Zinc 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:
Zinc Binding Sites:
The binding sites of Zinc 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 Zinc atom.
In total 10 binding sites of Zinc where determined in the
E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+, PDB code: 8rly:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 10 in 8rly
Go back to
Zinc Binding Sites List in 8rly
Zinc binding site 1 out
of 10 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn 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:Zn301
b:20.3
occ:1.00
|
O
|
A:HOH403
|
1.9
|
23.1
|
1.0
|
|
OE1
|
A:GLU145
|
2.1
|
17.1
|
1.0
|
|
NE2
|
A:HIS109
|
2.2
|
20.1
|
1.0
|
|
O3
|
A:SO4305
|
2.2
|
31.9
|
1.0
|
|
NE2
|
A:HIS69
|
2.2
|
17.1
|
1.0
|
|
CD
|
A:GLU145
|
3.0
|
16.5
|
1.0
|
|
CD2
|
A:HIS109
|
3.0
|
18.2
|
1.0
|
|
O2
|
A:SO4305
|
3.1
|
27.0
|
1.0
|
|
CD2
|
A:HIS69
|
3.1
|
14.8
|
1.0
|
|
HD2
|
A:HIS109
|
3.1
|
21.9
|
1.0
|
|
S
|
A:SO4305
|
3.2
|
31.1
|
1.0
|
|
CE1
|
A:HIS69
|
3.2
|
19.2
|
1.0
|
|
CE1
|
A:HIS109
|
3.2
|
21.6
|
1.0
|
|
OE2
|
A:GLU145
|
3.2
|
17.2
|
1.0
|
|
HD2
|
A:HIS69
|
3.3
|
17.8
|
1.0
|
|
HE1
|
A:HIS69
|
3.4
|
23.0
|
1.0
|
|
HD22
|
A:ASN107
|
3.4
|
18.7
|
1.0
|
|
FE
|
A:FE2302
|
3.5
|
20.4
|
1.0
|
|
HE1
|
A:HIS109
|
3.5
|
25.9
|
1.0
|
|
HE1
|
A:HIS182
|
3.5
|
17.8
|
1.0
|
|
HE1
|
A:HIS216
|
3.5
|
19.3
|
1.0
|
|
O4
|
A:SO4305
|
4.0
|
32.0
|
1.0
|
|
ND2
|
A:ASN107
|
4.1
|
15.6
|
1.0
|
|
HD21
|
A:ASN107
|
4.1
|
18.7
|
1.0
|
|
CG
|
A:HIS109
|
4.2
|
21.0
|
1.0
|
|
CE1
|
A:HIS216
|
4.2
|
16.1
|
1.0
|
|
ND1
|
A:HIS109
|
4.3
|
21.8
|
1.0
|
|
CG
|
A:HIS69
|
4.3
|
17.5
|
1.0
|
|
ND1
|
A:HIS69
|
4.3
|
18.3
|
1.0
|
|
OE2
|
A:GLU261
|
4.3
|
20.5
|
1.0
|
|
O1
|
A:SO4305
|
4.4
|
23.9
|
1.0
|
|
CG
|
A:GLU145
|
4.4
|
17.1
|
1.0
|
|
O
|
A:HOH425
|
4.4
|
28.0
|
1.0
|
|
ND1
|
A:HIS216
|
4.4
|
16.2
|
1.0
|
|
CE1
|
A:HIS182
|
4.4
|
14.8
|
1.0
|
|
HB3
|
A:GLU145
|
4.4
|
16.6
|
1.0
|
|
HB2
|
A:GLU145
|
4.8
|
16.6
|
1.0
|
|
CB
|
A:GLU145
|
4.8
|
13.8
|
1.0
|
|
OE1
|
A:GLU261
|
4.9
|
15.2
|
1.0
|
|
HG2
|
A:GLU145
|
4.9
|
20.6
|
1.0
|
|
HG3
|
A:GLU145
|
4.9
|
20.6
|
1.0
|
|
Zinc binding site 2 out
of 10 in 8rly
Go back to
Zinc Binding Sites List in 8rly
