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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

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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

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