Magnesium in PDB 7yzm: Mgadpnp-Bound Dccp:Dccp-R Complex
Protein crystallography data
The structure of Mgadpnp-Bound Dccp:Dccp-R Complex, PDB code: 7yzm
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)
|
26.72 /
1.82
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.12,
81.673,
121.377,
100.61,
97.13,
90
|
|
R / Rfree (%)
|
16.4 /
20.1
|
Other elements in 7yzm:
The structure of Mgadpnp-Bound Dccp:Dccp-R Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Mgadpnp-Bound Dccp:Dccp-R Complex
(pdb code 7yzm). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Mgadpnp-Bound Dccp:Dccp-R Complex, PDB code: 7yzm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7yzm
Go back to
Magnesium Binding Sites List in 7yzm
Magnesium binding site 1 out
of 4 in the Mgadpnp-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 Mgadpnp-Bound Dccp:Dccp-R Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg301
b:11.2
occ:1.00
|
O2B
|
G:ANP302
|
2.0
|
11.3
|
1.0
|
|
O3G
|
G:ANP302
|
2.0
|
9.5
|
1.0
|
|
O
|
G:HOH464
|
2.1
|
11.2
|
1.0
|
|
O
|
G:HOH454
|
2.1
|
13.2
|
1.0
|
|
O
|
G:HOH412
|
2.2
|
12.1
|
1.0
|
|
O
|
G:HOH444
|
2.2
|
10.5
|
1.0
|
|
HZ1
|
G:LYS96
|
3.1
|
15.4
|
1.0
|
|
PB
|
G:ANP302
|
3.3
|
11.1
|
1.0
|
|
PG
|
G:ANP302
|
3.3
|
13.4
|
1.0
|
|
HZ3
|
G:LYS13
|
3.4
|
16.7
|
1.0
|
|
N3B
|
G:ANP302
|
3.7
|
12.5
|
1.0
|
|
HZ3
|
G:LYS96
|
3.8
|
15.4
|
1.0
|
|
NZ
|
G:LYS96
|
3.8
|
12.8
|
1.0
|
|
OE1
|
G:GLU69
|
3.8
|
21.2
|
1.0
|
|
HZ1
|
G:LYS13
|
3.8
|
16.7
|
1.0
|
|
O1G
|
G:ANP302
|
4.0
|
13.6
|
1.0
|
|
O2A
|
G:ANP302
|
4.0
|
11.4
|
1.0
|
|
NZ
|
G:LYS13
|
4.0
|
13.9
|
1.0
|
|
HA3
|
G:GLY91
|
4.0
|
13.0
|
1.0
|
|
O3A
|
G:ANP302
|
4.1
|
12.1
|
1.0
|
|
HA3
|
G:GLY8
|
4.1
|
16.4
|
1.0
|
|
O
|
G:HOH422
|
4.1
|
14.1
|
1.0
|
|
O
|
G:HOH472
|
4.1
|
14.1
|
1.0
|
|
OD2
|
G:ASP6
|
4.2
|
15.5
|
1.0
|
|
HNB1
|
G:ANP302
|
4.3
|
15.0
|
1.0
|
|
HE2
|
G:LYS96
|
4.3
|
21.8
|
1.0
|
|
OD1
|
G:ASP6
|
4.4
|
14.3
|
1.0
|
|
HZ2
|
G:LYS13
|
4.4
|
16.7
|
1.0
|
|
HZ2
|
G:LYS96
|
4.4
|
15.4
|
1.0
|
|
HA2
|
G:GLY8
|
4.4
|
16.4
|
1.0
|
|
O1B
|
G:ANP302
|
4.5
|
12.6
|
1.0
|
|
OD2
|
G:ASP89
|
4.5
|
14.8
|
1.0
|
|
O2G
|
G:ANP302
|
4.5
|
12.2
|
1.0
|
|
OD1
|
G:ASP89
|
4.5
|
13.3
|
1.0
|
|
PA
|
G:ANP302
|
4.6
|
10.1
|
1.0
|
|
CE
|
G:LYS96
|
4.6
|
18.1
|
1.0
|
|
CG
|
G:ASP6
|
4.7
|
16.4
|
1.0
|
|
CA
|
G:GLY8
|
4.7
|
13.6
|
1.0
|
|
CD
|
G:GLU69
|
4.8
|
22.0
|
1.0
|
|
HA2
|
G:GLY91
|
4.8
|
13.0
|
1.0
|
|
CA
|
G:GLY91
|
4.9
|
10.8
|
1.0
|
|
H
|
G:SER9
|
4.9
|
17.4
|
1.0
|
|
HE3
|
G:LYS96
|
4.9
|
21.8
|
1.0
|
|
CG
|
G:ASP89
|
5.0
|
10.9
|
1.0
|
|
HB2
|
G:GLU69
|
5.0
|
16.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7yzm
Go back to
Magnesium Binding Sites List in 7yzm
Magnesium binding site 2 out
of 4 in the Mgadpnp-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 Mgadpnp-Bound Dccp:Dccp-R Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg302
b:15.8
occ:1.00
|
O1B
|
H:ANP303
|
1.9
|
17.1
|
1.0
|
|
O3G
|
H:ANP303
|
2.0
|
18.7
|
1.0
|
|
O
|
H:HOH445
|
2.0
|
15.8
|
1.0
|
|
O
|
H:HOH483
|
2.1
|
22.5
|
1.0
|
|
O
|
H:HOH440
|
2.1
|
22.2
|
1.0
|
|
O
|
H:HOH420
|
2.2
|
17.9
|
1.0
|
|
HZ1
|
H:LYS96
|
3.1
|
21.9
|
1.0
|
|
PB
|
H:ANP303
|
3.2
|
18.8
|
1.0
|
|
PG
|
H:ANP303
|
3.3
|
18.0
|
1.0
|
|
HZ3
|
H:LYS13
|
3.3
|
31.3
|
1.0
|
|
HZ1
|
H:LYS13
|
3.6
|
31.3
|
1.0
|
|
HZ3
|
H:LYS96
|
3.6
|
21.9
|
1.0
|
|
N3B
|
H:ANP303
|
3.7
|
19.6
|
1.0
|
|
NZ
|
H:LYS96
|
3.8
|
18.2
|
1.0
|
|
OE1
|
H:GLU69
|
3.8
|
32.1
|
1.0
|
|
NZ
|
H:LYS13
|
3.9
|
26.1
|
1.0
|
|
HA3
|
H:GLY91
|
3.9
|
20.7
|
1.0
|
|
O2A
|
H:ANP303
|
3.9
|
13.6
|
1.0
|
|
O3A
|
H:ANP303
|
3.9
|
18.0
|
1.0
|
|
O2G
|
H:ANP303
|
4.0
|
17.1
|
1.0
|
|
HZ2
|
H:LYS13
|
4.1
|
31.3
|
1.0
|
|
HA3
|
H:GLY8
|
4.1
|
27.7
|
1.0
|
|
O
|
H:HOH434
|
4.1
|
19.9
|
1.0
|
|
HNB1
|
H:ANP303
|
4.2
|
23.5
|
1.0
|
|
OD2
|
H:ASP6
|
4.2
|
22.3
|
1.0
|
|
O
|
H:HOH437
|
4.2
|
22.7
|
1.0
|
|
O2B
|
H:ANP303
|
4.4
|
22.2
|
1.0
|
|
HZ2
|
H:LYS96
|
4.4
|
21.9
|
1.0
|
|
O1G
|
H:ANP303
|
4.4
|
14.8
|
1.0
|
|
OD1
|
H:ASP6
|
4.4
|
23.4
|
1.0
|
|
HE2
|
H:LYS96
|
4.5
|
24.3
|
1.0
|
|
PA
|
H:ANP303
|
4.5
|
18.9
|
1.0
|
|
OD2
|
H:ASP89
|
4.5
|
20.5
|
1.0
|
|
OD1
|