Zinc binding site 2 out
of 10 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn 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:Zn303
b:19.2
occ:1.00
|
O1
|
A:SO4305
|
1.9
|
23.9
|
1.0
|
|
NE2
|
A:HIS182
|
2.1
|
16.5
|
1.0
|
|
NE2
|
A:HIS231
|
2.1
|
16.6
|
1.0
|
|
OD1
|
A:ASP229
|
2.3
|
14.7
|
1.0
|
|
OD2
|
A:ASP229
|
2.3
|
21.7
|
1.0
|
|
CG
|
A:ASP229
|
2.6
|
19.3
|
1.0
|
|
O2
|
A:SO4305
|
2.9
|
27.0
|
1.0
|
|
S
|
A:SO4305
|
3.0
|
31.1
|
1.0
|
|
CD2
|
A:HIS182
|
3.1
|
14.7
|
1.0
|
|
CE1
|
A:HIS231
|
3.1
|
18.2
|
1.0
|
|
CD2
|
A:HIS231
|
3.1
|
17.9
|
1.0
|
|
CE1
|
A:HIS182
|
3.2
|
14.8
|
1.0
|
|
HD2
|
A:HIS182
|
3.2
|
17.6
|
1.0
|
|
HD2
|
A:HIS231
|
3.3
|
21.4
|
1.0
|
|
HE1
|
A:HIS231
|
3.3
|
21.9
|
1.0
|
|
HE1
|
A:HIS182
|
3.4
|
17.8
|
1.0
|
|
O4
|
A:SO4305
|
3.8
|
32.0
|
1.0
|
|
CB
|
A:ASP229
|
4.1
|
15.6
|
1.0
|
|
O3
|
A:SO4305
|
4.2
|
31.9
|
1.0
|
|
ND1
|
A:HIS231
|
4.2
|
18.9
|
1.0
|
|
CG
|
A:HIS231
|
4.2
|
17.5
|
1.0
|
|
CG
|
A:HIS182
|
4.2
|
13.6
|
1.0
|
|
ND1
|
A:HIS182
|
4.2
|
14.2
|
1.0
|
|
OD2
|
A:ASP179
|
4.3
|
15.1
|
1.0
|
|
O
|
A:HOH556
|
4.5
|
16.7
|
1.0
|
|
HB2
|
A:ASP229
|
4.5
|
18.7
|
1.0
|
|
HB3
|
A:ASP229
|
4.6
|
18.7
|
1.0
|
|
O
|
A:HOH603
|
4.6
|
39.5
|
1.0
|
|
HE1
|
A:HIS109
|
4.7
|
25.9
|
1.0
|
|
FE
|
A:FE2302
|
4.7
|
20.4
|
1.0
|
|
HA
|
A:ASP229
|
4.8
|
18.5
|
1.0
|
|
HB3
|
A:CYS181
|
4.8
|
18.5
|
1.0
|
|
HG
|
A:CYS181
|
4.8
|
20.6
|
1.0
|
|
CA
|
A:ASP229
|
4.9
|
15.4
|
1.0
|
|
C
|
A:ASP229
|
4.9
|
13.8
|
1.0
|
|
CG
|
A:ASP179
|
4.9
|
13.4
|
1.0
|
|
HD1
|
A:HIS231
|
5.0
|
22.7
|
1.0
|
|
O
|
A:ASP229
|
5.0
|
17.9
|
1.0
|
|
HD21
|
A:ASN218
|
5.0
|
19.4
|
1.0
|
|
Zinc binding site 3 out
of 10 in 8rly
Go back to
Zinc Binding Sites List in 8rly
Zinc binding site 3 out
of 10 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn 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:Zn301
b:22.0
occ:1.00
|
O
|
B:HOH405
|
1.9
|
23.2
|
1.0
|
|
OE1
|
B:GLU145
|
2.1
|
16.6
|
1.0
|
|
NE2
|
B:HIS109
|
2.2
|
18.8
|
1.0
|
|
NE2
|
B:HIS69
|
2.2
|
18.1
|
1.0
|
|
O2
|
B:SO4304
|
2.3
|
27.2
|
1.0
|
|
CD
|
B:GLU145
|
3.0
|
18.0
|
1.0
|
|
CD2
|
B:HIS109
|
3.0
|
19.1
|
1.0
|
|
CD2
|
B:HIS69
|
3.1
|
17.8
|
1.0
|
|
O1
|
B:SO4304
|
3.1
|
22.6
|
