Magnesium in PDB 7yzq: Mgadp-ALF4-Bound Dccp:Dccp-R Complex
Protein crystallography data
The structure of Mgadp-ALF4-Bound Dccp:Dccp-R Complex, PDB code: 7yzq
was solved by
J.-H.Jeoung,
H.Dobbek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.16 /
1.96
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.032,
81.587,
121.485,
100.83,
96.92,
90.17
|
|
R / Rfree (%)
|
17.8 /
22.3
|
Other elements in 7yzq:
The structure of Mgadp-ALF4-Bound Dccp:Dccp-R Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Mgadp-ALF4-Bound Dccp:Dccp-R Complex
(pdb code 7yzq). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Mgadp-ALF4-Bound Dccp:Dccp-R Complex, PDB code: 7yzq:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7yzq
Go back to
Magnesium Binding Sites List in 7yzq
Magnesium binding site 1 out
of 4 in the Mgadp-ALF4-Bound Dccp:Dccp-R Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Mgadp-ALF4-Bound Dccp:Dccp-R Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg302
b:12.5
occ:1.00
|
F3
|
E:ALF303
|
2.0
|
12.6
|
1.0
|
|
O
|
E:HOH424
|
2.1
|
12.1
|
1.0
|
|
O
|
E:HOH496
|
2.1
|
10.8
|
1.0
|
|
O
|
E:HOH469
|
2.2
|
13.9
|
1.0
|
|
O1B
|
E:ADP301
|
2.2
|
12.2
|
1.0
|
|
O
|
E:HOH434
|
2.2
|
12.9
|
1.0
|
|
HZ3
|
E:LYS96
|
2.9
|
17.2
|
1.0
|
|
PB
|
E:ADP301
|
3.4
|
12.1
|
1.0
|
|
HZ1
|
E:LYS13
|
3.5
|
15.2
|
1.0
|
|
O3B
|
E:ADP301
|
3.6
|
14.1
|
1.0
|
|
AL
|
E:ALF303
|
3.6
|
14.6
|
1.0
|
|
F2
|
E:ALF303
|
3.8
|
8.3
|
1.0
|
|
NZ
|
E:LYS96
|
3.8
|
14.4
|
1.0
|
|
HZ3
|
E:LYS13
|
3.8
|
15.2
|
1.0
|
|
OE1
|
E:GLU69
|
3.9
|
14.5
|
1.0
|
|
O1A
|
E:ADP301
|
4.0
|
10.2
|
1.0
|
|
HZ1
|
E:LYS96
|
4.0
|
17.2
|
1.0
|
|
HA3
|
E:GLY91
|
4.0
|
16.9
|
1.0
|
|
HZ2
|
E:LYS96
|
4.1
|
17.2
|
1.0
|
|
NZ
|
E:LYS13
|
4.1
|
12.7
|
1.0
|
|
O
|
E:HOH460
|
4.1
|
10.8
|
1.0
|
|
OD2
|
E:ASP6
|
4.1
|
17.1
|
1.0
|
|
F1
|
E:ALF303
|
4.2
|
14.4
|
1.0
|
|
O
|
E:HOH493
|
4.2
|
10.9
|
1.0
|
|
O3A
|
E:ADP301
|
4.3
|
14.2
|
1.0
|
|
OD2
|
E:ASP89
|
4.3
|
10.4
|
1.0
|
|
OD1
|
E:ASP89
|
4.4
|
11.1
|
1.0
|
|
HA3
|
E:GLY8
|
4.4
|
22.3
|
1.0
|
|
HE2
|
E:LYS96
|
4.5
|
14.0
|
1.0
|
|
O
|
E:HOH417
|
4.5
|
13.9
|
1.0
|
|
O2B
|
E:ADP301
|
4.5
|
10.8
|
1.0
|
|
HB2
|
E:GLU69
|
4.6
|
10.9
|
1.0
|
|
OD1
|
E:ASP6
|
4.6
|
15.8
|
1.0
|
|
HE2
|
E:LYS13
|
4.6
|
12.1
|
1.0
|
|
HZ2
|
E:LYS13
|
4.7
|
15.2
|
1.0
|
|
CD
|
E:GLU69
|
4.7
|
13.0
|
1.0
|
|
PA
|
E:ADP301
|
4.7
|
14.2
|
1.0
|
|
HA2
|
E:GLY91
|
4.8
|
16.9
|
1.0
|
|
CE
|
E:LYS96
|
4.8
|
11.7
|
1.0
|
|
CG
|
E:ASP89
|
4.8
|
10.1
|
1.0
|
|
CG
|
E:ASP6
|
4.8
|
13.7
|
1.0
|
|
CA
|
E:GLY91
|
4.8
|
14.0
|
1.0
|
|
HA2
|
E:GLY8
|
5.0
|
22.3
|
1.0
|
|
CE
|
E:LYS13
|
5.0
|
10.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7yzq
Go back to
Magnesium Binding Sites List in 7yzq
Magnesium binding site 2 out
of 4 in the Mgadp-ALF4-Bound Dccp:Dccp-R Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Mgadp-ALF4-Bound Dccp:Dccp-R Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg303
b:21.3
occ:1.00
|
F4
|
F:ALF304
|
1.9
|
25.9
|
1.0
|
|
O
|
F:HOH444
|
2.1
|
23.6
|
1.0
|
|
O2B
|
F:ADP302
|
2.1
|
23.3
|
1.0
|
|
O
|
F:HOH473
|
2.1
|
21.7
|
1.0
|
|
O
|
F:HOH432
|
2.2
|
24.0
|
1.0
|
|
O
|
F:HOH431
|
2.2
|
21.5
|
1.0
|
|
HZ3
|
F:LYS96
|
2.9
|
26.9
|
1.0
|
|
HZ1
|
F:LYS13
|
3.3
|
31.6
|
1.0
|
|
PB
|
F:ADP302
|
3.4
|
22.4
|
1.0
|
|
HZ3
|
F:LYS13
|
3.5
|
31.6
|
1.0
|
|
AL
|
F:ALF304
|
3.6
|
23.4
|
1.0
|
|
O1B
|
F:ADP302
|
3.6
|
23.4
|
1.0
|
|
NZ
|
F:LYS96
|
3.7
|
22.4
|
1.0
|
|
HZ1
|
F:LYS96
|
3.8
|
26.9
|
1.0
|
|
NZ
|
F:LYS13
|
3.9
|
26.3
|
1.0
|
|
O1A
|
F:ADP302
|
3.9
|
17.8
|
1.0
|
|
HA3
|
F:GLY91
|
3.9
|
26.8
|
1.0
|
|
F2
|
F:ALF304
|
4.0
|
20.5
|
1.0
|
|
OE1
|
F:GLU69
|
4.0
|
25.4
|
1.0
|
|
OD2
|
F:ASP6
|
4.0
|
20.4
|
1.0
|
|
F1
|
F:ALF304
|
4.1
|
25.7
|
1.0
|
|
O
|
F:HOH422
|
4.1
|
20.0
|
1.0
|
|
HZ2
|
F:LYS96
|
4.2
|
26.9
|
1.0
|
|
O3A
|
F:ADP302
|
4.2
|
21.8
|
1.0
|
|
OD2
|
F:ASP89
|
4.3
|
24.8
|
1.0
|
|
HE2
|
F:LYS96
|
4.3
|
30.9
|
1.0
|
|
OD1
|
F:ASP89
|
4.4
|
21.6
|
1.0
|
|
HZ2
|
F:LYS13
|
4.4
|
31.6
|
1.0
|
|
HA3
|
F:GLY8
|
4.5
|
33.6
|
1.0
|
|
OD1
|
F:ASP6
|
4.5
|
28.5
|
1.0
|
|
O3B
|
F:ADP302
|
4.5
|
23.4
|
1.0
|
|
O
|
F:HOH421
|
4.6
|
21.2
|
1.0
|
|
PA
|
F:ADP302
|
4.6
|
24.0
|
1.0
|
|
CE
|
F:LYS96
|
4.6
|
25.8
|
1.0
|
|
HB2
|
F:GLU69
|
4.6
|
39.1
|
1.0
|
|
HE2
|
F:LYS13
|
4.7
|
35.5
|
1.0
|
|
O
|
F:HOH464
|
4.7
|
24.6
|
1.0
|
|
CG
|
F:ASP6
|
4.7
|
25.5
|
1.0
|
|
HA2
|
F:GLY91
|
4.7
|
26.8
|
1.0
|
|
CA
|
F:GLY91
|
4.7
|
22.3
|
1.0
|
|
CD
|
F:GLU69
|
4.8
|
28.8
|
1.0
|
|
CG
|
F:ASP89
|
4.8
|
31.1
|
1.0
|
|
CE
|
F:LYS13
|
4.9
|
29.6
|
1.0
|
|
HE21
|
F:GLN73
|
5.0
|
35.2
|
1.0
|
|
HB3
|
F:ALA232
|
5.0
|
38.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7yzq
Go back to
Magnesium Binding Sites List in 7yzq
Magnesium binding site 3 out
of 4 in the Mgadp-ALF4-Bound Dccp:Dccp-R Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Mgadp-ALF4-Bound Dccp:Dccp-R Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg302
b:10.7
occ:1.00
|
F2
|
G:ALF303
|
1.9
|
13.0
|
1.0
|
|
O
|
G:HOH492
|
2.0
|
11.9
|
1.0
|
|
O
|
G:HOH499
|
2.0
|
9.3
|
1.0
|
|
O2B
|
G:ADP301
|
2.1
|
10.9
|
1.0
|
|
O
|
G:HOH471
|
2.1
|
13.1
|
1.0
|
|
O
|
G:HOH462
|
2.1
|
13.3
|
1.0
|
|
HZ3
|
G:LYS96
|
3.0
|
13.4
|
1.0
|
|
PB
|
G:ADP301
|
3.3
|
11.8
|
1.0
|
|
HZ1
|
G:LYS13
|
3.4
|
15.2
|
1.0
|
|
AL
|
G:ALF303
|
3.5
|
16.5
|
1.0
|
|
F4
|
G:ALF303
|
3.7
|
11.1
|
1.0
|
|
O1B
|
G:ADP301
|
3.7
|
13.5
|
1.0
|
|
HZ3
|
G:LYS13
|
3.7
|
15.2
|
1.0
|
|
OE1
|
G:GLU69
|
3.8
|
12.9
|
1.0
|
|
NZ
|
G:LYS96
|
3.9
|
11.2
|
1.0
|
|
NZ
|
G:LYS13
|
4.0
|
12.7
|
1.0
|
|
O2A
|
G:ADP301
|
4.0
|
10.2
|
1.0
|
|
O
|
G:HOH472
|
4.0
|
10.3
|
1.0
|
|
HZ1
|
G:LYS96
|
4.1
|
13.4
|
1.0
|
|
HA3
|
G:GLY91
|
4.1
|
15.1
|
1.0
|
|
F3
|
G:ALF303
|
4.2
|
14.7
|
1.0
|
|
O
|
G:HOH535
|
4.2
|
11.8
|
1.0
|
|
OD2
|
G:ASP6
|
4.2
|
14.7
|
1.0
|
|
HZ2
|
G:LYS96
|
4.2
|
13.4
|
1.0
|
|
OD2
|
G:ASP89
|
4.2
|
10.1
|
1.0
|
|
O3A
|
G:ADP301
|
4.3
|
12.7
|
1.0
|
|
HA3
|
G:GLY8
|
4.4
|
20.9
|
1.0
|
|
OD1
|
G:ASP89
|
4.4
|
11.5
|
1.0
|
|
O
|
G:HOH430
|
4.4
|
12.8
|
1.0
|
|
O3B
|
G:ADP301
|
4.4
|
13.6
|
1.0
|
|
HE2
|
G:LYS96
|
4.5
|
15.7
|
1.0
|
|
HZ2
|
G:LYS13
|
4.5
|
15.2
|
1.0
|
|
OD1
|
G:ASP6
|
4.6
|
17.6
|
1.0
|
|
HB2
|
G:GLU69
|
4.6
|
11.8
|
1.0
|
|
CD
|
G:GLU69
|
4.7
|
15.0
|
1.0
|
|
PA
|
G:ADP301
|
4.7
|
12.5
|
1.0
|
|
HE2
|
G:LYS13
|
4.7
|
11.2
|
1.0
|
|
CG
|
G:ASP89
|
4.8
|
11.6
|
1.0
|
|
CE
|
G:LYS96
|
4.8
|
13.1
|
1.0
|
|
HA2
|
G:GLY91
|
4.8
|
15.1
|
1.0
|
|
CG
|
G:ASP6
|
4.8
|
16.3
|
1.0
|
|
CA
|
G:GLY91
|
4.9
|
12.5
|
1.0
|
|
HA2
|
G:GLY8
|
4.9
|
20.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7yzq
Go back to
Magnesium Binding Sites List in 7yzq
Magnesium binding site 4 out
of 4 in the Mgadp-ALF4-Bound Dccp:Dccp-R Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Mgadp-ALF4-Bound Dccp:Dccp-R Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg302
b:25.3
occ:1.00
|
O1B
|
H:ADP301
|
2.0
|
23.2
|
1.0
|
|
F1
|
H:ALF303
|
2.0
|
30.4
|
1.0
|
|
O
|
H:HOH450
|
2.0
|
25.3
|
1.0
|
|
O
|
H:HOH500
|
2.1
|
26.9
|
1.0
|
|
O
|
H:HOH435
|
2.2
|
27.3
|
1.0
|
|
O
|
H:HOH458
|
2.3
|
20.2
|
1.0
|
|
HZ3
|
H:LYS96
|
2.9
|
31.1
|
1.0
|
|
HZ1
|
H:LYS13
|
3.1
|
36.3
|
1.0
|
|
PB
|
H:ADP301
|
3.2
|
27.3
|
1.0
|
|
O3B
|
H:ADP301
|
3.4
|
26.3
|
1.0
|
|
HZ3
|
H:LYS13
|
3.5
|
36.3
|
1.0
|
|
AL
|
H:ALF303
|
3.6
|
29.5
|
1.0
|
|
O2A
|
H:ADP301
|
3.6
|
27.6
|
1.0
|
|
NZ
|
H:LYS13
|
3.7
|
30.3
|
1.0
|
|
NZ
|
H:LYS96
|
3.7
|
25.9
|
1.0
|
|
HZ1
|
H:LYS96
|
3.8
|
31.1
|
1.0
|
|
HA3
|
H:GLY91
|
3.8
|
26.7
|
1.0
|
|
F3
|
H:ALF303
|
3.9
|
21.9
|
1.0
|
|
O
|
H:HOH426
|
4.0
|
20.4
|
1.0
|
|
OE1
|
H:GLU69
|
4.1
|
26.1
|
1.0
|
|
F4
|
H:ALF303
|
4.1
|
26.2
|
1.0
|
|
OD2
|
H:ASP6
|
4.1
|
27.8
|
1.0
|
|
O3A
|
H:ADP301
|
4.1
|
24.5
|
1.0
|
|
HZ2
|
H:LYS96
|
4.2
|
31.1
|
1.0
|
|
HZ2
|
H:LYS13
|
4.2
|
36.3
|
1.0
|
|
O2B
|
H:ADP301
|
4.3
|
25.8
|
1.0
|
|
OD1
|
H:ASP89
|
4.4
|
28.0
|
1.0
|
|
OD2
|
H:ASP89
|
4.4
|
22.5
|
1.0
|
|
PA
|
H:ADP301
|
4.4
|
23.0
|
1.0
|
|
HE2
|
H:LYS96
|
4.5
|
30.0
|
1.0
|
|
HA2
|
H:GLY91
|
4.5
|
26.7
|
1.0
|
|
O
|
H:HOH424
|
4.6
|
25.5
|
1.0
|
|
CA
|
H:GLY91
|
4.6
|
22.2
|
1.0
|
|
OD1
|
H:ASP6
|
4.6
|
37.9
|
1.0
|
|
HA3
|
H:GLY8
|
4.6
|
42.0
|
1.0
|
|
O
|
H:HOH478
|
4.6
|
25.2
|
1.0
|
|
HE2
|
H:LYS13
|
4.6
|
37.4
|
1.0
|
|
CE
|
H:LYS96
|
4.7
|
25.0
|
1.0
|
|
CG
|
H:ASP6
|
4.8
|
32.7
|
1.0
|
|
CE
|
H:LYS13
|
4.8
|
31.1
|
1.0
|
|
HB2
|
H:GLU69
|
4.8
|
41.2
|
1.0
|
|
CG
|
H:ASP89
|
4.9
|
29.6
|
1.0
|
|
CD
|
H:GLU69
|
5.0
|
26.4
|
1.0
|
|
HA2
|
H:GLY8
|
5.0
|
42.0
|
1.0
|
|
Reference:
J.H.Jeoung,
S.Nicklisch,
H.Dobbek.
Structural Basis For Coupled Atp-Driven Electron Transfer in the Double-Cubane Cluster Protein. Proc.Natl.Acad.Sci.Usa V. 119 76119 2022.
ISSN: ESSN 1091-6490
PubMed: 35905315
DOI: 10.1073/PNAS.2203576119
Page generated: Thu Oct 3 16:10:59 2024
|
