Magnesium in PDB 6par: Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound
Protein crystallography data
The structure of Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound, PDB code: 6par
was solved by
C.Fan,
J.T.Kaiser,
D.C.Rees,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.62 /
3.35
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
169.648,
92.498,
237.691,
90.00,
110.34,
90.00
|
R / Rfree (%)
|
25.4 /
28.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound
(pdb code 6par). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound, PDB code: 6par:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6par
Go back to
Magnesium Binding Sites List in 6par
Magnesium binding site 1 out
of 6 in the Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg702
b:36.1
occ:1.00
|
OG
|
A:SER401
|
2.0
|
31.0
|
1.0
|
OE1
|
A:GLN442
|
2.1
|
60.1
|
1.0
|
N3B
|
A:ANP701
|
2.2
|
79.5
|
1.0
|
CD
|
A:GLN442
|
3.0
|
44.0
|
1.0
|
O2B
|
A:ANP701
|
3.1
|
45.8
|
1.0
|
CB
|
A:SER401
|
3.1
|
41.5
|
1.0
|
PB
|
A:ANP701
|
3.2
|
77.7
|
1.0
|
PG
|
A:ANP701
|
3.2
|
55.8
|
1.0
|
NE2
|
A:GLN442
|
3.4
|
53.9
|
1.0
|
O1A
|
A:ANP701
|
3.5
|
68.2
|
1.0
|
O1G
|
A:ANP701
|
3.5
|
38.5
|
1.0
|
O3G
|
A:ANP701
|
3.6
|
70.3
|
1.0
|
N
|
A:SER401
|
4.0
|
34.8
|
1.0
|
OD1
|
A:ASP522
|
4.1
|
55.3
|
1.0
|
CA
|
A:SER401
|
4.1
|
34.7
|
1.0
|
OD2
|
A:ASP522
|
4.2
|
49.8
|
1.0
|
O3A
|
A:ANP701
|
4.2
|
67.5
|
1.0
|
O1B
|
A:ANP701
|
4.3
|
78.9
|
1.0
|
CG
|
A:GLN442
|
4.3
|
30.7
|
1.0
|
PA
|
A:ANP701
|
4.4
|
83.3
|
1.0
|
CG
|
A:ASP522
|
4.6
|
54.2
|
1.0
|
CB
|
A:GLN442
|
4.6
|
32.3
|
1.0
|
O2G
|
A:ANP701
|
4.6
|
53.3
|
1.0
|
N
|
B:GLY500
|
4.7
|
44.1
|
1.0
|
CB
|
B:SER499
|
5.0
|
34.2
|
1.0
|
O2A
|
A:ANP701
|
5.0
|
73.9
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6par
Go back to
Magnesium Binding Sites List in 6par
Magnesium binding site 2 out
of 6 in the Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg702
b:49.8
occ:1.00
|
OE1
|
B:GLN442
|
2.0
|
61.1
|
1.0
|
OG
|
B:SER401
|
2.0
|
43.8
|
1.0
|
O1G
|
B:ANP701
|
2.1
|
71.7
|
1.0
|
O1B
|
B:ANP701
|
2.1
|
78.2
|
1.0
|
CD
|
B:GLN442
|
2.9
|
56.2
|
1.0
|
CB
|
B:SER401
|
3.1
|
52.8
|
1.0
|
NE2
|
B:GLN442
|
3.3
|
48.1
|
1.0
|
PG
|
B:ANP701
|
3.4
|
69.6
|
1.0
|
PB
|
B:ANP701
|
3.4
|
77.4
|
1.0
|
O1A
|
B:ANP701
|
3.6
|
83.0
|
1.0
|
N3B
|
B:ANP701
|
3.8
|
78.2
|
1.0
|
OD2
|
B:ASP522
|
4.0
|
68.8
|
1.0
|
OD1
|
B:ASP522
|
4.0
|
52.5
|
1.0
|
N
|
B:SER401
|
4.1
|
40.9
|
1.0
|
CA
|
B:SER401
|
4.2
|
42.6
|
1.0
|
CG
|
B:GLN442
|
4.2
|
55.2
|
1.0
|
O2G
|
B:ANP701
|
4.3
|
40.9
|
1.0
|
O2B
|
B:ANP701
|
4.4
|
49.7
|
1.0
|
O3G
|
B:ANP701
|
4.4
|
52.4
|
1.0
|
CG
|
B:ASP522
|
4.4
|
58.4
|
1.0
|
O3A
|
B:ANP701
|
4.5
|
72.2
|
1.0
|
CB
|
B:GLN442
|
4.5
|
44.4
|
1.0
|
PA
|
B:ANP701
|
4.5
|
81.0
|
1.0
|
N
|
A:GLY500
|
4.6
|
39.4
|
1.0
|
O2A
|
B:ANP701
|
5.0
|
55.5
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6par
Go back to
Magnesium Binding Sites List in 6par
Magnesium binding site 3 out
of 6 in the Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg702
b:0.8
occ:1.00
|
OG
|
C:SER401
|
2.2
|
1.0
|
1.0
|
N3B
|
C:ANP701
|
2.6
|
0.8
|
1.0
|
O1B
|
C:ANP701
|
2.7
|
0.4
|
1.0
|
OE1
|
C:GLN442
|
3.1
|
84.8
|
1.0
|
N
|
C:SER401
|
3.1
|
0.3
|
1.0
|
PB
|
C:ANP701
|
3.2
|
0.4
|
1.0
|
CB
|
C:SER401
|
3.3
|
0.0
|
1.0
|
O1G
|
C:ANP701
|
3.3
|
0.9
|
1.0
|
PG
|
C:ANP701
|
3.5
|
0.3
|
1.0
|
NE2
|
C:GLN442
|
3.5
|
88.2
|
1.0
|
CD
|
C:GLN442
|
3.5
|
87.8
|
1.0
|
OD1
|
C:ASP522
|
3.5
|
98.0
|
1.0
|
CA
|
C:SER401
|
3.7
|
0.7
|
1.0
|
O2A
|
C:ANP701
|
3.8
|
0.0
|
1.0
|
CB
|
C:LYS400
|
3.8
|
0.4
|
1.0
|
O3A
|
C:ANP701
|
3.9
|
0.6
|
1.0
|
O1A
|
C:ANP701
|
3.9
|
0.3
|
1.0
|
O3G
|
C:ANP701
|
4.0
|
0.5
|
1.0
|
OD2
|
C:ASP522
|
4.0
|
0.8
|
1.0
|
PA
|
C:ANP701
|
4.0
|
0.2
|
1.0
|
C
|
C:LYS400
|
4.1
|
0.1
|
1.0
|
CG
|
C:ASP522
|
4.2
|
97.6
|
1.0
|
CA
|
C:LYS400
|
4.4
|
0.1
|
1.0
|
CG2
|
C:ILE552
|
4.5
|
83.1
|
1.0
|
O2B
|
C:ANP701
|
4.6
|
0.1
|
1.0
|
N
|
C:LYS400
|
4.6
|
0.4
|
1.0
|
CD
|
C:LYS400
|
4.6
|
80.5
|
1.0
|
CG
|
C:LYS400
|
4.7
|
0.1
|
1.0
|
CG
|
C:GLN442
|
4.7
|
93.7
|
1.0
|
O2G
|
C:ANP701
|
4.9
|
0.8
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6par
Go back to
Magnesium Binding Sites List in 6par
Magnesium binding site 4 out
of 6 in the Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg702
b:87.2
occ:1.00
|
OG
|
D:SER401
|
2.1
|
95.7
|
1.0
|
OE1
|
D:GLN442
|
2.2
|
86.1
|
1.0
|
O2G
|
D:ANP701
|
2.2
|
0.1
|
1.0
|
O2B
|
D:ANP701
|
2.3
|
0.3
|
1.0
|
CD
|
D:GLN442
|
2.8
|
90.8
|
1.0
|
NE2
|
D:GLN442
|
2.8
|
86.5
|
1.0
|
PB
|
D:ANP701
|
3.2
|
0.5
|
1.0
|
PG
|
D:ANP701
|
3.2
|
0.1
|
1.0
|
CB
|
D:SER401
|
3.2
|
0.1
|
1.0
|
N3B
|
D:ANP701
|
3.4
|
0.3
|
1.0
|
O3A
|
D:ANP701
|
3.5
|
0.6
|
1.0
|
O1G
|
D:ANP701
|
3.7
|
0.2
|
1.0
|
O1A
|
D:ANP701
|
3.7
|
0.1
|
1.0
|
N
|
D:SER401
|
3.8
|
0.8
|
1.0
|
PA
|
D:ANP701
|
3.9
|
0.4
|
1.0
|
OD1
|
D:ASP522
|
4.0
|
1.0
|
1.0
|
CA
|
D:SER401
|
4.1
|
99.6
|
1.0
|
O2A
|
D:ANP701
|
4.1
|
0.6
|
1.0
|
CG
|
D:GLN442
|
4.1
|
0.4
|
1.0
|
OD2
|
D:ASP522
|
4.2
|
0.4
|
1.0
|
O1B
|
D:ANP701
|
4.5
|
0.0
|
1.0
|
CG
|
D:ASP522
|
4.5
|
0.7
|
1.0
|
O3G
|
D:ANP701
|
4.6
|
0.3
|
1.0
|
CB
|
D:GLN442
|
4.7
|
0.9
|
1.0
|
CB
|
D:LYS400
|
4.7
|
95.2
|
1.0
|
C
|
D:LYS400
|
4.8
|
0.8
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6par
Go back to
Magnesium Binding Sites List in 6par
Magnesium binding site 5 out
of 6 in the Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg702
b:52.9
occ:1.00
|
OE1
|
E:GLN442
|
1.9
|
86.2
|
1.0
|
OG
|
E:SER401
|
2.1
|
57.4
|
1.0
|
N3B
|
E:ANP701
|
2.6
|
0.6
|
1.0
|
CD
|
E:GLN442
|
2.9
|
82.9
|
1.0
|
O1G
|
E:ANP701
|
3.1
|
86.4
|
1.0
|
O1A
|
E:ANP701
|
3.2
|
0.6
|
1.0
|
PG
|
E:ANP701
|
3.3
|
0.8
|
1.0
|
O2B
|
E:ANP701
|
3.3
|
0.8
|
1.0
|
CB
|
E:SER401
|
3.3
|
61.1
|
1.0
|
NE2
|
E:GLN442
|
3.3
|
94.6
|
1.0
|
PB
|
E:ANP701
|
3.4
|
0.6
|
1.0
|
O3G
|
E:ANP701
|
3.6
|
90.3
|
1.0
|
O3A
|
E:ANP701
|
3.8
|
0.9
|
1.0
|
OD1
|
E:ASP522
|
4.0
|
89.3
|
1.0
|
N
|
E:SER401
|
4.0
|
60.8
|
1.0
|
OD2
|
E:ASP522
|
4.0
|
99.0
|
1.0
|
PA
|
E:ANP701
|
4.0
|
0.7
|
1.0
|
CG
|
E:GLN442
|
4.2
|
83.1
|
1.0
|
CA
|
E:SER401
|
4.2
|
57.3
|
1.0
|
CG
|
E:ASP522
|
4.4
|
91.0
|
1.0
|
CB
|
E:GLN442
|
4.5
|
79.2
|
1.0
|
O2A
|
E:ANP701
|
4.7
|
0.6
|
1.0
|
N
|
F:GLY500
|
4.7
|
60.3
|
1.0
|
O2G
|
E:ANP701
|
4.8
|
0.1
|
1.0
|
O1B
|
E:ANP701
|
4.8
|
0.9
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6par
Go back to
Magnesium Binding Sites List in 6par
Magnesium binding site 6 out
of 6 in the Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of A Bacterial ATM1-Family Abc Exporter with Mgamppnp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg702
b:64.8
occ:1.00
|
OE1
|
F:GLN442
|
2.0
|
94.9
|
1.0
|
OG
|
F:SER401
|
2.0
|
55.6
|
1.0
|
O1B
|
F:ANP701
|
2.3
|
0.5
|
1.0
|
O1G
|
F:ANP701
|
2.6
|
77.4
|
1.0
|
CD
|
F:GLN442
|
2.7
|
83.6
|
1.0
|
O2G
|
F:ANP701
|
2.9
|
97.8
|
1.0
|
NE2
|
F:GLN442
|
3.0
|
94.3
|
1.0
|
CB
|
F:SER401
|
3.1
|
48.7
|
1.0
|
PG
|
F:ANP701
|
3.2
|
0.5
|
1.0
|
O1A
|
F:ANP701
|
3.2
|
0.3
|
1.0
|
PB
|
F:ANP701
|
3.4
|
98.6
|
1.0
|
N3B
|
F:ANP701
|
3.8
|
99.0
|
1.0
|
N
|
F:SER401
|
4.0
|
68.9
|
1.0
|
OD1
|
F:ASP522
|
4.0
|
83.0
|
1.0
|
PA
|
F:ANP701
|
4.1
|
97.5
|
1.0
|
CA
|
F:SER401
|
4.1
|
55.2
|
1.0
|
CG
|
F:GLN442
|
4.1
|
70.0
|
1.0
|
O3A
|
F:ANP701
|
4.2
|
0.2
|
1.0
|
OD2
|
F:ASP522
|
4.3
|
73.8
|
1.0
|
O2A
|
F:ANP701
|
4.5
|
0.0
|
1.0
|
CB
|
F:GLN442
|
4.6
|
70.9
|
1.0
|
O3G
|
F:ANP701
|
4.6
|
85.4
|
1.0
|
CG
|
F:ASP522
|
4.6
|
79.9
|
1.0
|
O2B
|
F:ANP701
|
4.7
|
89.5
|
1.0
|
N
|
E:GLY500
|
4.8
|
66.6
|
1.0
|
CB
|
E:SER499
|
5.0
|
96.5
|
1.0
|
|
Reference:
C.Fan,
J.T.Kaiser,
D.C.Rees.
A Structural and Kinetic Framework For the Transport Cycle of A Bacterial Abc Exporter To Be Published.
Page generated: Tue Oct 1 14:00:54 2024
|