1.0
|
|
HD2
|
B:HIS109
|
3.1
|
22.9
|
1.0
|
|
OE2
|
B:GLU145
|
3.2
|
14.4
|
1.0
|
|
HD2
|
B:HIS69
|
3.2
|
21.3
|
1.0
|
|
S
|
B:SO4304
|
3.2
|
27.8
|
1.0
|
|
CE1
|
B:HIS69
|
3.2
|
21.1
|
1.0
|
|
CE1
|
B:HIS109
|
3.3
|
27.5
|
1.0
|
|
HD22
|
B:ASN107
|
3.4
|
22.4
|
1.0
|
|
FE
|
B:FE2302
|
3.4
|
21.7
|
1.0
|
|
HE1
|
B:HIS69
|
3.5
|
25.3
|
1.0
|
|
HE1
|
B:HIS182
|
3.5
|
21.4
|
1.0
|
|
HE1
|
B:HIS109
|
3.5
|
33.1
|
1.0
|
|
HE1
|
B:HIS216
|
3.6
|
21.7
|
1.0
|
|
HE1
|
B:TYR72
|
3.6
|
46.2
|
1.0
|
|
ND2
|
B:ASN107
|
4.0
|
18.7
|
1.0
|
|
HD21
|
B:ASN107
|
4.1
|
22.4
|
1.0
|
|
O4
|
B:SO4304
|
4.1
|
26.9
|
1.0
|
|
CG
|
B:HIS109
|
4.2
|
22.3
|
1.0
|
|
CE1
|
B:HIS216
|
4.3
|
18.1
|
1.0
|
|
CG
|
B:HIS69
|
4.3
|
15.3
|
1.0
|
|
OH
|
B:TYR72
|
4.3
|
42.1
|
1.0
|
|
ND1
|
B:HIS109
|
4.3
|
29.1
|
1.0
|
|
ND1
|
B:HIS69
|
4.3
|
20.6
|
1.0
|
|
O3
|
B:SO4304
|
4.4
|
22.0
|
1.0
|
|
CG
|
B:GLU145
|
4.4
|
19.5
|
1.0
|
|
OE2
|
B:GLU261
|
4.4
|
16.0
|
1.0
|
|
CE1
|
B:HIS182
|
4.4
|
17.8
|
1.0
|
|
ND1
|
B:HIS216
|
4.4
|
17.9
|
1.0
|
|
HB3
|
B:GLU145
|
4.5
|
17.7
|
1.0
|
|
CE1
|
B:TYR72
|
4.5
|
38.5
|
1.0
|
|
HB2
|
B:GLU145
|
4.8
|
17.7
|
1.0
|
|
CB
|
B:GLU145
|
4.8
|
14.7
|
1.0
|
|
HG2
|
B:GLU145
|
4.9
|
23.4
|
1.0
|
|
HG3
|
B:GLU145
|
4.9
|
23.4
|
1.0
|
|
OE1
|
B:GLU261
|
4.9
|
14.5
|
1.0
|
|
CZ
|
B:TYR72
|
4.9
|
39.3
|
1.0
|
|
HH
|
B:TYR72
|
5.0
|
50.6
|
1.0
|
|
Zinc binding site 4 out
of 10 in 8rly
Go back to
Zinc Binding Sites List in 8rly
Zinc binding site 4 out
of 10 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn 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
|
B:Zn303
b:19.8
occ:1.00
|
O3
|
B:SO4304
|
1.9
|
22.0
|
1.0
|
|
OD1
|
B:ASP229
|
2.1
|
19.2
|
1.0
|
|
NE2
|
B:HIS182
|
2.2
|
17.7
|
1.0
|
|
NE2
|
B:HIS231
|
2.2
|
17.6
|
1.0
|
|
OD2
|
B:ASP229
|
2.4
|
23.6
|
1.0
|
|
CG
|
B:ASP229
|
2.6
|
22.8
|
1.0
|
|
O1
|
B:SO4304
|
2.9
|
22.6
|
1.0
|
|
S
|
B:SO4304
|
3.0
|
27.8
|
1.0
|
|
CD2
|
B:HIS182
|
3.1
|
20.3
|
1.0
|
|
CE1
|
B:HIS231
|
3.1
|
16.0
|
1.0
|
|
CD2
|
B:HIS231
|
3.2
|
17.2
|
1.0
|
|
CE1
|
B:HIS182
|
3.2
|
17.8
|
1.0
|
|
HD2
|
B:HIS182
|
3.2
|
24.4
|
1.0
|
|
HE1
|
B:HIS231
|
3.3
|
19.2
|
1.0
|
|
HD2
|
B:HIS231
|
3.3
|
20.6
|
1.0
|
|
HE1
|
B:HIS182
|
3.4
|
