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:
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
|