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Manganese in PDB 6z1a: Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna

Enzymatic activity of Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna

All present enzymatic activity of Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna:
5.6.2.2;

Protein crystallography data

The structure of Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna, PDB code: 6z1a was solved by A.Kolaric, T.Germe, M.Hrast, C.E.M.Stevenson, D.M.Lawson, N.Burton, J.Voros, A.Maxwell, N.Minovski, M.Anderluh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.32 / 2.30
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 92.592, 92.592, 405.464, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 21.7

Other elements in 6z1a:

The structure of Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna (pdb code 6z1a). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna, PDB code: 6z1a:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6z1a

Go back to Manganese Binding Sites List in 6z1a
Manganese binding site 1 out of 4 in the Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1702

b:51.3
occ:1.00
 OD2 B:ASP510 2.0 47.6 1.0
O B:HOH1869 2.0 54.7 1.0
O B:HOH1815 2.0 47.3 1.0
O B:HOH1834 2.0 46.5 1.0
O B:HOH1861 2.0 41.5 1.0
OD2 B:ASP508 2.1 59.9 1.0
CG B:ASP510 3.0 44.5 1.0
CG B:ASP508 3.1 54.7 1.0
OD1 B:ASP510 3.4 41.7 1.0
CB B:ASP508 3.5 51.1 1.0
OE1 B:GLU435 3.9 45.4 1.0
O B:HOH1801 3.9 26.6 1.0
O B:HOH1819 4.1 43.7 1.0
O B:LYS581 4.2 99.3 1.0
OD1 B:ASP508 4.3 56.9 1.0
CB B:ASP510 4.3 47.1 1.0
CD B:GLU435 4.7 47.0 1.0
CA B:GLY582 4.7 88.8 1.0
OP1 E:DG8 4.8 45.1 1.0
NH1 D:ARG1122 4.8 50.4 1.0
OE2 B:GLU435 4.8 44.4 1.0
C B:LYS581 5.0 99.3 1.0

Manganese binding site 2 out of 4 in 6z1a

Go back to Manganese Binding Sites List in 6z1a
Manganese binding site 2 out of 4 in the Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1605

b:48.4
occ:1.00
 OP2 H:DG2009 2.0 72.7 1.0
OD2 D:ASP508 2.0 55.6 1.0
OE2 D:GLU435 2.0 49.9 1.0
O D:HOH1777 2.0 38.1 1.0
O D:HOH1705 2.0 48.3 1.0
CD D:GLU435 3.0 46.3 1.0
O3' F:DG8 3.1 51.9 1.0
CG D:ASP508 3.1 55.0 1.0
C3' F:DG8 3.3 47.7 1.0
P H:DG2009 3.3 65.2 1.0
OE1 D:GLU435 3.4 45.7 1.0
OP3 H:DG2009 3.6 62.5 1.0
O D:HOH1738 3.6 44.6 1.0
CB D:ASP508 3.7 52.6 1.0
CG D:GLU435 4.1 47.4 1.0
OD1 D:ASP508 4.2 52.2 1.0
CB D:GLU435 4.2 48.1 1.0
O F:HOH102 4.3 48.4 1.0
O5' H:DG2009 4.3 62.5 1.0
OP1 H:DG2009 4.3 65.1 1.0
C4' F:DG8 4.4 44.4 1.0
O D:LYS581 4.4 64.2 1.0
C2' F:DG8 4.5 48.3 1.0
OD2 D:ASP510 4.5 48.4 1.0
CZ B:PHE1123 4.5 47.7 1.0
C5' H:DG2009 4.5 61.5 1.0
NH1 B:ARG1122 4.7 54.4 1.0
OD1 D:ASP510 4.7 51.6 1.0
C5' F:DG8 4.9 40.6 1.0

Manganese binding site 3 out of 4 in 6z1a

Go back to Manganese Binding Sites List in 6z1a
Manganese binding site 3 out of 4 in the Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1606

b:66.1
occ:1.00
 O D:HOH1836 2.0 61.8 1.0
O D:HOH1853 2.0 68.6 1.0
O D:HOH1840 2.0 57.3 1.0
NE2 D:HIS1390 2.0 52.6 1.0
CE1 D:HIS1390 2.8 51.9 1.0
CD2 D:HIS1390 3.2 48.3 1.0
ND1 D:HIS1390 4.0 50.4 1.0
CG D:HIS1390 4.2 47.4 1.0
OD2 D:ASP1389 4.5 45.4 1.0
CB D:ASP1389 4.6 42.4 1.0

Manganese binding site 4 out of 4 in 6z1a

Go back to Manganese Binding Sites List in 6z1a
Manganese binding site 4 out of 4 in the Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Ternary Complex of Staphylococcus Aureus Dna Gyrase with AMK12 and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn2102

b:65.2
occ:1.00
 O G:HOH2204 2.0 50.2 1.0
O E:HOH1704 2.0 45.1 1.0
O G:HOH2201 2.0 55.7 1.0
O G:HOH2208 2.0 53.5 1.0
O E:HOH1708 2.0 53.9 1.0
N7 G:DG2009 2.1 55.4 1.0
C8 G:DG2009 3.0 51.3 1.0
C5 G:DG2009 3.2 48.0 1.0
O6 G:DG2009 3.6 50.1 1.0
O6 E:DG8 3.7 41.2 1.0
C6 G:DG2009 3.7 50.8 1.0
OP1 G:DG2009 3.8 58.5 1.0
N9 G:DG2009 4.2 50.7 1.0
OP2 G:DG2009 4.3 62.5 1.0
C4 G:DG2009 4.3 49.3 1.0
O B:HOH1907 4.4 43.4 1.0
P G:DG2009 4.4 60.3 1.0
C6 E:DG8 4.5 42.2 1.0
N7 E:DG8 4.5 43.0 1.0
CB B:SER1084 4.6 44.1 1.0
O5' G:DG2009 4.6 58.6 1.0
O4 G:DT2010 4.7 55.7 1.0
C5 E:DG8 4.8 42.1 1.0
OG B:SER1084 4.9 50.1 1.0

Reference:

A.Kolaric, T.Germe, M.Hrast, C.E.M.Stevenson, D.M.Lawson, N.Burton, J.Voros, A.Maxwell, N.Minovski, M.Anderluh. Potent Novel Dna Gyrase Inhibitors Bind Asymmetrically to Their Target Using Unforeseen Symmetrical Halogen Bonds To Be Published.
Page generated: Sun Oct 6 07:56:56 2024

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