21.4
|
1.0
|
|
O4
|
B:SO4304
|
3.9
|
26.9
|
1.0
|
|
CB
|
B:ASP229
|
4.1
|
17.0
|
1.0
|
|
O2
|
B:SO4304
|
4.1
|
27.2
|
1.0
|
|
CG
|
B:HIS182
|
4.2
|
17.5
|
1.0
|
|
ND1
|
B:HIS231
|
4.2
|
16.3
|
1.0
|
|
ND1
|
B:HIS182
|
4.3
|
18.0
|
1.0
|
|
OD2
|
B:ASP179
|
4.3
|
17.3
|
1.0
|
|
CG
|
B:HIS231
|
4.3
|
19.0
|
1.0
|
|
HB2
|
B:ASP229
|
4.5
|
20.4
|
1.0
|
|
HE1
|
B:HIS109
|
4.6
|
33.1
|
1.0
|
|
FE
|
B:FE2302
|
4.6
|
21.7
|
1.0
|
|
HB3
|
B:ASP229
|
4.6
|
20.4
|
1.0
|
|
O
|
B:HOH502
|
4.7
|
19.6
|
1.0
|
|
HA
|
B:ASP229
|
4.7
|
25.8
|
1.0
|
|
HB3
|
B:CYS181
|
4.8
|
18.8
|
1.0
|
|
HG
|
B:CYS181
|
4.8
|
23.7
|
1.0
|
|
CA
|
B:ASP229
|
4.9
|
21.5
|
1.0
|
|
CG
|
B:ASP179
|
4.9
|
18.0
|
1.0
|
|
HD21
|
B:ASN218
|
5.0
|
19.1
|
1.0
|
|
C
|
B:ASP229
|
5.0
|
14.7
|
1.0
|
|
Zinc binding site 5 out
of 10 in 8rly
Go back to
Zinc Binding Sites List in 8rly
Zinc binding site 5 out
of 10 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn 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
|
C:Zn301
b:20.3
occ:1.00
|
O
|
C:HOH407
|
1.8
|
22.8
|
1.0
|
|
O4
|
C:SO4304
|
2.1
|
30.1
|
1.0
|
|
OE1
|
C:GLU145
|
2.2
|
16.1
|
1.0
|
|
NE2
|
C:HIS69
|
2.2
|
12.6
|
1.0
|
|
NE2
|
C:HIS109
|
2.2
|
18.6
|
1.0
|
|
CD
|
C:GLU145
|
3.0
|
18.2
|
1.0
|
|
CD2
|
C:HIS109
|
3.0
|
16.6
|
1.0
|
|
CD2
|
C:HIS69
|
3.1
|
17.6
|
1.0
|
|
HD2
|
C:HIS109
|
3.1
|
19.9
|
1.0
|
|
OE2
|
C:GLU145
|
3.1
|
14.0
|
1.0
|
|
HD2
|
C:HIS69
|
3.2
|
21.1
|
1.0
|
|
CE1
|
C:HIS69
|
3.2
|
17.0
|
1.0
|
|
O2
|
C:SO4304
|
3.2
|
28.8
|
1.0
|
|
S
|
C:SO4304
|
3.3
|
28.4
|
1.0
|
|
CE1
|
C:HIS109
|
3.3
|
26.6
|
1.0
|
|
HD22
|
C:ASN107
|
3.4
|
19.3
|
1.0
|
|
HE1
|
C:HIS69
|
3.4
|
20.4
|
1.0
|
|
HE1
|
C:HIS182
|
3.4
|
25.8
|
1.0
|
|
FE
|
C:FE2302
|
3.4
|
20.9
|
1.0
|
|
HE1
|
C:HIS109
|
3.5
|
32.0
|
1.0
|
|
HE1
|
C:HIS216
|
3.6
|
23.3
|
1.0
|
|
ND2
|
C:ASN107
|
4.0
|
16.1
|
1.0
|
|
HD21
|
C:ASN107
|
4.0
|
19.3
|
1.0
|
|
O
|
C:HOH579
|
4.1
|
35.4
|
1.0
|
|
O1
|
C:SO4304
|
4.1
|
26.9
|
1.0
|
|
CG
|
C:HIS109
|
4.2
|
16.6
|
1.0
|
|
CG
|
C:HIS69
|
4.3
|
15.1
|
1.0
|
|
ND1
|
C:HIS69
|
4.3
|
16.3
|
1.0
|
|
OE2
|
C:GLU261
|
4.3
|
15.1
|
1.0
|
|
ND1
|
C:HIS109
|
4.3
|
21.7
|
1.0
|
|
CE1
|
C:HIS216
|
4.3
|
19.4
|
1.0
|
|
CE1
|
C:HIS182
|
4.4
