Atomistry » Manganese » PDB 5nha-5raa » 5npk
Atomistry »
  Manganese »
    PDB 5nha-5raa »
      5npk »

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

Go back to Manganese Binding Sites List in 5npk
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

Go back to Manganese Binding Sites List in 5npk
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

Go back to Manganese Binding Sites List in 5npk
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

Go back to Manganese Binding Sites List in 5npk
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

Go back to Manganese Binding Sites List in 5npk
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: Tue Dec 15 04:44:51 2020

Last articles

Cl in 6COG
Cl in 6CST
Cl in 6CTW
Cl in 6CTZ
Cl in 6CTT
Cl in 6CSP
Cl in 6CU9
Cl in 6CTX
Cl in 6CTU
Cl in 6CTP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy