Atomistry » Sodium » PDB 5cd1-5cwl » 5cdo
Atomistry »
  Sodium »
    PDB 5cd1-5cwl »
      5cdo »

Sodium in PDB 5cdo: 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna

Enzymatic activity of 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna

All present enzymatic activity of 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna:
5.99.1.3;

Protein crystallography data

The structure of 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna, PDB code: 5cdo was solved by B.D.Bax, V.Srikannathasan, P.F.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.42 / 3.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.472, 170.211, 124.579, 90.00, 102.75, 90.00
R / Rfree (%) 21.5 / 24.7

Other elements in 5cdo:

The structure of 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna (pdb code 5cdo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna, PDB code: 5cdo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5cdo

Go back to Sodium Binding Sites List in 5cdo
Sodium binding site 1 out of 5 in the 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:40.0
occ:1.00
 O A:THR325 3.0 43.1 1.0
O A:TYR322 3.0 45.3 1.0
O A:GLN328 3.1 42.2 1.0
O A:LYS323 3.4 45.3 1.0
C A:LYS323 3.6 45.4 1.0
HA A:LYS323 3.8 52.1 1.0
C A:THR325 3.9 43.0 1.0
HA A:PRO326 4.1 46.4 1.0
N A:GLN324 4.1 47.1 1.0
C A:TYR322 4.1 45.1 1.0
HB3 A:GLN328 4.1 53.7 1.0
H A:GLN328 4.2 51.5 1.0
H A:THR325 4.2 55.6 1.0
N A:THR325 4.2 46.3 1.0
CA A:LYS323 4.2 43.4 1.0
C A:GLN328 4.3 42.0 1.0
C A:GLN324 4.4 48.6 1.0
H A:GLN324 4.5 56.6 1.0
HA A:GLN324 4.6 58.4 1.0
CA A:GLN324 4.6 48.7 1.0
CA A:THR325 4.6 45.2 1.0
N A:LYS323 4.6 42.3 1.0
N A:PRO326 4.7 41.4 1.0
HA A:THR329 4.8 47.3 1.0
CA A:PRO326 4.8 38.7 1.0
N A:GLN328 4.9 42.9 1.0
O A:GLN324 4.9 50.0 1.0
HA A:THR325 4.9 54.2 1.0
CB A:GLN328 5.0 44.7 1.0
CA A:GLN328 5.0 42.8 1.0

Sodium binding site 2 out of 5 in 5cdo

Go back to Sodium Binding Sites List in 5cdo
Sodium binding site 2 out of 5 in the 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:19.7
occ:1.00
 O C:ASN153 3.2 51.1 1.0
HG2 C:ARG155 3.2 54.5 1.0
HA C:GLU154 3.2 54.8 1.0
C C:ASN153 3.4 50.6 1.0
O C:GLY152 3.6 55.3 1.0
N C:GLU154 3.6 47.7 1.0
CA C:GLU154 3.7 45.6 1.0
C C:GLU154 3.8 44.2 1.0
HA C:ASN153 3.9 62.9 1.0
CG C:ARG155 4.1 45.5 1.0
O C:GLU154 4.1 44.4 1.0
H C:GLU154 4.1 57.3 1.0
CA C:ASN153 4.2 52.4 1.0
HG3 C:ARG155 4.2 54.5 1.0
N C:ARG155 4.3 41.4 1.0
H C:ARG155 4.5 49.7 1.0
C C:GLY152 4.5 54.5 1.0
HD3 C:ARG155 4.5 57.8 1.0
N C:ASN153 4.7 52.2 1.0
CD C:ARG155 4.8 48.1 1.0

Sodium binding site 3 out of 5 in 5cdo

Go back to Sodium Binding Sites List in 5cdo
Sodium binding site 3 out of 5 in the 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:30.9
occ:1.00
 O C:THR325 2.6 35.0 1.0
O C:TYR322 2.7 36.9 1.0
O C:GLN328 2.8 32.2 1.0
O C:LYS323 3.2 43.5 1.0
C C:LYS323 3.6 42.6 1.0
HA C:LYS323 3.6 51.0 1.0
H C:THR325 3.6 46.8 1.0
C C:THR325 3.6 36.7 1.0
H C:GLN328 3.7 39.1 1.0
HA C:PRO326 3.7 43.0 1.0
HB3 C:GLN328 3.8 41.9 1.0
C C:TYR322 3.8 37.6 1.0
C C:GLN328 3.9 31.0 1.0
N C:THR325 4.0 39.0 1.0
CA C:LYS323 4.0 42.5 1.0
N C:GLN324 4.2 40.0 1.0
N C:LYS323 4.4 40.6 1.0
N C:GLN328 4.4 32.6 1.0
CA C:THR325 4.4 37.7 1.0
CA C:PRO326 4.5 35.8 1.0
N C:PRO326 4.5 38.0 1.0
CA C:GLN328 4.5 31.9 1.0
CB C:GLN328 4.6 34.9 1.0
HA C:THR329 4.6 37.0 1.0
C C:GLN324 4.6 41.2 1.0
HD2 C:LYS323 4.6 66.6 1.0
H C:GLN324 4.7 48.0 1.0
HA C:THR325 4.8 45.3 1.0
H C:LEU327 4.8 43.7 1.0
CA C:GLN324 4.8 41.9 1.0
O C:LEU321 4.9 38.3 1.0
HA C:TYR322 4.9 43.0 1.0
HA C:GLN324 4.9 50.2 1.0

