0
CB A:GLN150 3.8 17.0 1.0
HD22 A:ASN153 3.8 25.0 1.0
HB3 A:ASN153 3.9 25.9 1.0
CB A:ASN153 3.9 21.6 1.0
N A:ALA148 3.9 18.6 1.0
HA2 A:GLY149 4.0 21.2 1.0
CB A:THR147 4.0 17.2 1.0
CA A:GLY149 4.0 17.7 1.0
CA A:GLN150 4.0 17.1 1.0
HB2 A:ASP229 4.1 18.7 1.0
CG A:ASN153 4.1 20.9 1.0
C A:GLY149 4.1 17.0 1.0
CG A:GLN150 4.2 17.0 1.0
C A:ALA148 4.2 18.4 1.0
HG1 A:THR147 4.3 20.4 1.0
CB A:ALA148 4.3 16.1 1.0
O A:GLN150 4.3 18.4 1.0
CA A:ALA148 4.4 15.3 1.0
OG1 A:THR147 4.5 17.0 1.0
HB3 A:GLN150 4.6 20.4 1.0
HG21 A:THR147 4.6 23.9 1.0
C A:GLN150 4.6 17.7 1.0
C A:THR147 4.7 17.2 1.0
CG2 A:THR147 4.8 19.9 1.0
HD1 A:HIS109 4.8 26.2 1.0
CA A:THR147 4.8 15.6 1.0
HA A:THR147 4.8 18.8 1.0
HG22 A:THR147 4.8 23.9 1.0
HB2 A:ALA148 4.8 19.4 1.0
HB3 A:ASP229 4.8 18.7 1.0
HA A:GLN150 4.9 20.6 1.0
CB A:ASP229 4.9 15.6 1.0
HG2 A:GLN150 4.9 20.4 1.0
HB1 A:ALA148 4.9 19.4 1.0
CD A:GLN150 5.0 19.2 1.0
HA3 A:GLY149 5.0 21.2 1.0

Chlorine binding site 2 out of 5 in 8rly

Go back to Chlorine Binding Sites List in 8rly
Chlorine 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 Chlorine with other atoms in the Cl 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
A:Cl308

b:23.2
occ:1.00
H A:PHE224 2.5 22.2 1.0
HB3 A:ASN238 2.9 26.1 1.0
O A:HOH653 2.9 27.6 1.0
HA A:THR223 3.0 22.7 1.0
HB A:THR223 3.0 21.3 1.0
HZ A:PHE184 3.1 19.7 1.0
N A:PHE224 3.3 18.5 1.0
HG22 A:THR223 3.3 23.7 1.0
HB2 A:PHE224 3.5 18.2 1.0
HE2 A:PHE184 3.6 20.2 1.0
HH11 A:ARG191 3.6 31.6 1.0
CB A:ASN238 3.6 21.8 1.0
CA A:THR223 3.6 18.9 1.0
CB A:THR223 3.6 17.8 1.0
HB3 A:PHE224 3.7 18.2 1.0
CG A:ASN238 3.8 23.3 1.0
CZ A:PHE184 3.8 16.4 1.0
CG2 A:THR223 3.9 19.8 1.0
HB2 A:ASN238 3.9 26.1 1.0
CB A:PHE224 4.0 15.2 1.0
C A:THR223 4.0 19.4 1.0
NH1 A:ARG191 4.0 26.4 1.0
HH12 A:ARG191 4.0 31.6 1.0
CE2 A:PHE184 4.1 16.8 1.0
ND2 A:ASN238 4.2 19.7 1.0
HD3 A:ARG191 4.2 25.0 1.0
OD1 A:ASN238 4.2 19.3 1.0
CA A:PHE224 4.2 21.3 1.0
HD21 A:ASN238 4.3 23.6 1.0
HG21 A:THR223 4.3 23.7 1.0
HD22 A:ASN238 4.6 23.6 1.0
HA A:PHE224 4.7 25.6 1.0
HG23 A:THR223 4.7 23.7 1.0
O A:ASN238 4.8 15.7 1.0
CZ A:ARG191 4.9 22.9 1.0
CA A:ASN238 4.9 17.9 1.0
N A:THR223 4.9 15.5 1.0
OG1 A:THR223 5.0 17.5 1.0
HA A:ASN238 5.0 21.6 1.0

