Potassium in PDB 9gef: Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Enzymatic activity of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
All present enzymatic activity of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex:
5.6.2.2;
Protein crystallography data
The structure of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex, PDB code: 9gef
was solved by
B.Wang,
S.Najmudin,
X.-S.Pan,
V.Mykhaylyk,
C.Orr,
A.Wagner,
L.Govada,
N.E.Chayen,
L.M.Fisher,
M.R.Sanderson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
79.39 /
2.62
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
158.533,
158.533,
210.82,
90,
90,
120
|
R / Rfree (%)
|
18 /
20.9
|
Other elements in 9gef:
The structure of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
(pdb code 9gef). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the
Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex, PDB code: 9gef:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Potassium binding site 1 out
of 8 in 9gef
Go back to
Potassium Binding Sites List in 9gef
Potassium binding site 1 out
of 8 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1504
b:39.5
occ:1.00
|
OD1
|
B:ASN587
|
2.6
|
57.0
|
1.0
|
O
|
A:GLY1103
|
2.6
|
40.6
|
1.0
|
O
|
A:HOH1630
|
2.9
|
21.7
|
1.0
|
OD1
|
A:ASN1105
|
2.9
|
39.2
|
1.0
|
O
|
A:MET1101
|
2.9
|
35.9
|
1.0
|
CG
|
A:ASN1105
|
3.4
|
36.7
|
1.0
|
CG
|
B:ASN587
|
3.5
|
55.2
|
1.0
|
C
|
A:GLY1103
|
3.7
|
37.6
|
1.0
|
N
|
A:GLY1103
|
3.8
|
37.6
|
1.0
|
O
|
B:HOH1644
|
3.9
|
28.6
|
1.0
|
C
|
A:MET1101
|
4.0
|
34.4
|
1.0
|
ND2
|
A:ASN1105
|
4.0
|
35.9
|
1.0
|
CB
|
B:ASN587
|
4.2
|
55.8
|
1.0
|
CB
|
A:ASN1105
|
4.2
|
36.9
|
1.0
|
C
|
A:HIS1102
|
4.3
|
37.4
|
1.0
|
CA
|
A:GLY1103
|
4.3
|
38.1
|
1.0
|
N
|
A:ASN1105
|
4.3
|
38.2
|
1.0
|
CA
|
A:HIS1102
|
4.4
|
38.4
|
1.0
|
ND2
|
B:ASN587
|
4.5
|
55.4
|
1.0
|
CA
|
B:ASN587
|
4.5
|
54.0
|
1.0
|
N
|
A:HIS1102
|
4.7
|
36.9
|
1.0
|
N
|
A:ASN1104
|
4.8
|
37.1
|
1.0
|
CA
|
A:ASN1105
|
5.0
|
37.4
|
1.0
|
|
Potassium binding site 2 out
of 8 in 9gef
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Potassium Binding Sites List in 9gef
Potassium binding site 2 out
of 8 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1505
b:67.2
occ:1.00
|
N
|
A:GLN1423
|
3.5
|
28.9
|
1.0
|
NE
|
A:ARG1426
|
3.6
|
47.0
|
1.0
|
NE2
|
A:GLN1423
|
4.0
|
29.6
|
1.0
|
CB
|
A:GLN1423
|
4.0
|
29.7
|
1.0
|
CG
|
A:ARG1426
|
4.0
|
41.2
|
1.0
|
CG
|
A:GLN1423
|
4.1
|
29.8
|
1.0
|
NH2
|
A:ARG1426
|
4.1
|
49.2
|
1.0
|
O2
|
A:MPD1501
|
4.1
|
63.3
|
1.0
|
CA
|
A:LEU1422
|
4.1
|
27.9
|
1.0
|
CD
|
A:GLN1423
|
4.2
|
29.8
|
1.0
|
C
|
A:LEU1422
|
4.3
|
28.9
|
1.0
|
CZ
|
A:ARG1426
|
4.3
|
50.1
|
1.0
|
CD2
|
A:LEU1422
|
4.3
|
27.6
|
1.0
|
CD
|
A:ARG1426
|
4.3
|
44.0
|
1.0
|
CA
|
A:GLN1423
|
4.4
|
29.8
|
1.0
|
O
|
A:THR1421
|
4.4
|
26.7
|
1.0
|
CB
|
A:LEU1422
|
4.9
|
28.2
|
1.0
|
OH
|
A:TYR1425
|
4.9
|
31.8
|
1.0
|
|
Potassium binding site 3 out
of 8 in 9gef
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Potassium Binding Sites List in 9gef
Potassium binding site 3 out
of 8 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1506
b:34.7
occ:1.00
|
O
|
A:GLN1322
|
2.5
|
42.6
|
1.0
|
O
|
A:THR1319
|
2.6
|
43.5
|
1.0
|
O
|
A:PHE1316
|
2.6
|
43.6
|
1.0
|
O
|
A:HOH1642
|
2.8
|
17.7
|
1.0
|
O
|
A:LYS1317
|
2.8
|
43.4
|
1.0
|
O
|
A:HOH1613
|
2.8
|
35.7
|
1.0
|
C
|
A:LYS1317
|
3.4
|
41.3
|
1.0
|
C
|
A:GLN1322
|
3.7
|
39.2
|
1.0
|
C
|
A:THR1319
|
3.7
|
39.3
|
1.0
|
C
|
A:PHE1316
|
3.8
|
40.9
|
1.0
|
CA
|
A:LYS1317
|
4.0
|
41.7
|
1.0
|
N
|
A:THR1319
|
4.2
|
39.5
|
1.0
|
N
|
A:TYR1318
|
4.2
|
40.9
|
1.0
|
N
|
A:LYS1317
|
4.3
|
41.5
|
1.0
|
O
|
A:HOH1623
|
4.5
|
29.6
|
1.0
|
N
|
A:GLN1322
|
4.5
|
38.4
|
1.0
|
CA
|
A:GLN1322
|
4.5
|
39.0
|
1.0
|
N
|
A:ASP1320
|
4.6
|
38.4
|
1.0
|
CA
|
A:ASP1320
|
4.6
|
37.4
|
1.0
|
CB
|
A:GLN1322
|
4.6
|
40.1
|
1.0
|
CA
|
A:THR1319
|
4.6
|
39.0
|
1.0
|
N
|
A:ILE1323
|
4.6
|
38.2
|
1.0
|
C
|
A:TYR1318
|
4.7
|
39.7
|
1.0
|
CA
|
A:ILE1323
|
4.7
|
37.6
|
1.0
|
CA
|
A:TYR1318
|
4.7
|
40.1
|
1.0
|
OD1
|
A:ASP1320
|
4.9
|
37.2
|
1.0
|
CA
|
A:PHE1316
|
4.9
|
40.4
|
1.0
|
|
Potassium binding site 4 out
of 8 in 9gef
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Potassium Binding Sites List in 9gef
Potassium binding site 4 out
of 8 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1504
b:45.2
occ:1.00
|
O
|
B:GLY1103
|
2.5
|
40.4
|
1.0
|
OD1
|
B:ASN1105
|
2.6
|
46.4
|
1.0
|
OD1
|
A:ASN587
|
2.9
|
57.3
|
1.0
|
O
|
B:MET1101
|
3.4
|
32.0
|
1.0
|
CG
|
B:ASN1105
|
3.4
|
41.3
|
1.0
|
C
|
B:GLY1103
|
3.7
|
35.5
|
1.0
|
CG
|
A:ASN587
|
3.7
|
55.2
|
1.0
|
N
|
B:GLY1103
|
4.0
|
34.4
|
1.0
|
ND2
|
B:ASN1105
|
4.1
|
41.5
|
1.0
|
N
|
B:ASN1105
|
4.2
|
36.6
|
1.0
|
CB
|
B:ASN1105
|
4.3
|
39.4
|
1.0
|
CB
|
A:ASN587
|
4.3
|
55.4
|
1.0
|
CA
|
B:GLY1103
|
4.4
|
35.4
|
1.0
|
C
|
B:MET1101
|
4.5
|
31.8
|
1.0
|
CA
|
A:ASN587
|
4.6
|
53.8
|
1.0
|
C
|
B:HIS1102
|
4.6
|
34.6
|
1.0
|
N
|
B:ASN1104
|
4.7
|
35.1
|
1.0
|
ND2
|
A:ASN587
|
4.7
|
55.7
|
1.0
|
CA
|
B:ASN1104
|
4.9
|
34.8
|
1.0
|
CA
|
B:ASN1105
|
4.9
|
37.9
|
1.0
|
CA
|
B:HIS1102
|
4.9
|
35.8
|
1.0
|
C
|
B:ASN1104
|
5.0
|
35.0
|
1.0
|
|
Potassium binding site 5 out
of 8 in 9gef
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Potassium Binding Sites List in 9gef
Potassium binding site 5 out
of 8 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1505
b:68.5
occ:1.00
|
O
|
B:GLU1396
|
3.0
|
58.5
|
1.0
|
CA
|
A:ASN1429
|
4.0
|
55.6
|
1.0
|
C
|
B:GLU1396
|
4.0
|
51.6
|
1.0
|
O
|
A:THR1428
|
4.1
|
49.4
|
1.0
|
OE1
|
B:GLU1396
|
4.2
|
55.9
|
1.0
|
N
|
A:ASN1429
|
4.2
|
51.3
|
1.0
|
C
|
A:THR1428
|
4.3
|
46.9
|
1.0
|
CA
|
B:GLU1396
|
4.4
|
51.2
|
1.0
|
N
|
A:THR1430
|
4.4
|
58.8
|
1.0
|
C
|
A:ASN1429
|
4.7
|
55.9
|
1.0
|
CB
|
B:GLU1396
|
5.0
|
53.0
|
1.0
|
CD
|
B:GLU1396
|
5.0
|
55.4
|
1.0
|
CB
|
A:ASN1429
|
5.0
|
58.0
|
1.0
|
|
Potassium binding site 6 out
of 8 in 9gef
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Potassium Binding Sites List in 9gef
Potassium binding site 6 out
of 8 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1506
b:69.0
occ:1.00
|
O
|
B:ASP495
|
2.6
|
93.7
|
1.0
|
OD1
|
B:ASN497
|
3.2
|
74.3
|
1.0
|
C
|
B:ASP495
|
3.5
|
87.3
|
1.0
|
O
|
B:GLY484
|
3.7
|
78.2
|
1.0
|
CA
|
B:ASP495
|
3.9
|
87.8
|
1.0
|
CB
|
B:ASP495
|
4.1
|
86.7
|
1.0
|
CG
|
B:ASN497
|
4.2
|
72.4
|
1.0
|
ND2
|
B:ASN497
|
4.5
|
70.4
|
1.0
|
O
|
B:ALA496
|
4.5
|
81.7
|
1.0
|
C
|
B:GLY484
|
4.6
|
76.4
|
1.0
|
N
|
B:ALA496
|
4.7
|
84.4
|
1.0
|
C
|
B:ALA496
|
4.7
|
79.4
|
1.0
|
CG
|
B:ASP495
|
4.8
|
88.0
|
1.0
|
CA
|
B:GLY484
|
5.0
|
74.8
|
1.0
|
OD1
|
B:ASP495
|
5.0
|
90.0
|
1.0
|
|
Potassium binding site 7 out
of 8 in 9gef
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Potassium Binding Sites List in 9gef
Potassium binding site 7 out
of 8 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1507
b:79.7
occ:1.00
|
N
|
B:GLN1423
