Magnesium in PDB 5d7c: Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
Enzymatic activity of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
All present enzymatic activity of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand:
5.99.1.3;
Protein crystallography data
The structure of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand, PDB code: 5d7c
was solved by
J.Zhang,
Q.Yang,
J.B.Cross,
J.A.C.Romero,
M.D.Ryan,
B.Lippa,
R.E.Dolle,
O.A.Andersen,
J.Barker,
R.K.Cheng,
J.Kahmann,
B.Felicetti,
M.Wood,
C.Scheich,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.78 /
1.55
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
142.803,
55.485,
51.422,
90.00,
100.77,
90.00
|
R / Rfree (%)
|
17.1 /
19.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
(pdb code 5d7c). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand, PDB code: 5d7c:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 5d7c
Go back to
Magnesium Binding Sites List in 5d7c
Magnesium binding site 1 out
of 8 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg304
b:31.1
occ:1.00
|
O
|
A:HOH532
|
2.0
|
37.2
|
1.0
|
O
|
A:HOH477
|
2.2
|
25.9
|
1.0
|
OE1
|
A:GLU50
|
2.3
|
27.4
|
1.0
|
O
|
A:HOH416
|
2.7
|
44.7
|
1.0
|
CD
|
A:GLU50
|
3.4
|
29.2
|
1.0
|
OE2
|
A:GLU50
|
3.9
|
45.8
|
1.0
|
OD1
|
A:ASP53
|
4.5
|
29.1
|
1.0
|
CG
|
A:GLU50
|
4.6
|
21.5
|
1.0
|
O
|
A:GLU50
|
4.7
|
20.1
|
1.0
|
OD1
|
A:ASN54
|
4.8
|
33.8
|
1.0
|
CB
|
A:GLU50
|
4.8
|
19.0
|
1.0
|
CA
|
A:GLU50
|
5.0
|
16.8
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 5d7c
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Magnesium Binding Sites List in 5d7c
Magnesium binding site 2 out
of 8 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg304
b:41.4
occ:1.00
|
O
|
B:HOH447
|
2.2
|
40.2
|
1.0
|
O
|
B:HOH426
|
2.3
|
26.7
|
1.0
|
OD1
|
B:ASP53
|
2.4
|
20.9
|
0.5
|
OD2
|
B:ASP57
|
2.5
|
27.4
|
1.0
|
O
|
B:HOH501
|
2.6
|
31.1
|
1.0
|
OD2
|
B:ASP53
|
2.7
|
20.5
|
0.5
|
O
|
B:HOH406
|
2.9
|
45.6
|
1.0
|
CG
|
B:ASP53
|
2.9
|
18.1
|
0.5
|
CG
|
B:ASP57
|
3.3
|
24.4
|
1.0
|
OD1
|
B:ASP57
|
3.5
|
25.1
|
1.0
|
O
|
B:ASP53
|
4.0
|
17.2
|
1.0
|
O
|
B:HOH429
|
4.2
|
30.2
|
1.0
|
CG
|
B:ASP53
|
4.3
|
24.8
|
0.5
|
CB
|
B:ASP53
|
4.3
|
20.2
|
0.5
|
CB
|
B:ASP53
|
4.3
|
16.7
|
0.5
|
OD2
|
B:ASP53
|
4.5
|
29.4
|
0.5
|
CB
|
B:ASP57
|
4.7
|
17.8
|
1.0
|
OD1
|
B:ASP53
|
4.7
|
32.2
|
0.5
|
MG
|
B:MG310
|
4.7
|
40.7
|
1.0
|
C
|
B:ASP53
|
4.7
|
16.2
|
1.0
|
O
|
B:HOH401
|
4.8
|
20.0
|
0.5
|
CA
|
B:ASP53
|
4.8
|
18.6
|
0.5
|
CA
|
B:ASP53
|
4.8
|
17.1
|
0.5
|
N
|
B:ASP57
|
4.8
|
16.3
|
1.0
|
CA
|
B:ASP57
|
5.0
|
17.7
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 5d7c
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Magnesium Binding Sites List in 5d7c
Magnesium binding site 3 out
of 8 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg305
b:28.9
occ:1.00
|
O
|
B:HOH531
|
2.2
|
33.1
|
1.0
|
OE1
|
B:GLU164
|
2.5
|
35.4
|
1.0
|
O
|
B:HOH538
|
2.6
|
47.5
|
1.0
|
OE2
|
B:GLU164
|
2.6
|
34.3
|
1.0
|
CD
|
B:GLU164
|
2.8
|
28.5
|
1.0
|
CG
|
B:GLU164
|
4.3
|
23.8
|
1.0
|
O
|
B:HOH425
|
4.3
|
35.8
|
1.0
|
O
|
B:HOH403
|
4.3
|
43.0
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 5d7c
Go back to
Magnesium Binding Sites List in 5d7c
Magnesium binding site 4 out
of 8 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg306
b:27.5
occ:1.00
|
O
|
B:HOH503
|
2.1
|
52.4
|
1.0
|
O
|
B:HOH565
|
2.2
|
53.4
|
1.0
|
O
|
B:LEU60
|
2.3
|
20.5
|
1.0
|
O
|
B:HOH505
|
2.6
|
31.8
|
1.0
|
C
|
B:LEU60
|
3.5
|
18.7
|
1.0
|
N
|
B:ALA61
|
4.3
|
19.0
|
1.0
|
CA
|
B:LEU60
|
4.4
|
17.0
|
1.0
|
O
|
B:HOH551
|
4.4
|
46.8
|
1.0
|
CA
|
B:ALA61
|
4.4
|
19.1
|
1.0
|
C
|
B:ALA61
|
4.7
|
19.2
|
1.0
|
CB
|
B:LEU60
|
4.7
|
17.2
|
1.0
|
O
|
B:HOH454
|
4.9
|
37.9
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 5d7c
Go back to
Magnesium Binding Sites List in 5d7c
Magnesium binding site 5 out
of 8 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg307
b:41.2
occ:1.00
|
O
|
B:HOH562
|
2.1
|
42.2
|
1.0
|
O
|
B:HOH429
|
2.2
|
30.2
|
1.0
|
O
|
B:HOH506
|
2.2
|
37.3
|
1.0
|
O
|
B:HOH542
|
2.3
|
37.1
|
1.0
|
O
|
B:HOH421
|
2.3
|
27.5
|
1.0
|
OD1
|
B:ASN54
|
2.4
|
24.5
|
1.0
|
MG
|
B:MG310
|
2.4
|
40.7
|
1.0
|
CG
|
B:ASN54
|
3.6
|
21.9
|
1.0
|
O
|
B:HOH485
|
4.0
|
26.2
|
1.0
|
O
|
B:HOH406
|
4.2
|
45.6
|
1.0
|
OD2
|
B:ASP53
|
4.3
|
20.5
|
0.5
|
O
|
B:GLU50
|
4.3
|
19.7
|
1.0
|
N
|
B:ASN54
|
4.5
|
16.9
|
1.0
|
ND2
|
B:ASN54
|
4.5
|
23.6
|
1.0
|
O
|
B:HOH432
|
4.5
|
47.6
|
1.0
|
CA
|
B:ASN54
|
4.5
|
17.5
|
1.0
|
OD1
|
B:ASP57
|
4.6
|
25.1
|
1.0
|
CB
|
B:ASN54
|
4.6
|
19.2
|
1.0
|
O
|
B:HOH537
|
4.7
|
40.0
|
1.0
|
OE2
|
B:GLU50
|
4.7
|
28.9
|
1.0
|
CB
|
B:ASP53
|
4.9
|
20.2
|
0.5
|
C
|
B:ASP53
|
4.9
|
16.2
|
1.0
|
C20
|
B:57W303
|
5.0
|
23.7
|
1.0
|
CB
|
B:ASP53
|
5.0
|
16.7
|
0.5
|
|
Magnesium binding site 6 out
of 8 in 5d7c
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Magnesium Binding Sites List in 5d7c
Magnesium binding site 6 out
of 8 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg308
b:28.7
occ:1.00
|
OG1
|
B:THR171
|
2.0
|
22.4
|
1.0
|
O
|
B:ASN82
|
2.3
|
16.1
|
1.0
|
O
|
B:HOH504
|
2.3
|
36.9
|
1.0
|
O
|
B:HOH479
|
2.5
|
28.0
|
1.0
|
O
|
B:GLY83
|
2.7
|
14.7
|
1.0
|
O
|
B:THR171
|
2.9
|
18.2
|
1.0
|
O
|
B:HOH514
|
3.0
|
36.8
|
1.0
|
C
|
B:ASN82
|
3.2
|
13.4
|
1.0
|
CB
|
B:THR171
|
3.2
|
21.4
|
1.0
|
C
|
B:THR171
|
3.4
|
15.0
|
1.0
|
C
|
B:GLY83
|
3.5
|
15.2
|
1.0
|
CA
|
B:THR171
|
3.7
|
16.8
|
1.0
|
N
|
B:THR171
|
3.9
|
18.0
|
1.0
|
N
|
B:GLY83
|
3.9
|
13.3
|
1.0
|
CA
|
B:GLY83
|
3.9
|
14.6
|
1.0
|
CA
|
B:ASN82
|
4.1
|
13.9
|
1.0
|
N
|
B:GLY172
|
4.3
|
13.7
|
1.0
|
CB
|
B:ASN82
|
4.4
|
15.1
|
1.0
|
CG2
|
B:THR171
|
4.4
|
23.4
|
1.0
|
O
|
B:TYR63
|
4.6
|
23.0
|
1.0
|
N
|
B:ARG84
|
4.6
|
14.2
|
1.0
|
O
|
B:HOH568
|
4.6
|
35.0
|
1.0
|
O
|
B:HOH536
|
4.7
|
42.1
|
1.0
|
CA
|
B:ARG84
|
4.8
|
14.4
|
1.0
|
CA
|
B:GLY172
|
4.9
|
14.1
|
1.0
|
CG
|
B:ASN82
|
4.9
|
15.7
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 5d7c
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Magnesium Binding Sites List in 5d7c
Magnesium binding site 7 out
of 8 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg309
b:35.4
occ:1.00
|
O
|
B:HOH478
|
2.2
|
27.6
|
1.0
|
O
|
B:HOH519
|
2.2
|
41.0
|
1.0
|
O
|
B:GLY208
|
2.4
|
22.4
|
1.0
|
NE2
|
B:HIS228
|
2.8
|
32.6
|
1.0
|
CE1
|
B:HIS228
|
3.2
|
38.8
|
1.0
|
O
|
B:HOH486
|
3.4
|
42.1
|
1.0
|
C
|
B:GLY208
|
3.4
|
19.3
|
1.0
|
CD2
|
B:HIS228
|
3.8
|
31.4
|
1.0
|
CA
|
B:GLY208
|
4.0
|
20.6
|
1.0
|
O
|
B:HOH510
|
4.3
|
39.1
|
1.0
|
ND1
|
B:HIS228
|
4.4
|
34.9
|
1.0
|
N
|
B:ILE209
|
4.5
|
16.4
|
1.0
|
CB
|
B:ASN65
|
4.6
|
18.8
|
1.0
|
O
|
B:ASN65
|
4.7
|
15.9
|
1.0
|
O
|
B:HOH525
|
4.7
|
46.2
|
1.0
|
ND2
|
B:ASN65
|
4.7
|
26.9
|
1.0
|
CG
|
B:HIS228
|
4.8
|
26.6
|
1.0
|
CA
|
B:ILE209
|
4.8
|
17.4
|
1.0
|
CG
|
B:ASN65
|
4.9
|
20.3
|
1.0
|
N
|
B:GLN210
|
5.0
|
15.7
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 5d7c
Go back to
Magnesium Binding Sites List in 5d7c
Magnesium binding site 8 out
of 8 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg310
b:40.7
occ:1.00
|
O
|
B:HOH562
|
2.0
|
42.2
|
1.0
|
O
|
B:HOH429
|
2.3
|
30.2
|
1.0
|
MG
|
B:MG307
|
2.4
|
41.2
|
1.0
|
O
|
B:HOH432
|
2.5
|
47.6
|
1.0
|
O
|
B:HOH421
|
2.5
|
27.5
|
1.0
|
OD2
|
B:ASP53
|
2.6
|
20.5
|
0.5
|
O
|
B:HOH406
|
3.0
|
45.6
|
1.0
|
O
|
B:HOH521
|
3.6
|
54.2
|
1.0
|
CG
|
B:ASP53
|
3.6
|
18.1
|
0.5
|
CB
|
B:ASP53
|
3.9
|
20.2
|
0.5
|
CB
|
B:ASP53
|
4.0
|
16.7
|
0.5
|
O
|
B:HOH542
|
4.0
|
37.1
|
1.0
|
O
|
B:HOH447
|
4.1
|
40.2
|
1.0
|
OE2
|
B:GLU50
|
4.2
|
28.9
|
1.0
|
OD1
|
B:ASP53
|
4.3
|
32.2
|
0.5
|
O
|
B:HOH506
|
4.3
|
37.3
|
1.0
|
OD1
|
B:ASN54
|
4.4
|
24.5
|
1.0
|
OD1
|
B:ASP57
|
4.5
|
25.1
|
1.0
|
CG
|
B:ASP53
|
4.6
|
24.8
|
0.5
|
MG
|
B:MG304
|
4.7
|
41.4
|
1.0
|
OD1
|
B:ASP53
|
4.7
|
20.9
|
0.5
|
O
|
B:GLU50
|
4.8
|
19.7
|
1.0
|
C
|
B:ASP53
|
5.0
|
16.2
|
1.0
|
|
Reference:
J.Zhang,
Q.Yang,
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PubMed: 26460684
DOI: 10.1021/ACS.JMEDCHEM.5B00961
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