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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:

Chlorine (Cl) 4 atoms
Magnesium (Mg) 4 atoms
Fluorine (F) 6 atoms

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

Go back to 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

Go back to 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 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

Go back to 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

Go back to 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

Go back to 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

Go back to 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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