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Manganese in PDB 5npk: 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna

Enzymatic activity of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna

All present enzymatic activity of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna:
5.99.1.3;

Protein crystallography data

The structure of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna, PDB code: 5npk was solved by B.D.Bax, P.F.Chan, R.A.Stavenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.442, 120.680, 168.899, 90.00, 90.05, 90.00
R / Rfree (%) 15.4 / 18.3

Other elements in 5npk:

The structure of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna (pdb code 5npk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna, PDB code: 5npk:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 5npk

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Manganese binding site 1 out of 5 in the 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1501

b:25.8
occ:1.00
 OD2 B:ASP508 2.1 24.6 1.0
O B:HOH1724 2.2 23.5 1.0
O B:HOH1840 2.2 27.3 1.0
OD2 B:ASP510 2.2 22.3 1.0
O B:HOH1990 2.2 24.9 1.0
O E:HOH132 2.4 27.3 1.0
CG B:ASP508 3.1 24.1 1.0
CG B:ASP510 3.2 23.1 1.0
CB B:ASP508 3.4 24.0 1.0
OD1 B:ASP510 3.5 22.7 1.0
O B:HOH1958 4.0 39.5 1.0
O B:HOH1853 4.0 33.5 1.0
OE2 B:GLU435 4.0 24.4 1.0
O B:HOH1927 4.0 28.9 1.0
O B:HOH1744 4.1 27.6 1.0
O B:HOH1977 4.2 24.1 1.0
OD1 B:ASP508 4.3 24.8 1.0
O E:HOH146 4.4 28.2 1.0
O B:HOH1759 4.5 29.4 1.0
CB B:ASP510 4.5 23.0 1.0
OP1 E:DG-1 4.7 24.1 1.0
CD B:GLU435 4.9 24.7 1.0
CA B:ASP508 5.0 25.8 1.0

Manganese binding site 2 out of 5 in 5npk

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Manganese binding site 2 out of 5 in the 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1501

b:27.9
occ:1.00
 OD2 D:ASP510 2.2 22.7 1.0
O D:HOH1968 2.2 24.6 1.0
O D:HOH1632 2.2 20.1 1.0
OD2 D:ASP508 2.3 24.5 1.0
O D:HOH1961 2.4 22.3 1.0
O F:HOH106 2.5 21.5 1.0
CG D:ASP510 3.2 25.8 1.0
CG D:ASP508 3.2 27.0 1.0
OD1 D:ASP510 3.5 23.6 1.0
CB D:ASP508 3.5 27.1 1.0
O D:HOH1727 4.0 30.6 1.0
OE2 D:GLU435 4.1 26.6 1.0
O D:HOH1880 4.1 40.9 1.0
O D:HOH1977 4.2 25.9 1.0
O D:HOH1877 4.3 24.2 1.0
O D:HOH1806 4.3 42.2 1.0
O D:HOH1916 4.3 30.6 1.0
O F:HOH133 4.4 36.4 1.0
OD1 D:ASP508 4.4 26.2 1.0
CB D:ASP510 4.5 25.0 1.0
OP1 F:DG-1 4.7 23.8 1.0
C5' F:DG-1 4.9 24.6 1.0
CD D:GLU435 4.9 26.2 1.0

Manganese binding site 3 out of 5 in 5npk

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Manganese binding site 3 out of 5 in the 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mn1501

b:24.2
occ:1.00
 O b:HOH1935 2.2 20.3 1.0
O b:HOH1962 2.2 25.3 1.0
O b:HOH1641 2.2 23.4 1.0
OD2 b:ASP510 2.2 22.2 1.0
OD2 b:ASP508 2.3 24.9 1.0
O e:HOH224 2.4 21.9 1.0
CG b:ASP508 3.2 24.7 1.0
CG b:ASP510 3.2 22.5 1.0
CB b:ASP508 3.5 23.1 1.0
OD1 b:ASP510 3.5 23.6 1.0
O b:HOH1886 4.0 40.7 1.0
OE2 b:GLU435 4.0 24.5 1.0
O b:HOH1625 4.1 30.7 1.0
O b:HOH1970 4.2 27.6 1.0
O b:HOH1880 4.2 22.8 1.0
O b:HOH1661 4.2 41.6 1.0
O b:HOH1841 4.3 31.7 1.0
O b:HOH1697 4.4 31.8 1.0
OD1 b:ASP508 4.4 25.7 1.0
CB b:ASP510 4.5 23.1 1.0
O1 b:GOL1503 4.6 47.3 1.0
OP1 e:DG-1 4.7 22.2 1.0
CD b:GLU435 4.8 23.5 1.0
C5' e:DG-1 4.9 23.9 1.0

Manganese binding site 4 out of 5 in 5npk

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Manganese binding site 4 out of 5 in the 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Mn1501

b:27.6
occ:1.00
 O d:HOH1879 2.0 28.6 1.0
O d:HOH1843 2.1 31.9 1.0
O d:HOH1649 2.2 25.0 1.0
OD2 d:ASP510 2.2 25.4 1.0
O f:HOH131 2.2 25.8 1.0
OD2 d:ASP508 2.3 28.4 1.0
CG d:ASP510 3.2 29.7 1.0
CG d:ASP508 3.3 27.3 1.0
OD1 d:ASP510 3.4 29.3 1.0
CB d:ASP508 3.5 27.4 1.0
OE2 d:GLU435 4.0 29.1 1.0
O d:HOH1672 4.0 37.9 1.0
O d:HOH1867 4.1 31.1 1.0
O d:HOH1752 4.1 39.7 1.0
O d:HOH1668 4.2 26.4 1.0
O d:HOH1825 4.2 27.1 1.0
O b:HOH1706 4.2 31.6 1.0
O b:HOH1655 4.3 29.2 1.0
OD1 d:ASP508 4.4 26.7 1.0
CB d:ASP510 4.5 28.8 1.0
OP1 f:DG-1 4.7 23.7 1.0
C5' f:DG-1 4.9 25.3 1.0
CD d:GLU435 4.9 27.1 1.0

Manganese binding site 5 out of 5 in 5npk

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Manganese binding site 5 out of 5 in the 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Mn1505

b:84.4
occ:1.00
 NE2 d:HIS1390 2.3 46.8 1.0
CE1 d:HIS1390 3.0 46.4 1.0
CD2 d:HIS1390 3.4 44.7 1.0
ND1 d:HIS1390 4.2 44.6 1.0
CG d:HIS1390 4.4 45.0 1.0
OD2 d:ASP1389 4.5 40.1 1.0
CB d:ASP1389 4.6 39.2 1.0

Reference:

P.F.Chan, T.Germe, B.D.Bax, J.Huang, R.K.Thalji, E.Bacque, A.Checchia, D.Chen, H.Cui, X.Ding, K.Ingraham, L.Mccloskey, K.Raha, V.Srikannathasan, A.Maxwell, R.A.Stavenger. Thiophene Antibacterials That Allosterically Stabilize Dna-Cleavage Complexes with Dna Gyrase. Proc. Natl. Acad. Sci. V. 114 E4492 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28507124
DOI: 10.1073/PNAS.1700721114
Page generated: Sun Oct 6 02:03:59 2024

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