H:ASP89
|
4.6
|
19.7
|
1.0
|
|
HA2
|
H:GLY8
|
4.6
|
27.7
|
1.0
|
|
HA2
|
H:GLY91
|
4.7
|
20.7
|
1.0
|
|
CA
|
H:GLY91
|
4.7
|
17.2
|
1.0
|
|
CE
|
H:LYS96
|
4.7
|
20.3
|
1.0
|
|
CG
|
H:ASP6
|
4.8
|
32.5
|
1.0
|
|
CA
|
H:GLY8
|
4.9
|
23.1
|
1.0
|
|
CD
|
H:GLU69
|
4.9
|
36.5
|
1.0
|
|
H
|
H:GLY92
|
5.0
|
21.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7yzm
Go back to
Magnesium Binding Sites List in 7yzm
Magnesium binding site 3 out
of 4 in the Mgadpnp-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 Mgadpnp-Bound Dccp:Dccp-R Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg302
b:17.5
occ:1.00
|
O1B
|
E:ANP303
|
2.0
|
18.6
|
1.0
|
|
O2G
|
E:ANP303
|
2.0
|
19.2
|
1.0
|
|
O
|
E:HOH483
|
2.1
|
22.3
|
1.0
|
|
O
|
E:HOH419
|
2.1
|
17.6
|
1.0
|
|
O
|
E:HOH463
|
2.1
|
19.2
|
1.0
|
|
O
|
E:HOH422
|
2.1
|
20.6
|
1.0
|
|
HZ3
|
E:LYS96
|
3.1
|
26.2
|
1.0
|
|
PB
|
E:ANP303
|
3.3
|
18.6
|
1.0
|
|
PG
|
E:ANP303
|
3.3
|
19.4
|
1.0
|
|
HZ2
|
E:LYS13
|
3.5
|
32.5
|
1.0
|
|
HZ2
|
E:LYS96
|
3.5
|
26.2
|
1.0
|
|
N3B
|
E:ANP303
|
3.7
|
17.5
|
1.0
|
|
NZ
|
E:LYS96
|
3.8
|
21.8
|
1.0
|
|
HZ3
|
E:LYS13
|
3.8
|
32.5
|
1.0
|
|
O2A
|
E:ANP303
|
3.8
|
16.5
|
1.0
|
|
OE1
|
E:GLU69
|
3.9
|
33.1
|
1.0
|
|
O1G
|
E:ANP303
|
4.0
|
18.7
|
1.0
|
|
HA3
|
E:GLY91
|
4.0
|
21.7
|
1.0
|
|
O3A
|
E:ANP303
|
4.0
|
18.5
|
1.0
|
|
O
|
E:HOH441
|
4.0
|
23.2
|
1.0
|
|
NZ
|
E:LYS13
|
4.1
|
27.1
|
1.0
|
|
HNB1
|
E:ANP303
|
4.2
|
21.0
|
1.0
|
|
HA3
|
E:GLY8
|
4.2
|
27.9
|
1.0
|
|
OD2
|
E:ASP6
|
4.2
|
26.6
|
1.0
|
|
O
|
E:HOH431
|
4.3
|
23.5
|
1.0
|
|
HZ1
|
E:LYS96
|
4.4
|
26.2
|
1.0
|
|
OD2
|
E:ASP89
|
4.4
|
26.6
|
1.0
|
|
HE2
|
E:LYS96
|
4.4
|
26.2
|
1.0
|
|
O2B
|
E:ANP303
|
4.4
|
21.4
|
1.0
|
|
O3G
|
E:ANP303
|
4.5
|
20.1
|
1.0
|
|
OD1
|
E:ASP89
|
4.5
|
22.3
|
1.0
|
|
PA
|
E:ANP303
|
4.5
|
18.1
|
1.0
|
|
HZ1
|
E:LYS13
|
4.5
|
32.5
|
1.0
|
|
OD1
|
E:ASP6
|
4.5
|
27.6
|
1.0
|
|
HA2
|
E:GLY8
|
4.6
|
27.9
|
1.0
|
|
CE
|
E:LYS96
|
4.7
|
21.8
|
1.0
|
|
HA2
|
E:GLY91
|
4.7
|
21.7
|
1.0
|
|
CA
|
E:GLY91
|
4.8
|
18.1
|
1.0
|
|
CG
|
E:ASP6
|
4.8
|
32.3
|
1.0
|
|
CD
|
E:GLU69
|
4.9
|
34.4
|
1.0
|
|
CA
|
E:GLY8
|
4.9
|
23.2
|
1.0
|
|
CG
|
E:ASP89
|
4.9
|
22.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7yzm
Go back to
Magnesium Binding Sites List in 7yzm
Magnesium binding site 4 out
of 4 in the Mgadpnp-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 Mgadpnp-Bound Dccp:Dccp-R Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg302
b:10.4
occ:1.00
|
O2B
|
F:ANP303
|
2.0
|
10.2
|
1.0
|
|
O
|
F:HOH495
|
2.0
|
11.2
|
1.0
|
|
O1G
|
F:ANP303
|
2.1
|
11.2
|
1.0
|
|
O
|
F:HOH463
|
2.1
|
15.7
|
1.0
|
|
O
|
F:HOH415
|
2.1
|
14.2
|
1.0
|
|
O
|
F:HOH442
|
2.2
|
10.8
|
1.0
|
|
HZ1
|
F:LYS96
|
3.2
|
16.1
|
1.0
|
|
PB
|
F:ANP303
|
3.3
|
10.3
|
1.0
|
|
PG
|
F:ANP303
|
3.3
|
12.8
|
1.0
|
|
HZ2
|
F:LYS13
|
3.4
|
19.4
|
1.0
|
|
HZ3
|
F:LYS96
|
3.7
|
16.1
|
1.0
|
|
N3B
|
F:ANP303
|
3.7
|
8.5
|
1.0
|
|
NZ
|
F:LYS96
|
3.8
|
13.4
|
1.0
|
|
OE1
|
F:GLU69
|
3.9
|
19.6
|
1.0
|
|
O2A
|
F:ANP303
|
3.9
|
12.6
|
1.0
|
|
HZ3
|
F:LYS13
|
4.0
|
19.4
|
1.0
|
|
O3A
|
F:ANP303
|
4.0
|
10.7
|
1.0
|
|
O2G
|
F:ANP303
|
4.1
|
13.0
|
1.0
|
|
HA3
|
F:GLY91
|
4.1
|
13.1
|
1.0
|
|
NZ
|
F:LYS13
|
4.1
|
16.1
|
1.0
|
|
O
|
F:HOH469
|
4.1
|
12.0
|
1.0
|
|
O
|
F:HOH420
|
4.1
|
12.1
|
1.0
|
|
HA3
|
F:GLY8
|
4.1
|
16.2
|
1.0
|
|
HNB1
|
F:ANP303
|
4.1
|
10.2
|
1.0
|
|
OD2
|
F:ASP6
|
4.2
|
15.7
|
1.0
|
|
OD2
|
F:ASP89
|
4.4
|
14.1
|
1.0
|
|
OD1
|
F:ASP6
|
4.4
|
13.2
|
1.0
|
|
HE2
|
F:LYS96
|
4.4
|
19.3
|
1.0
|
|
HZ1
|
F:LYS13
|
4.4
|
19.4
|
1.0
|
|
HZ2
|
F:LYS96
|
4.4
|
16.1
|
1.0
|
|
HA2
|
F:GLY8
|
4.5
|
16.2
|
1.0
|
|
O1B
|
F:ANP303
|
4.5
|
12.4
|
1.0
|
|
O3G
|
F:ANP303
|
4.5
|
13.3
|
1.0
|
|
OD1
|
F:ASP89
|
4.5
|
12.6
|
1.0
|
|
PA
|
F:ANP303
|
4.6
|
10.8
|
1.0
|
|
CG
|
F:ASP6
|
4.7
|
16.4
|
1.0
|
|
CE
|
F:LYS96
|
4.7
|
16.1
|
1.0
|
|
HA2
|
F:GLY91
|
4.8
|
13.1
|
1.0
|
|
CA
|
F:GLY8
|
4.8
|
13.5
|
1.0
|
|
CD
|
F:GLU69
|
4.8
|
22.6
|
1.0
|
|
CA
|
F:GLY91
|
4.9
|
10.9
|
1.0
|
|
CG
|
F:ASP89
|
4.9
|
11.7
|
1.0
|
|
H
|
F:SER9
|
4.9
|
13.7
|
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: Fri Apr 7 03:38:00 2023
|
