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Magnesium in PDB 5cdq: 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna

Enzymatic activity of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna

All present enzymatic activity of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna:
5.99.1.3;

Protein crystallography data

The structure of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna, PDB code: 5cdq 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) 19.99 / 2.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.930, 170.550, 125.670, 90.00, 103.30, 90.00
R / Rfree (%) 17.5 / 21.8

Other elements in 5cdq:

The structure of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna (pdb code 5cdq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna, PDB code: 5cdq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 5cdq

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Magnesium binding site 1 out of 14 in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:76.8
occ:1.00
 O E:MFX2101 1.9 76.5 1.0
O E:HOH2211 2.0 70.6 1.0
O E:HOH2201 2.0 82.5 1.0
O02 E:MFX2101 2.0 72.0 1.0
O E:HOH2213 2.1 81.3 1.0
O F:HOH2214 2.2 79.4 1.0
C20 E:MFX2101 3.0 75.4 1.0
C19 E:MFX2101 3.0 69.7 1.0
C18 E:MFX2101 3.5 70.7 1.0
O4 F:DT8 4.0 67.1 1.0
O6 F:DG2009 4.1 82.2 1.0
O03 E:MFX2101 4.1 77.9 1.0
OG A:SER84 4.2 88.6 1.0
O F:HOH2216 4.4 88.9 1.0
C14 E:MFX2101 4.4 67.8 1.0
OE2 A:GLU88 4.4 0.9 1.0
N6 E:DA2013 4.5 75.4 1.0
CB A:SER84 4.6 79.6 1.0
N4 E:DC2012 4.6 80.3 1.0
C17 E:MFX2101 4.8 67.9 1.0
C6 F:DG2009 4.8 81.9 1.0
OE1 A:GLU88 4.8 0.1 1.0
C16 E:MFX2101 4.8 67.2 1.0
N7 F:DG2009 5.0 83.3 1.0

Magnesium binding site 2 out of 14 in 5cdq

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Magnesium binding site 2 out of 14 in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:84.8
occ:1.00
 O A:GLN328 2.5 0.9 1.0
O A:TYR322 2.5 0.2 1.0
O A:THR325 3.0 0.7 1.0
C A:GLN328 3.5 0.1 1.0
O A:LYS323 3.5 0.8 1.0
C A:TYR322 3.7 0.8 1.0
C A:LYS323 3.9 0.3 1.0
C A:THR325 4.0 0.3 1.0
CB A:GLN328 4.0 0.7 1.0
CA A:GLN328 4.2 0.2 1.0
CA A:LYS323 4.2 0.3 1.0
N A:GLN328 4.3 0.2 1.0
N A:LYS323 4.4 0.4 1.0
N A:THR325 4.5 0.4 1.0
N A:THR329 4.6 97.4 1.0
N A:GLN324 4.7 0.7 1.0
CA A:PRO326 4.7 98.5 1.0
N A:PRO326 4.8 99.8 1.0
CA A:TYR322 4.8 0.8 1.0
CA A:THR325 4.9 0.0 1.0
CA A:THR329 5.0 94.5 1.0

Magnesium binding site 3 out of 14 in 5cdq

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Magnesium binding site 3 out of 14 in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:42.2
occ:1.00
 O B:HOH1116 1.9 70.1 1.0
OD2 B:ASP510 2.0 76.2 1.0
O B:HOH1107 2.1 49.1 1.0
OD2 B:ASP508 2.2 88.9 1.0
O B:HOH1111 2.9 67.5 1.0
CG B:ASP510 3.0 72.3 1.0
O B:HOH1114 3.2 80.5 1.0
CG B:ASP508 3.3 84.1 1.0
OD1 B:ASP510 3.4 70.4 1.0
CB B:ASP508 3.7 73.5 1.0
OE2 B:GLU435 4.3 72.6 1.0
CB B:ASP510 4.3 69.1 1.0
OD1 B:ASP508 4.3 86.6 1.0
OP1 F:DT8 4.4 72.0 1.0
C5' F:DT8 4.8 67.2 1.0
CA B:GLY582 5.0 93.1 1.0

Magnesium binding site 4 out of 14 in 5cdq

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Magnesium binding site 4 out of 14 in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:94.9
occ:1.00
 O F:HOH2201 1.9 94.5 1.0
O F:HOH2208 2.0 91.6 1.0
O F:MFX2101 2.0 94.7 1.0
O02 F:MFX2101 2.0 92.7 1.0
O F:HOH2213 2.1 99.5 1.0
O E:HOH2214 2.1 97.9 1.0
C20 F:MFX2101 3.0 93.5 1.0
C19 F:MFX2101 3.1 90.9 1.0
C18 F:MFX2101 3.5 91.3 1.0
O4 E:DT8 4.0 83.6 1.0
O6 E:DG2009 4.0 79.0 1.0
O03 F:MFX2101 4.1 94.1 1.0
OG C:SER84 4.2 0.7 1.0
OE2 C:GLU88 4.4 0.4 1.0
C14 F:MFX2101 4.4 88.8 1.0
N4 F:DC2012 4.5 90.7 1.0
N6 F:DA2013 4.6 76.2 1.0
CB C:SER84 4.7 89.2 1.0
C6 E:DG2009 4.8 78.8 1.0
OE1 C:GLU88 4.8 81.5 1.0
C17 F:MFX2101 4.8 89.2 1.0
C16 F:MFX2101 4.9 89.4 1.0
N7 E:DG2009 5.0 79.7 1.0

Magnesium binding site 5 out of 14 in 5cdq

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Magnesium binding site 5 out of 14 in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:66.3
occ:1.00
 O C:GLN328 2.3 81.3 1.0
O C:TYR322 2.5 84.8 1.0
O C:THR325 2.8 82.7 1.0
C C:GLN328 3.4 80.5 1.0
O C:LYS323 3.7 93.1 1.0
C C:TYR322 3.7 85.2 1.0
C C:THR325 3.9 82.6 1.0
C C:LYS323 4.0 91.8 1.0
CB C:GLN328 4.1 80.2 1.0
CA C:GLN328 4.1 76.6 1.0
N C:GLN328 4.2 77.1 1.0
CA C:LYS323 4.3 86.3 1.0
N C:THR329 4.4 76.3 1.0
N C:LYS323 4.5 83.7 1.0
N C:THR325 4.5 82.8 1.0
CA C:PRO326 4.6 75.9 1.0
N C:PRO326 4.7 77.8 1.0
CA C:THR329 4.7 76.4 1.0
N C:GLN324 4.8 88.8 1.0
CA C:THR325 4.8 79.9 1.0
CA C:TYR322 4.9 79.8 1.0

Magnesium binding site 6 out of 14 in 5cdq

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Magnesium binding site 6 out of 14 in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:66.3
occ:1.00
 OD2 D:ASP510 1.9 96.9 1.0
O D:HOH1101 1.9 85.6 1.0
OD2 D:ASP508 2.2 100.0 1.0
O D:HOH1104 2.3 76.6 1.0
O D:HOH1102 2.4 69.5 1.0
O D:HOH1103 2.5 71.7 1.0
CG D:ASP510 3.0 95.2 1.0
CG D:ASP508 3.2 0.3 1.0
OD1 D:ASP510 3.3 96.3 1.0
CB D:ASP508 3.6 93.6 1.0
OD1 D:ASP508 4.3 0.3 1.0
CB D:ASP510 4.3 87.3 1.0
OP1 E:DT8 4.4 82.4 1.0
C5' E:DT8 4.7 85.4 1.0
OE2 D:GLU435 4.7 0.4 1.0

Magnesium binding site 7 out of 14 in 5cdq

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Magnesium binding site 7 out of 14 in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2102

b:69.1
occ:1.00
 O02 F:MFX2103 2.0 70.2 1.0
O F:MFX2103 2.0 69.5 1.0
O F:HOH2207 2.1 71.1 1.0
O F:HOH2212 2.1 68.4 1.0
C20 F:MFX2103 2.9 71.8 1.0
C19 F:MFX2103 3.0 70.0 1.0
C18 F:MFX2103 3.4 70.2 1.0
O03 F:MFX2103 4.0 73.1 1.0
N6 F:DA2 4.0 90.6 1.0
C14 F:MFX2103 4.3 70.0 1.0
N7 F:DA2 4.5 91.1 1.0
N2 F:DG1 4.7 88.6 1.0
C6 F:DA2 4.7 90.4 1.0
C17 F:MFX2103 4.7 72.6 1.0
C16 F:MFX2103 4.8 68.2 1.0
C5 F:DA2 4.9 90.8 1.0

Magnesium binding site 8 out of 14 in 5cdq

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Magnesium binding site 8 out of 14 in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg4301

b:73.8
occ:1.00
 O V:MFX2101 1.9 74.3 1.0
O V:HOH2201 2.0 80.4 1.0
O V:HOH2204 2.0 70.0 1.0
O02 V:MFX2101 2.1 69.0 1.0
O V:HOH2206 2.1 75.9 1.0
O W:HOH2210 2.1 81.2 1.0
C20 V:MFX2101 3.0 73.2 1.0
C19 V:MFX2101 3.1 68.1 1.0
C18 V:MFX2101 3.5 69.5 1.0
O4 W:DT8 3.9 69.7 1.0
O03 V:MFX2101 4.1 74.6 1.0
O6 W:DG2009 4.1 79.4 1.0
OG R:SER84 4.2 88.1 1.0
O W:HOH2205 4.2 86.0 1.0
C14 V:MFX2101 4.4 67.4 1.0
OE2 R:GLU88 4.4 93.7 1.0
N6 V:DA2013 4.6 74.5 1.0
CB R:SER84 4.6 75.0 1.0
N4 V:DC2012 4.7 79.8 1.0
C17 V:MFX2101 4.8 68.4 1.0
C16 V:MFX2101 4.9 67.0 1.0
OE1 R:GLU88 4.9 99.2 1.0
C6 W:DG2009 4.9 78.8 1.0
C4 W:DT8 5.0 67.9 1.0

Magnesium binding site 9 out of 14 in 5cdq

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Magnesium binding site 9 out of 14 in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg1001

b:52.1
occ:1.00
 OD2 S:ASP510 1.9 79.0 1.0
OD2 S:ASP508 2.0 76.7 1.0
O S:HOH1110 2.1 58.8 1.0
O S:HOH1102 2.2 41.2 1.0
O S:HOH1108 2.4 48.3 1.0
O S:HOH1107 2.5 84.3 1.0
CG S:ASP510 2.9 76.8 1.0
CG S:ASP508 2.9 73.4 1.0
CB S:ASP508 3.2 64.9 1.0
OD1 S:ASP510 3.2 76.9 1.0
OD1 S:ASP508 4.1 75.3 1.0
OE2 S:GLU435 4.3 59.3 1.0
CB S:ASP510 4.3 70.8 1.0
O S:HOH1114 4.5 54.7 1.0
CA S:ASP508 4.7 65.3 1.0
CA S:GLY582 4.8 91.2 1.0
OP1 W:DT8 4.9 65.9 1.0
OE1 S:GLU435 4.9 52.2 1.0
CD S:GLU435 5.0 73.0 1.0

Magnesium binding site 10 out of 14 in 5cdq

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Magnesium binding site 10 out of 14 in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg4501

b:84.0
occ:1.00
 O W:HOH2201 1.9 85.3 1.0
O W:MFX2101 1.9 81.9 1.0
O W:HOH2208 2.0 80.5 1.0
O02 W:MFX2101 2.1 82.7 1.0
O W:HOH2209 2.1 89.0 1.0
O V:HOH2207 2.1 87.5 1.0
C20 W:MFX2101 3.0 80.2 1.0
C19 W:MFX2101 3.1 79.7 1.0
C18 W:MFX2101 3.5 78.8 1.0
O4 V:DT8 3.9 73.7 1.0
O6 V:DG2009 4.0 85.6 1.0
O03 W:MFX2101 4.1 79.5 1.0
OG T:SER84 4.2 0.8 1.0
OE2 T:GLU88 4.4 92.6 1.0
C14 W:MFX2101 4.4 79.0 1.0
O T:HOH4621 4.4 53.0 1.0
CB T:SER84 4.6 91.4 1.0
N4 W:DC2012 4.6 85.8 1.0
O W:HOH2212 4.6 62.8 1.0
N6 W:DA2013 4.6 85.7 1.0
OE1 T:GLU88 4.8 75.4 1.0
C17 W:MFX2101 4.8 81.7 1.0
C6 V:DG2009 4.8 85.5 1.0
C16 W:MFX2101 4.9 76.8 1.0
CD T:GLU88 5.0 97.6 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: Sun Sep 29 02:04:13 2024

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