|
21.5
|
1.0
|
|
CG
|
C:GLU145
|
4.4
|
15.6
|
1.0
|
|
O3
|
C:SO4304
|
4.4
|
21.5
|
1.0
|
|
HB3
|
C:GLU145
|
4.5
|
16.9
|
1.0
|
|
ND1
|
C:HIS216
|
4.5
|
15.3
|
1.0
|
|
HB2
|
C:GLU145
|
4.8
|
16.9
|
1.0
|
|
CB
|
C:GLU145
|
4.8
|
14.1
|
1.0
|
|
HG2
|
C:GLU145
|
4.8
|
18.8
|
1.0
|
|
OE1
|
C:GLU261
|
4.9
|
11.8
|
1.0
|
|
HG3
|
C:GLU145
|
4.9
|
18.8
|
1.0
|
|
Zinc binding site 6 out
of 10 in 8rly
Go back to
Zinc Binding Sites List in 8rly
Zinc binding site 6 out
of 10 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn303
b:19.9
occ:1.00
|
O3
|
C:SO4304
|
1.9
|
21.5
|
1.0
|
|
NE2
|
C:HIS182
|
2.2
|
13.5
|
1.0
|
|
OD1
|
C:ASP229
|
2.2
|
14.8
|
1.0
|
|
NE2
|
C:HIS231
|
2.2
|
18.7
|
1.0
|
|
OD2
|
C:ASP229
|
2.4
|
19.6
|
1.0
|
|
CG
|
C:ASP229
|
2.6
|
17.1
|
1.0
|
|
O2
|
C:SO4304
|
2.8
|
28.8
|
1.0
|
|
S
|
C:SO4304
|
2.9
|
28.4
|
1.0
|
|
CD2
|
C:HIS182
|
3.1
|
14.4
|
1.0
|
|
CD2
|
C:HIS231
|
3.1
|
18.7
|
1.0
|
|
CE1
|
C:HIS231
|
3.1
|
18.7
|
1.0
|
|
HD2
|
C:HIS182
|
3.2
|
17.3
|
1.0
|
|
CE1
|
C:HIS182
|
3.2
|
21.5
|
1.0
|
|
HD2
|
C:HIS231
|
3.3
|
22.4
|
1.0
|
|
HE1
|
C:HIS231
|
3.3
|
22.4
|
1.0
|
|
HE1
|
C:HIS182
|
3.4
|
25.8
|
1.0
|
|
O1
|
C:SO4304
|
3.9
|
26.9
|
1.0
|
|
O4
|
C:SO4304
|
4.1
|
30.1
|
1.0
|
|
CB
|
C:ASP229
|
4.1
|
20.1
|
1.0
|
|
ND1
|
C:HIS231
|
4.2
|
17.8
|
1.0
|
|
CG
|
C:HIS182
|
4.2
|
17.0
|
1.0
|
|
OD2
|
C:ASP179
|
4.3
|
15.2
|
1.0
|
|
CG
|
C:HIS231
|
4.3
|
18.0
|
1.0
|
|
ND1
|
C:HIS182
|
4.3
|
15.4
|
1.0
|
|
O
|
C:HOH569
|
4.4
|
21.0
|
1.0
|
|
HB2
|
C:ASP229
|
4.5
|
24.1
|
1.0
|
|
HE1
|
C:HIS109
|
4.6
|
32.0
|
1.0
|
|
HB3
|
C:ASP229
|
4.6
|
24.1
|
1.0
|
|
HA
|
C:ASP229
|
4.7
|
24.3
|
1.0
|
|
FE
|
C:FE2302
|
4.7
|
20.9
|
1.0
|
|
HB3
|
C:CYS181
|
4.7
|
19.4
|
1.0
|
|
HG
|
C:CYS181
|
4.7
|
20.0
|
1.0
|
|
CA
|
C:ASP229
|
4.8
|
20.2
|
1.0
|
|
C
|
C:ASP229
|
5.0
|
15.5
|
1.0
|
|
CG
|
C:ASP179
|
5.0
|
13.8
|
1.0
|
|
O
|
C:ASP229
|
5.0
|
19.0
|
1.0
|
|
Zinc binding site 7 out
of 10 in 8rly
Go back to
Zinc Binding Sites List in 8rly
Zinc binding site 7 out
of 10 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:24.2
occ:1.00
|
O
|
D:HOH405
|
1.9
|
28.0
|
1.0
|
|
OE1
|
D:GLU145
|
2.1
|
21.9
|
1.0
|
|
O3
|
D:SO4304
|
2.2
|
29.6
|
1.0
|
|
NE2
|
D:HIS69
|
2.2
|
21.4
|
1.0
|
|
NE2
|
D:HIS109
|
2.2
|
23.1
|
1.0
|
|
CD
|
D:GLU145
|
2.9
|
21.1
|
1.0
|
|
CD2
|
D:HIS109
|
3.1
|
24.4
|
1.0
|
|
O2
|
D:SO4304
|
3.1
|
33.0
|
1.0
|
|
CD2
|
D:HIS69
|
3.1
|
21.6
|
1.0
|
|
HD2
|
D:HIS109
|
3.1
|
29.3
|
1.0
|
|
OE2
|
D:GLU145
|
3.2
|
17.2
|
1.0
|
|
S
|
D:SO4304
|
3.2
|
31.0
|
1.0
|
|
CE1
|
D:HIS69
|
3.2
|
25.6
|
1.0
|
|
HD2
|
D:HIS69
|
3.3
|
25.9
|
1.0
|
|
CE1
|
D:HIS109
|
3.3
|
23.6
|
1.0
|
|
HD22
|
D:ASN107
|
3.4
|
27.5
|
1.0
|
|
HE1
|
D:HIS69
|
3.4
|
30.8
|
1.0
|
|
FE
|
D:FE2302
|
3.4
|
27.5
|
1.0
|
|
HE1
|
D:HIS182
|
3.4
|
26.8
|
1.0
|
|
HE1
|
D:HIS109
|
3.5
|
28.3
|
1.0
|
|
HE1
|
D:HIS216
|
3.7
|
22.0
|
1.0
|
|
OH
|
D:TYR72
|
3.8
|
54.3
|
1.0
|
|
HE1
|
D:TYR72
|
3.9
|
40.6
|
1.0
|
|
ND2
|
D:ASN107
|
4.0
|
22.9
|
1.0
|
|
O4
|
D:SO4304
|
4.1
|
30.6
|
1.0
|
|
HD21
|
D:ASN107
|
4.1
|
27.5
|
1.0
|
|
CG
|
D:HIS109
|
4.2
|
23.5
|
1.0
|
|
HH
|
D:TYR72
|
4.3
|
65.1
|
1.0
|
|
O1
|
D:SO4304
|
4.3
|
25.8
|
1.0
|
|
CG
|
D:HIS69
|
4.3
|
22.0
|
1.0
|
|
ND1
|
D:HIS69
|
4.3
|
21.2
|
1.0
|
|
ND1
|
D:HIS109
|
4.3
|
23.3
|
1.0
|
|
CE1
|
D:HIS182
|
4.3
|
22.4
|
1.0
|
|
CG
|
D:GLU145
|
4.3
|
18.1
|
1.0
|
|
OE2
|
D:GLU261
|
4.4
|
24.8
|
1.0
|
|
CE1
|
D:HIS216
|
4.4
|
18.3
|
1.0
|
|
HB3
|
D:GLU145
|
4.4
|
26.1
|
1.0
|
|
CE1
|
D:TYR72
|
4.5
|
33.8
|
1.0
|
|
ND1
|
D:HIS216
|
4.5
|
18.1
|
1.0
|
|
CZ
|
D:TYR72
|
4.5
|
50.0
|
1.0
|
|
HB2
|
D:GLU145
|
4.8
|
26.1
|
1.0
|
|
CB
|
D:GLU145
|
4.8
|
21.8
|
1.0
|
|
HG2
|
D:GLU145
|
4.8
|
21.7
|
1.0
|
|
HG3
|
D:GLU145
|
4.9
|
21.7
|
1.0
|
|
OE1
|
D:GLU261
|
4.9
|
23.3
|
1.0
|
|
Zinc binding site 8 out
of 10 in 8rly
Go back to
Zinc Binding Sites List in 8rly
Zinc binding site 8 out
of 10 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn303
b:25.1
occ:1.00
|
OD2
|
D:ASP229
|
1.8
|
23.2
|
1.0
|
|
O1
|
D:SO4304
|
2.0
|
25.8
|
1.0
|
|
NE2
|
D:HIS231
|
2.1
|
22.0
|
1.0
|
|
NE2
|
D:HIS182
|
2.2
|
20.1
|
1.0
|
|
CG
|
D:ASP229
|
2.6
|
24.8
|
1.0
|
|
OD1
|
D:ASP229
|
2.7
|
26.8
|
1.0
|
|
O2
|
D:SO4304
|
2.8
|
33.0
|
1.0
|
|
S
|
D:SO4304
|
3.0
|
31.0
|
1.0
|
|
CD2
|
D:HIS182
|
3.0
|
24.1
|
1.0
|
|
CD2
|
D:HIS231
|
3.1
|
19.9
|
1.0
|
|
CE1
|
D:HIS231
|
3.1
|
28.6
|
1.0
|
|
HD2
|
D:HIS182
|
3.1
|
29.0
|
1.0
|
|
CE1
|
D:HIS182
|
3.2
|
22.4
|
1.0
|
|
HD2
|
D:HIS231
|
3.3
|
23.9
|
1.0
|
|
HE1
|
D:HIS231
|
3.3
|
34.3
|
1.0
|
|
HE1
|
D:HIS182
|
3.5
|
26.8
|
1.0
|
|
O4
|
D:SO4304
|
3.8
|
30.6
|
1.0
|
|
CB
|
D:ASP229
|
4.0
|
29.2
|
1.0
|
|
O3
|
D:SO4304
|
4.2
|
29.6
|
1.0
|
|
OD2
|
D:ASP179
|
4.2
|
18.1
|
1.0
|
|
ND1
|
D:HIS231
|
4.2
|
20.5
|
1.0
|
|
CG
|
D:HIS182
|
4.2
|
20.4
|
1.0
|
|
CG
|
D:HIS231
|
4.2
|
21.9
|
1.0
|
|
ND1
|
D:HIS182
|
4.3
|
23.0
|
1.0
|
|
HB3
|
D:ASP229
|
4.3
|
35.0
|
1.0
|
|
HB2
|
D:ASP229
|
4.4
|
35.0
|
1.0
|
|
FE
|
D:FE2302
|
4.5
|
27.5
|
1.0
|
|
O
|
D:HOH498
|
4.6
|
25.9
|
1.0
|
|
HB3
|
D:CYS181
|
4.6
|
28.7
|
1.0
|
|
HE1
|
D:HIS109
|
4.8
|
28.3
|
1.0
|
|
HG
|
D:CYS181
|
4.8
|
27.8
|
1.0
|
|
CG
|
D:ASP179
|
4.8
|
19.7
|
1.0
|
|
HD21
|
D:ASN218
|
4.9
|
22.5
|
1.0
|
|
OE1
|
D:GLU261
|
5.0
|
23.3
|
1.0
|
|
OD1
|
D:ASP179
|
5.0
|
20.6
|
1.0
|
|
HD1
|
D:HIS231
|
5.0
|
24.6
|
1.0
|
|
Zinc binding site 9 out
of 10 in 8rly
Go back to
Zinc Binding Sites List in 8rly
Zinc binding site 9 out
of 10 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn301
b:22.9
occ:1.00
|
O
|
E:HOH405
|
2.0
|
27.8
|
1.0
|
|
O3
|
E:SO4304
|
2.1
|
27.4
|
1.0
|
|
OE1
|
E:GLU145
|
2.2
|
16.4
|
1.0
|
|
NE2
|
E:HIS69
|
2.2
|
19.4
|
1.0
|
|
NE2
|
E:HIS109
|
2.2
|
24.8
|
1.0
|
|
O1
|
E:SO4304
|
2.9
|
30.1
|
1.0
|
|
CD
|
E:GLU145
|
3.0
|
18.3
|
1.0
|
|
CD2
|
E:HIS109
|
3.0
|
19.5
|
1.0
|
|
S
|
E:SO4304
|
3.1
|
30.7
|
1.0
|
|
CD2
|
E:HIS69
|
3.1
|
20.4
|
1.0
|
|
HD2
|
E:HIS109
|
3.1
|
23.5
|
1.0
|
|
HD2
|
E:HIS69
|
3.2
|
24.5
|
1.0
|
|
OE2
|
E:GLU145
|
3.2
|
16.9
|
1.0
|
|
CE1
|
E:HIS69
|
3.2
|
21.9
|
1.0
|
|
CE1
|
E:HIS109
|
3.3
|
25.6
|
1.0
|
|
HD22
|
E:ASN107
|
3.4
|
23.6
|
1.0
|
|
FE
|
E:FE2302
|
3.4
|
23.1
|
1.0
|
|
HE1
|
E:HIS69
|
3.5
|
26.3
|
1.0
|
|
HH
|
E:TYR72
|
3.5
|
42.1
|
1.0
|
|
HE1
|
E:HIS216
|
3.5
|
17.6
|
1.0
|
|
HE1
|
E:HIS109
|
3.5
|
30.7
|
1.0
|
|
HE1
|
E:HIS182
|
3.5
|
26.9
|
1.0
|
|
HE2
|
E:TYR72
|
3.6
|
43.0
|
1.0
|
|
O2
|
E:SO4304
|
3.9
|
31.4
|
1.0
|
|
ND2
|
E:ASN107
|
4.0
|
19.6
|
1.0
|
|
HD21
|
E:ASN107
|
4.0
|
23.6
|
1.0
|
|
CE1
|
E:HIS216
|
4.2
|
14.7
|
1.0
|
|
O4
|
E:SO4304
|
4.2
|
18.8
|
1.0
|
|
OH
|
E:TYR72
|
4.2
|
35.1
|
1.0
|
|
CG
|
E:HIS109
|
4.2
|
24.0
|
1.0
|
|
CG
|
E:HIS69
|
4.3
|
19.0
|
1.0
|
|
ND1
|
E:HIS69
|
4.3
|
18.9
|
1.0
|
|
ND1
|
E:HIS109
|
4.3
|
23.8
|
1.0
|
|
CE2
|
E:TYR72
|
4.3
|
35.8
|
1.0
|
|
OE2
|
E:GLU261
|
4.3
|
20.6
|
1.0
|
|
CG
|
E:GLU145
|
4.4
|
15.8
|
1.0
|
|
HB3
|
E:GLU145
|
4.4
|
19.4
|
1.0
|
|
ND1
|
E:HIS216
|
4.4
|
14.4
|
1.0
|
|
CE1
|
E:HIS182
|
4.4
|
22.4
|
1.0
|
|
CZ
|
E:TYR72
|
4.7
|
43.2
|
1.0
|
|
HB2
|
E:GLU145
|
4.8
|
19.4
|
1.0
|
|
CB
|
E:GLU145
|
4.8
|
16.1
|
1.0
|
|
OE1
|
E:GLU261
|
4.9
|
17.6
|
1.0
|
|
HG2
|
E:GLU145
|
4.9
|
18.9
|
1.0
|
|
HG3
|
E:GLU145
|
4.9
|
18.9
|
1.0
|
|
Zinc binding site 10 out
of 10 in 8rly
Go back to
Zinc Binding Sites List in 8rly
Zinc binding site 10 out
of 10 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn303
b:21.0
occ:1.00
|
O4
|
E:SO4304
|
2.0
|
18.8
|
1.0
|
|
OD2
|
E:ASP229
|
2.0
|
30.6
|
1.0
|
|
NE2
|
E:HIS231
|
2.2
|
20.3
|
1.0
|
|
NE2
|
E:HIS182
|
2.2
|
19.9
|
1.0
|
|
OD1
|
E:ASP229
|
2.4
|
25.1
|
1.0
|
|
CG
|
E:ASP229
|
2.5
|
22.1
|
1.0
|
|
O1
|
E:SO4304
|
3.0
|
30.1
|
1.0
|
|
S
|
E:SO4304
|
3.0
|
30.7
|
1.0
|
|
CE1
|
E:HIS231
|
3.1
|
19.8
|
1.0
|
|
CD2
|
E:HIS182
|
3.1
|
23.0
|
1.0
|
|
CD2
|
E:HIS231
|
3.2
|
16.6
|
1.0
|
|
HD2
|
E:HIS182
|
3.2
|
27.7
|
1.0
|
|
HE1
|
E:HIS231
|
3.2
|
23.8
|
1.0
|
|
CE1
|
E:HIS182
|
3.2
|
22.4
|
1.0
|
|
HD2
|
E:HIS231
|
3.4
|
20.0
|
1.0
|
|
HE1
|
E:HIS182
|
3.5
|
26.9
|
1.0
|
|
O2
|
E:SO4304
|
3.8
|
31.4
|
1.0
|
|
CB
|
E:ASP229
|
4.1
|
23.7
|
1.0
|
|
ND1
|
E:HIS231
|
4.2
|
20.5
|
1.0
|
|
CG
|
E:HIS231
|
4.3
|
20.0
|
1.0
|
|
O3
|
E:SO4304
|
4.3
|
27.4
|
1.0
|
|
CG
|
E:HIS182
|
4.3
|
20.0
|
1.0
|
|
OD2
|
E:ASP179
|
4.3
|
16.5
|
1.0
|
|
ND1
|
E:HIS182
|
4.3
|
18.2
|
1.0
|
|
HB2
|
E:ASP229
|
4.3
|
28.4
|
1.0
|
|
O
|
E:HOH538
|
4.5
|
22.6
|
1.0
|
|
HB3
|
E:ASP229
|
4.5
|
28.4
|
1.0
|
|
HE1
|
E:HIS109
|
4.6
|
30.7
|
1.0
|
|
FE
|
E:FE2302
|
4.6
|
23.1
|
1.0
|
|
HB3
|
E:CYS181
|
4.9
|
21.5
|
1.0
|
|
HD21
|
E:ASN218
|
4.9
|
19.3
|
1.0
|
|
HG
|
E:CYS181
|
4.9
|
22.8
|
1.0
|
|
HA
|
E:ASP229
|
4.9
|
23.2
|
1.0
|
|
HD1
|
E:HIS231
|
4.9
|
24.6
|
1.0
|
|
CG
|
E:ASP179
|
5.0
|
18.5
|
1.0
|
|
CA
|
E:ASP229
|
5.0
|
19.3
|
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 12:13:36 2024
|