|
3.6
|
29.1
|
1.0
|
NE
|
B:ARG1426
|
3.8
|
46.4
|
1.0
|
CZ
|
B:ARG1426
|
3.8
|
49.9
|
1.0
|
NE2
|
B:GLN1423
|
3.9
|
32.1
|
1.0
|
CM
|
B:MPD1501
|
4.0
|
52.8
|
1.0
|
CA
|
B:LEU1422
|
4.0
|
27.7
|
1.0
|
NH1
|
B:ARG1426
|
4.1
|
52.2
|
1.0
|
CG
|
B:ARG1426
|
4.1
|
41.2
|
1.0
|
CG
|
B:GLN1423
|
4.2
|
30.5
|
1.0
|
CB
|
B:GLN1423
|
4.2
|
30.0
|
1.0
|
NH2
|
B:ARG1426
|
4.3
|
51.0
|
1.0
|
CD2
|
B:LEU1422
|
4.3
|
26.9
|
1.0
|
C
|
B:LEU1422
|
4.3
|
28.8
|
1.0
|
O
|
B:THR1421
|
4.3
|
26.1
|
1.0
|
CD
|
B:GLN1423
|
4.4
|
31.3
|
1.0
|
CD
|
B:ARG1426
|
4.5
|
43.4
|
1.0
|
CA
|
B:GLN1423
|
4.5
|
29.8
|
1.0
|
CB
|
B:LEU1422
|
4.8
|
27.7
|
1.0
|
|
Potassium binding site 8 out
of 8 in 9gef
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Potassium Binding Sites List in 9gef
Potassium binding site 8 out
of 8 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1508
b:29.9
occ:1.00
|
O
|
B:THR1319
|
2.6
|
40.9
|
1.0
|
O
|
B:GLN1322
|
2.6
|
38.3
|
1.0
|
O
|
B:PHE1316
|
2.6
|
40.4
|
1.0
|
O
|
B:HOH1638
|
2.8
|
29.7
|
1.0
|
O
|
B:LYS1317
|
2.9
|
41.1
|
1.0
|
O
|
B:HOH1640
|
3.1
|
30.4
|
1.0
|
C
|
B:LYS1317
|
3.4
|
39.2
|
1.0
|
C
|
B:THR1319
|
3.7
|
38.2
|
1.0
|
C
|
B:GLN1322
|
3.7
|
35.6
|
1.0
|
C
|
B:PHE1316
|
3.7
|
37.8
|
1.0
|
CA
|
B:LYS1317
|
4.0
|
39.2
|
1.0
|
N
|
B:THR1319
|
4.1
|
37.8
|
1.0
|
N
|
B:TYR1318
|
4.2
|
39.2
|
1.0
|
N
|
B:LYS1317
|
4.3
|
38.6
|
1.0
|
N
|
B:GLN1322
|
4.4
|
35.8
|
1.0
|
CA
|
B:GLN1322
|
4.4
|
35.9
|
1.0
|
CB
|
B:GLN1322
|
4.4
|
37.0
|
1.0
|
CA
|
B:THR1319
|
4.5
|
37.6
|
1.0
|
N
|
B:ASP1320
|
4.6
|
38.7
|
1.0
|
NE2
|
B:GLN1322
|
4.6
|
38.5
|
1.0
|
C
|
B:TYR1318
|
4.6
|
37.9
|
1.0
|
N
|
B:ILE1323
|
4.7
|
34.5
|
1.0
|
CA
|
B:ASP1320
|
4.7
|
38.5
|
1.0
|
CA
|
B:TYR1318
|
4.7
|
39.0
|
1.0
|
CA
|
B:ILE1323
|
4.9
|
34.3
|
1.0
|
CA
|
B:PHE1316
|
4.9
|
36.7
|
1.0
|
O
|
B:LEU1315
|
5.0
|
35.3
|
1.0
|
CG
|
B:GLN1322
|
5.0
|
37.3
|
1.0
|
|
Reference:
B.Wang,
S.Najmudin,
X.S.Pan,
V.Mykhaylyk,
C.Orr,
A.Wagner,
L.Govada,
N.E.Chayen,
L.M.Fisher,
M.R.Sanderson.
Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in Type II Dna Topoisomerases. Proc.Natl.Acad.Sci.Usa V. 121 57121 2024.
ISSN: ESSN 1091-6490
PubMed: 39361644
DOI: 10.1073/PNAS.2413357121
Page generated: Thu Oct 31 21:36:27 2024
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