Chlorine binding site 3 out of 5 in 8rly

Go back to Chlorine Binding Sites List in 8rly
Chlorine 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 Chlorine with other atoms in the Cl 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
B:Cl307

b:24.8
occ:1.00
H B:GLN150 2.4 20.8 1.0
H B:GLY149 2.8 23.1 1.0
O B:HOH502 2.9 19.6 1.0
O B:HOH626 2.9 39.0 1.0
HB B:THR147 2.9 20.4 1.0
HB2 B:GLN150 2.9 25.5 1.0
N B:GLN150 3.2 17.3 1.0
HB2 B:ASN153 3.2 24.5 1.0
H B:ALA148 3.2 24.1 1.0
HB3 B:ALA148 3.3 24.1 1.0
N B:GLY149 3.4 19.3 1.0
HG3 B:GLN150 3.4 37.5 1.0
O B:HOH442 3.5 31.4 1.0
HB3 B:ASN153 3.5 24.5 1.0
HD21 B:ASN153 3.6 24.8 1.0
ND2 B:ASN153 3.6 20.6 1.0
CB B:ASN153 3.6 20.4 1.0
CG B:ASN153 3.6 25.5 1.0
CB B:GLN150 3.7 21.2 1.0
N B:ALA148 3.7 20.1 1.0
CB B:THR147 3.9 17.0 1.0
CA B:GLN150 4.0 20.2 1.0
HD22 B:ASN153 4.0 24.8 1.0
CG B:GLN150 4.0 31.2 1.0
CA B:GLY149 4.0 16.8 1.0
C B:GLY149 4.1 18.5 1.0
HA2 B:GLY149 4.1 20.2 1.0
HB2 B:ASP229 4.1 20.4 1.0
CB B:ALA148 4.1 20.0 1.0
C B:ALA148 4.2 19.8 1.0
CA B:ALA148 4.2 16.4 1.0
O B:GLN150 4.2 17.2 1.0
OD1 B:ASN153 4.3 30.2 1.0
HG1 B:THR147 4.4 21.8 1.0
OG1 B:THR147 4.4 18.2 1.0
HB3 B:GLN150 4.5 25.5 1.0
HG21 B:THR147 4.5 21.3 1.0
C B:GLN150 4.6 20.3 1.0
C B:THR147 4.6 17.8 1.0
HB2 B:ALA148 4.6 24.1 1.0
CG2 B:THR147 4.7 17.7 1.0
CA B:THR147 4.7 19.6 1.0
HG2 B:GLN150 4.7 37.5 1.0
HA B:THR147 4.7 23.5 1.0
HG22 B:THR147 4.8 21.3 1.0
HB1 B:ALA148 4.8 24.1 1.0
HA B:GLN150 4.8 24.3 1.0
HD1 B:HIS109 4.8 35.0 1.0
HA3 B:GLY149 5.0 20.2 1.0
CB B:ASP229 5.0 17.0 1.0
CD B:GLN150 5.0 35.0 1.0

Chlorine binding site 4 out of 5 in 8rly

Go back to Chlorine Binding Sites List in 8rly
Chlorine 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 Chlorine with other atoms in the Cl 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
C:Cl307

b:19.6
occ:1.00
H C:GLN150 2.4 21.7 1.0
H C:GLY149 2.8 21.2 1.0
HB C:THR147 2.8 20.8 1.0
O C:HOH569 3.1 21.0 1.0
HB2 C:GLN150 3.1 26.3 1.0
N C:GLN150 3.2 18.1 1.0
HB2 C:ASN153 3.2 17.3 1.0
O C:HOH415 3.3 27.6 1.0
H C:ALA148 3.4 19.4 1.0
HG3 C:GLN150 3.4 30.6 1.0
HB3 C:ALA148 3.4 17.7 1.0
N C:GLY149 3.4 17.7 1.0
HD21 C:ASN153 3.6 25.7 1.0
HB3 C:ASN153 3.6 17.3 1.0
CB C:ASN153 3.7 14.4 1.0
ND2 C:ASN153 3.7 21.4 1.0
CB C:THR147 3.8 17.3 1.0
CB C:GLN150 3.8 21.9 1.0
CG C:ASN153 3.8 25.7 1.0
N C:ALA148 3.8 16.2 1.0
CA C:GLN150 4.0 19.4 1.0
HA2 C:GLY149 4.0 21.5 1.0
CG C:GLN150 4.0 25.5 1.0
CA C:GLY149 4.0 17.9 1.0
C C:GLY149 4.1 15.8 1.0
HD22 C:ASN153 4.1 25.7 1.0
O C:GLN150 4.2 16.5 1.0
HE21 C:GLN150 4.2 34.0 1.0
CB C:ALA148 4.2 14.8 1.0
HB2 C:ASP229 4.2 24.1 1.0
C C:ALA148 4.2 15.8 1.0
OG1 C:THR147 4.3 16.3 1.0
CA C:ALA148 4.3 16.7 1.0
HG1 C:THR147 4.3 19.6 1.0
HG21 C:THR147 4.4 21.3 1.0
OD1 C:ASN153 4.4 28.1 1.0
HD1 C:HIS109 4.5 26.1 1.0
C C:GLN150 4.5 22.2 1.0
CG2 C:THR147 4.5 17.8 1.0
C C:THR147 4.6 16.0 1.0
CA C:THR147 4.6 14.9 1.0
HG22 C:THR147 4.6 21.3 1.0
HB3 C:GLN150 4.6 26.3 1.0
HA C:THR147 4.6 17.9 1.0
HB2 C:ALA148 4.7 17.7 1.0
NE2 C:GLN150 4.7 28.3 1.0
CD C:GLN150 4.7 22.7 1.0
HG2 C:GLN150 4.8 30.6 1.0
HA C:GLN150 4.8 23.4 1.0
HB1 C:ALA148 4.9 17.7 1.0
HA3 C:GLY149 5.0 21.5 1.0
O C:HOH611 5.0 26.4 1.0

Chlorine binding site 5 out of 5 in 8rly

Go back to Chlorine Binding Sites List in 8rly
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl306

b:27.7
occ:1.00
H E:GLN150 2.3 27.6 1.0
HD21 E:ASN153 2.4 38.4 1.0
H E:GLY149 2.8 23.1 1.0
HB E:THR147 2.9 25.8 1.0
O E:HOH538 3.0 22.6 1.0
HB2 E:GLN150 3.1 34.8 1.0
HB2 E:ASN153 3.1 24.9 1.0
N E:GLN150 3.2 23.0 1.0
ND2 E:ASN153 3.2 32.0 1.0
HE21 E:GLN150 3.2 48.0 1.0
O E:HOH467 3.2 29.2 1.0
HG3 E:GLN150 3.3 43.6 1.0
H E:ALA148 3.3 26.8 1.0
N E:GLY149 3.4 19.2 1.0
HB3 E:ALA148 3.4 21.1 1.0
CB E:GLN150 3.7 29.0 1.0
CB E:ASN153 3.7 20.8 1.0
HB3 E:ASN153 3.7 24.9 1.0
HD22 E:ASN153 3.8 38.4 1.0
CB E:THR147 3.8 21.5 1.0
N E:ALA148 3.8 22.4 1.0
CG E:GLN150 3.9 36.3 1.0
NE2 E:GLN150 3.9 40.0 1.0
CG E:ASN153 3.9 25.1 1.0
CA E:GLN150 3.9 29.5 1.0
HA2 E:GLY149 4.0 30.8 1.0
CA E:GLY149 4.0 25.6 1.0
C E:GLY149 4.0 28.1 1.0
O E:GLN150 4.2 25.6 1.0
C E:ALA148 4.2 21.2 1.0
CB E:ALA148 4.2 17.6 1.0
HG1 E:THR147 4.2 28.8 1.0
CA E:ALA148 4.3 18.2 1.0
OG1 E:THR147 4.3 24.0 1.0
CD E:GLN150 4.4 34.8 1.0
HG21 E:THR147 4.4 25.2 1.0
HB2 E:ASP229 4.4 28.4 1.0
HE22 E:GLN150 4.5 48.0 1.0
C E:GLN150 4.5 27.1 1.0
CG2 E:THR147 4.6 21.0 1.0
C E:THR147 4.6 21.4 1.0
HB3 E:GLN150 4.6 34.8 1.0
HG22 E:THR147 4.6 25.2 1.0
CA E:THR147 4.7 23.9 1.0
HB2 E:ALA148 4.7 21.1 1.0
HA E:THR147 4.7 28.6 1.0
HG2 E:GLN150 4.8 43.6 1.0
HA E:GLN150 4.8 35.5 1.0
HD1 E:HIS109 4.8 28.5 1.0
HB1 E:ALA148 4.9 21.1 1.0
HA3 E:GLY149 4.9 30.8 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 10:13:41 2024

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