Sodium binding site 4 out of 5 in 5cdo

Go back to Sodium Binding Sites List in 5cdo
Sodium binding site 4 out of 5 in the 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na501

b:40.3
occ:1.00
 O R:GLN328 2.5 53.1 1.0
O R:TYR322 2.7 67.7 1.0
O R:THR325 3.3 63.2 1.0
HB3 R:GLN328 3.4 66.5 1.0
C R:GLN328 3.6 51.2 1.0
H R:GLN328 3.7 64.6 1.0
C R:TYR322 3.9 69.6 1.0
O R:LYS323 3.9 73.5 1.0
HA R:PRO326 4.0 69.8 1.0
HA R:LYS323 4.0 88.4 1.0
CB R:GLN328 4.2 55.4 1.0
HA R:THR329 4.2 62.8 1.0
C R:LYS323 4.2 73.7 1.0
C R:THR325 4.2 62.9 1.0
CA R:GLN328 4.3 52.5 1.0
N R:GLN328 4.4 53.8 1.0
CA R:LYS323 4.5 73.6 1.0
HG2 R:GLN328 4.5 71.8 1.0
N R:LYS323 4.6 72.5 1.0
N R:THR329 4.7 52.3 1.0
HA R:TYR322 4.7 81.6 1.0
CA R:PRO326 4.7 58.2 1.0
CG R:GLN328 4.8 59.8 1.0
N R:PRO326 4.9 61.0 1.0
H R:THR325 4.9 81.5 1.0
CA R:TYR322 4.9 68.0 1.0
HB2 R:GLN328 4.9 66.5 1.0
CA R:THR329 4.9 52.4 1.0
CD R:GLN328 4.9 67.7 1.0
N R:GLN324 4.9 74.2 1.0
N R:THR325 5.0 68.0 1.0
HE21 R:GLN328 5.0 80.0 1.0

Sodium binding site 5 out of 5 in 5cdo

Go back to Sodium Binding Sites List in 5cdo
Sodium binding site 5 out of 5 in the 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 3.15A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na503

b:43.9
occ:1.00
 O T:HOH615 2.4 41.7 1.0
O T:TYR322 2.7 50.4 1.0
O T:THR325 2.8 47.1 1.0
O T:GLN328 2.8 42.8 1.0
HB3 T:GLN328 3.4 53.3 1.0
H T:GLN328 3.6 49.6 1.0
C T:GLN328 3.7 40.9 1.0
O T:LYS323 3.9 54.9 1.0
HA T:PRO326 3.9 58.9 1.0
C T:TYR322 3.9 53.0 1.0
C T:THR325 4.0 48.5 1.0
C T:LYS323 4.1 55.2 1.0
HA T:LYS323 4.2 66.6 1.0
CB T:GLN328 4.2 44.4 1.0
N T:GLN328 4.2 41.3 1.0
CA T:GLN328 4.3 41.9 1.0
HA T:THR329 4.3 46.8 1.0
N T:GLN324 4.5 54.6 1.0
CA T:LYS323 4.5 55.5 1.0
N T:THR325 4.6 53.3 1.0
HE21 T:GLN328 4.6 63.1 1.0
C T:GLN324 4.6 55.3 1.0
CA T:PRO326 4.6 49.0 1.0
N T:THR329 4.7 40.0 1.0
N T:LYS323 4.7 55.4 1.0
H T:THR325 4.7 63.9 1.0
N T:PRO326 4.7 51.6 1.0
HA T:TYR322 4.7 63.3 1.0
HB2 T:GLN328 4.7 53.3 1.0
H T:LEU327 4.7 56.6 1.0
H T:GLN324 4.8 65.5 1.0
O T:GLN324 4.9 55.7 1.0
CA T:THR325 4.9 50.8 1.0
NE2 T:GLN328 5.0 52.6 1.0
CA T:TYR322 5.0 52.7 1.0
CA T:THR329 5.0 39.0 1.0

Reference:

P.F.Chan, V.Srikannathasan, J.Huang, H.Cui, A.P.Fosberry, M.Gu, M.M.Hann, M.Hibbs, P.Homes, K.Ingraham, J.Pizzollo, C.Shen, A.J.Shillings, C.E.Spitzfaden, R.Tanner, A.J.Theobald, R.A.Stavenger, B.D.Bax, M.N.Gwynn. Structural Basis of Dna Gyrase Inhibition By Antibacterial Qpt-1, Anticancer Drug Etoposide and Moxifloxacin. Nat Commun V. 6 10048 2015.
ISSN: ESSN 2041-1723
PubMed: 26640131
DOI: 10.1038/NCOMMS10048
Page generated: Mon Oct 7 20:19:15 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy