Magnesium in PDB 4g73: Crystal Structure of Ndh with Nadh and Quinone
Enzymatic activity of Crystal Structure of Ndh with Nadh and Quinone
All present enzymatic activity of Crystal Structure of Ndh with Nadh and Quinone:
1.6.5.9;
Protein crystallography data
The structure of Crystal Structure of Ndh with Nadh and Quinone, PDB code: 4g73
was solved by
W.Li,
Y.Feng,
J.Ge,
M.Yang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
38.36 /
2.52
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
127.406,
230.186,
112.921,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18.9 /
21.7
|
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of Ndh with Nadh and Quinone
(pdb code 4g73). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the
Crystal Structure of Ndh with Nadh and Quinone, PDB code: 4g73:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 11 in 4g73
Go back to
Magnesium Binding Sites List in 4g73
Magnesium binding site 1 out
of 11 in the Crystal Structure of Ndh with Nadh and Quinone
 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 Ndh with Nadh and Quinone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:70.5
occ:1.00
|
O
|
A:LYS53
|
2.7
|
48.1
|
1.0
|
|
OD1
|
A:ASN55
|
3.2
|
56.7
|
1.0
|
|
O
|
A:SER51
|
3.2
|
81.9
|
1.0
|
|
OE1
|
A:GLN49
|
3.2
|
98.9
|
1.0
|
|
O
|
A:PRO48
|
3.3
|
76.5
|
1.0
|
|
CG
|
A:ASN55
|
3.7
|
55.7
|
1.0
|
|
ND2
|
A:ASN55
|
3.7
|
69.2
|
1.0
|
|
CD
|
A:GLN49
|
3.8
|
93.1
|
1.0
|
|
C
|
A:LYS53
|
3.9
|
49.7
|
1.0
|
|
NE2
|
A:GLN49
|
4.0
|
76.4
|
1.0
|
|
C
|
A:SER51
|
4.1
|
74.5
|
1.0
|
|
O
|
A:HOH827
|
4.2
|
62.2
|
1.0
|
|
OD2
|
A:ASP170
|
4.2
|
49.6
|
1.0
|
|
N
|
A:ASN55
|
4.4
|
37.8
|
1.0
|
|
CA
|
A:GLN49
|
4.4
|
90.0
|
1.0
|
|
C
|
A:PRO48
|
4.4
|
85.5
|
1.0
|
|
OG
|
A:SER51
|
4.5
|
81.3
|
1.0
|
|
N
|
A:LYS53
|
4.6
|
70.3
|
1.0
|
|
CA
|
A:PRO54
|
4.6
|
46.5
|
1.0
|
|
C
|
A:PRO54
|
4.7
|
49.5
|
1.0
|
|
CA
|
A:ASP52
|
4.7
|
75.5
|
1.0
|
|
N
|
A:PRO54
|
4.7
|
42.5
|
1.0
|
|
C
|
A:ASP52
|
4.7
|
75.0
|
1.0
|
|
N
|
A:ASP52
|
4.8
|
69.8
|
1.0
|
|
CB
|
A:ASN55
|
4.9
|
42.1
|
1.0
|
|
CA
|
A:LYS53
|
4.9
|
52.6
|
1.0
|
|
N
|
A:GLN49
|
4.9
|
91.8
|
1.0
|
|
N
|
A:SER51
|
4.9
|
85.0
|
1.0
|
|
CA
|
A:SER51
|
5.0
|
78.7
|
1.0
|
|
Magnesium binding site 2 out
of 11 in 4g73
Go back to
Magnesium Binding Sites List in 4g73
Magnesium binding site 2 out
of 11 in the Crystal Structure of Ndh with Nadh and Quinone
 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 Ndh with Nadh and Quinone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg606
b:38.2
occ:1.00
|
O1P
|
A:FAD605
|
2.6
|
26.7
|
1.0
|
|
O
|
A:ILE381
|
2.8
|
33.0
|
1.0
|
|
N
|
A:ASN384
|
2.9
|
32.5
|
1.0
|
|
N
|
A:GLY177
|
2.9
|
27.8
|
1.0
|
|
ND2
|
A:ASN384
|
3.0
|
29.6
|
1.0
|
|
CG
|
A:ASN384
|
3.1
|
29.4
|
1.0
|
|
CA
|
A:GLY177
|
3.2
|
28.2
|
1.0
|
|
N
|
A:ASP383
|
3.3
|
30.2
|
1.0
|
|
CB
|
A:ASN384
|
3.4
|
29.2
|
1.0
|
|
CA
|
A:ALA175
|
3.4
|
26.2
|
1.0
|
|
C
|
A:ALA175
|
3.4
|
29.3
|
1.0
|
|
C
|
A:GLY382
|
3.5
|
36.4
|
1.0
|
|
N
|
A:VAL176
|
3.6
|
23.6
|
1.0
|
|
CA
|
A:ASN384
|
3.6
|
33.4
|
1.0
|
|
CA
|
A:GLY382
|
3.7
|
28.1
|
1.0
|
|
OD1
|
A:ASN384
|
3.8
|
26.0
|
1.0
|
|
C
|
A:ASP383
|
3.8
|
37.4
|
1.0
|
|
P
|
A:FAD605
|
3.8
|
26.5
|
1.0
|
|
C
|
A:ILE381
|
3.9
|
35.7
|
1.0
|
|
O
|
A:ALA175
|
4.0
|
25.1
|
1.0
|
|
CA
|
A:ASP383
|
4.0
|
30.1
|
1.0
|
|
C
|
A:VAL176
|
4.1
|
36.4
|
1.0
|
|
O
|
A:GLY382
|
4.1
|
32.9
|
1.0
|
|
CB
|
A:ALA175
|
4.1
|
23.1
|
1.0
|
|
C
|
A:GLY177
|
4.2
|
33.2
|
1.0
|
|
N
|
A:GLY382
|
4.3
|
35.6
|
1.0
|
|
O
|
A:GLY177
|
4.3
|
34.5
|
1.0
|
|
O2P
|
A:FAD605
|
4.3
|
26.4
|
1.0
|
|
O3P
|
A:FAD605
|
4.3
|
35.7
|
1.0
|
|
O
|
A:SER174
|
4.4
|
32.2
|
1.0
|
|
CA
|
A:VAL176
|
4.5
|
29.3
|
1.0
|
|
N
|
A:ALA175
|
4.5
|
35.9
|
1.0
|
|
CB
|
A:ASP383
|
4.6
|
35.5
|
1.0
|
|
C
|
A:ASN384
|
4.6
|
38.5
|
1.0
|
|
N
|
A:ALA385
|
4.7
|
33.7
|
1.0
|
|
C
|
A:SER174
|
4.9
|
29.5
|
1.0
|
|
O
|
A:ASP383
|
5.0
|
37.7
|
1.0
|
|
Magnesium binding site 3 out
of 11 in 4g73
Go back to
Magnesium Binding Sites List in 4g73
Magnesium binding site 3 out
of 11 in the Crystal Structure of Ndh with Nadh and Quinone
 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 Ndh with Nadh and Quinone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:42.3
occ:1.00
|
O2P
|
A:FAD605
|
2.6
|
26.4
|
1.0
|
|
O
|
A:ALA175
|
2.7
|
25.1
|
1.0
|
|
N
|
A:ALA65
|
2.9
|
29.0
|
1.0
|
|
N
|
A:GLY62
|
3.0
|
27.2
|
1.0
|
|
CB
|
A:ALA65
|
3.2
|
24.3
|
1.0
|
|
CB
|
A:ALA175
|
3.3
|
23.1
|
1.0
|
|
C
|
A:GLY62
|
3.3
|
24.8
|
1.0
|
|
CA
|
A:GLY62
|
3.4
|
23.4
|
1.0
|
|
O5B
|
A:FAD605
|
3.4
|
32.7
|
1.0
|
|
N
|
A:GLY64
|
3.5
|
26.7
|
1.0
|
|
O
|
A:GLY62
|
3.6
|
26.1
|
1.0
|
|
CA
|
A:ALA65
|
3.7
|
30.1
|
1.0
|
|
C5B
|
A:FAD605
|
3.7
|
26.6
|
1.0
|
|
C
|
A:ALA175
|
3.8
|
29.3
|
1.0
|
|
N
|
A:TRP63
|
3.8
|
28.5
|
1.0
|
|
C4B
|
A:FAD605
|
3.9
|
30.9
|
1.0
|
|
C
|
A:GLY64
|
3.9
|
32.1
|
1.0
|
|
CA
|
A:GLY64
|
3.9
|
29.6
|
1.0
|
|
P
|
A:FAD605
|
4.0
|
26.5
|
1.0
|
|
N
|
A:SER61
|
4.1
|
31.6
|
1.0
|
|
CA
|
A:ALA175
|
4.2
|
26.2
|
1.0
|
|
C
|
A:GLY60
|
4.2
|
30.0
|
1.0
|
|
C
|
A:SER61
|
4.2
|
29.7
|
1.0
|
|
C
|
A:TRP63
|
4.3
|
29.5
|
1.0
|
|
O3P
|
A:FAD605
|
4.3
|
35.7
|
1.0
|
|
CA
|
A:GLY60
|
4.3
|
26.0
|
1.0
|
|
PA
|
A:FAD605
|
4.4
|
25.9
|
1.0
|
|
O4B
|
A:FAD605
|
4.4
|
27.0
|
1.0
|
|
O
|
A:LEU59
|
4.5
|
24.5
|
1.0
|
|
CA
|
A:SER61
|
4.6
|
22.5
|
1.0
|
|
O2A
|
A:FAD605
|
4.6
|
28.6
|
1.0
|
|
CA
|
A:TRP63
|
4.6
|
33.4
|
1.0
|
|
O
|
A:GLY60
|
4.7
|
26.4
|
1.0
|
|
N
|
A:ILE66
|
4.8
|
30.1
|
1.0
|
|
C
|
A:ALA65
|
4.8
|
27.8
|
1.0
|
|
O1P
|
A:FAD605
|
4.8
|
26.7
|
1.0
|
|
N
|
A:VAL176
|
5.0
|
23.6
|
1.0
|
|
Magnesium binding site 4 out
of 11 in 4g73
Go back to
Magnesium Binding Sites List in 4g73
Magnesium binding site 4 out
of 11 in the Crystal Structure of Ndh with Nadh and Quinone
 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 Ndh with Nadh and Quinone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg608
b:41.3
occ:1.00
|
O
|
A:HOH702
|
2.8
|
28.2
|
1.0
|
|
O
|
A:LEU89
|
2.9
|
23.6
|
1.0
|
|
NH2
|
A:ARG85
|
3.0
|
21.5
|
1.0
|
|
O2A
|
A:FAD605
|
3.2
|
28.6
|
1.0
|
|
CA
|
A:GLY62
|
3.3
|
23.4
|
1.0
|
|
N
|
A:LEU89
|
3.7
|
25.1
|
1.0
|
|
N
|
A:TRP63
|
3.7
|
28.5
|
1.0
|
|
C
|
A:LEU89
|
3.8
|
31.5
|
1.0
|
|
CB
|
A:LEU89
|
3.8
|
22.0
|
1.0
|
|
CE1
|
A:PHE88
|
3.9
|
27.5
|
1.0
|
|
CD1
|
A:TRP63
|
3.9
|
26.3
|
1.0
|
|
CG2
|
A:THR91
|
3.9
|
28.2
|
1.0
|
|
C
|
A:GLY62
|
3.9
|
24.8
|
1.0
|
|
CZ
|
A:ARG85
|
3.9
|
26.0
|
1.0
|
|
CA
|
A:LEU89
|
4.0
|
24.7
|
1.0
|
|
NH1
|
A:ARG85
|
4.0
|
27.2
|
1.0
|
|
CD1
|
A:PHE88
|
4.0
|
24.1
|
1.0
|
|
PA
|
A:FAD605
|
4.0
|
25.9
|
1.0
|
|
O5B
|
A:FAD605
|
4.2
|
32.7
|
1.0
|
|
NE1
|
A:TRP63
|
4.3
|
23.0
|
1.0
|
|
O1A
|
A:FAD605
|
4.3
|
24.4
|
1.0
|
|
O4'
|
A:FAD605
|
4.4
|
32.8
|
1.0
|
|
CG
|
A:LEU89
|
4.5
|
23.4
|
1.0
|
|
N
|
A:GLY62
|
4.6
|
27.2
|
1.0
|
|
CG
|
A:TRP63
|
4.6
|
31.4
|
1.0
|
|
O
|
A:SER61
|
4.7
|
28.6
|
1.0
|
|
CZ
|
A:PHE88
|
4.7
|
22.7
|
1.0
|
|
CA
|
A:TRP63
|
4.8
|
33.4
|
1.0
|
|
C
|
A:PHE88
|
4.9
|
24.4
|
1.0
|
|
N
|
A:THR91
|
4.9
|
23.5
|
1.0
|
|
CG
|
A:PHE88
|
4.9
|
23.0
|
1.0
|
|
O
|
A:GLY62
|
4.9
|
26.1
|
1.0
|
|
CD2
|
A:LEU89
|
5.0
|
22.5
|
1.0
|
|
Magnesium binding site 5 out
of 11 in 4g73
Go back to
Magnesium Binding Sites List in 4g73
Magnesium binding site 5 out
of 11 in the Crystal Structure of Ndh with Nadh and Quinone
 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 Ndh with Nadh and Quinone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg609
b:51.2
occ:1.00
|
N
|
A:ALA178
|
2.9
|
28.5
|
1.0
|
|
NZ
|
A:LYS196
|
3.0
|
31.7
|
1.0
|
|
O1A
|
A:FAD605
|
3.1
|
24.4
|
1.0
|
|
OD2
|
A:ASP383
|
3.2
|
42.3
|
1.0
|
|
O
|
A:ALA178
|
3.3
|
33.7
|
1.0
|
|
CE
|
A:LYS196
|
3.5
|
32.7
|
1.0
|
|
O
|
A:HOH727
|
3.6
|
27.3
|
1.0
|
|
O3P
|
A:FAD605
|
3.7
|
35.7
|
1.0
|
|
CA
|
A:GLY177
|
3.7
|
28.2
|
1.0
|
|
C
|
A:GLY177
|
3.7
|
33.2
|
1.0
|
|
CA
|
A:ALA178
|
3.8
|
30.3
|
1.0
|
|
C
|
A:ALA178
|
3.9
|
30.6
|
1.0
|
|
PA
|
A:FAD605
|
4.0
|
25.9
|
1.0
|
|
CG
|
A:ASP383
|
4.0
|
40.6
|
1.0
|
|
CB
|
A:ALA178
|
4.2
|
26.7
|
1.0
|
|
CB
|
A:ASP383
|
4.2
|
35.5
|
1.0
|
|
O
|
A:HOH760
|
4.3
|
30.4
|
1.0
|
|
C5'
|
A:FAD605
|
4.5
|
27.9
|
1.0
|
|
O4'
|
A:FAD605
|
4.6
|
32.8
|
1.0
|
|
O
|
A:HOH751
|
4.7
|
31.2
|
1.0
|
|
NH1
|
A:ARG344
|
4.8
|
27.4
|
1.0
|
|
C3'
|
A:FAD605
|
4.9
|
33.4
|
1.0
|
|
ND2
|
A:ASN341
|
4.9
|
51.1
|
1.0
|
|
C4'
|
A:FAD605
|
4.9
|
32.2
|
1.0
|
|
P
|
A:FAD605
|
4.9
|
26.5
|
1.0
|
|
O
|
A:GLY177
|
4.9
|
34.5
|
1.0
|
|
CD
|
A:LYS196
|
5.0
|
29.3
|
1.0
|
|
Magnesium binding site 6 out
of 11 in 4g73
Go back to
Magnesium Binding Sites List in 4g73
Magnesium binding site 6 out
of 11 in the Crystal Structure of Ndh with Nadh and Quinone
 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 Ndh with Nadh and Quinone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:23.3
occ:1.00
|
O
|
B:GLY333
|
2.7
|
32.3
|
1.0
|
|
O
|
B:HOH720
|
3.0
|
27.4
|
1.0
|
|
O
|
B:HOH847
|
3.0
|
45.4
|
1.0
|
|
O
|
B:HOH716
|
3.2
|
33.0
|
1.0
|
|
O
|
B:HOH714
|
3.3
|
36.8
|
1.0
|
|
C
|
B:GLY333
|
3.8
|
35.1
|
1.0
|
|
O
|
B:HOH785
|
4.0
|
46.1
|
1.0
|
|
CG2
|
B:THR207
|
4.2
|
30.6
|
1.0
|
|
CE1
|
B:TYR332
|
4.4
|
30.4
|
1.0
|
|
O
|
B:GLU311
|
4.5
|
44.9
|
1.0
|
|
O
|
B:TYR191
|
4.6
|
30.0
|
1.0
|
|
N
|
B:THR334
|
4.7
|
25.7
|
1.0
|
|
CA
|
B:GLY333
|
4.7
|
27.8
|
1.0
|
|
CA
|
B:THR334
|
4.7
|
26.3
|
1.0
|
|
ND2
|
B:ASN211
|
4.8
|
22.1
|
1.0
|
|
CD1
|
B:TYR332
|
4.9
|
24.0
|
1.0
|
|
Magnesium binding site 7 out
of 11 in 4g73
Go back to
Magnesium Binding Sites List in 4g73
Magnesium binding site 7 out
of 11 in the Crystal Structure of Ndh with Nadh and Quinone
 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 Ndh with Nadh and Quinone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:60.1
occ:1.00
|
O
|
B:LYS118
|
2.9
|
49.4
|
1.0
|
|
O
|
B:LEU116
|
2.9
|
45.6
|
1.0
|
|
O
|
B:HOH721
|
3.1
|
35.0
|
1.0
|
|
C
|
B:LEU116
|
3.9
|
41.9
|
1.0
|
|
C
|
B:LYS118
|
4.0
|
51.6
|
1.0
|
|
CA
|
B:LEU116
|
4.6
|
38.1
|
1.0
|
|
N
|
B:LYS118
|
4.6
|
47.8
|
1.0
|
|
CA
|
B:LYS119
|
4.7
|
52.7
|
1.0
|
|
N
|
B:LYS119
|
4.8
|
54.8
|
1.0
|
|
C
|
B:LYS117
|
4.8
|
47.8
|
1.0
|
|
O
|
B:ALA115
|
4.9
|
43.3
|
1.0
|
|
O
|
B:LYS119
|
4.9
|
56.6
|
1.0
|
|
N
|
B:LYS117
|
5.0
|
39.1
|
1.0
|
|
CA
|
B:LYS118
|
5.0
|
46.4
|
1.0
|
|
Magnesium binding site 8 out
of 11 in 4g73
Go back to
Magnesium Binding Sites List in 4g73
Magnesium binding site 8 out
of 11 in the Crystal Structure of Ndh with Nadh and Quinone
 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 Ndh with Nadh and Quinone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg607
b:42.2
occ:1.00
|
O1P
|
B:FAD606
|
2.5
|
40.1
|
1.0
|
|
O
|
B:ILE381
|
2.8
|
32.1
|
1.0
|
|
N
|
B:GLY177
|
2.9
|
27.4
|
1.0
|
|
N
|
B:ASN384
|
2.9
|
32.3
|
1.0
|
|
ND2
|
B:ASN384
|
2.9
|
29.6
|
1.0
|
|
CG
|
B:ASN384
|
3.1
|
31.7
|
1.0
|
|
CA
|
B:GLY177
|
3.3
|
27.1
|
1.0
|
|
N
|
B:ASP383
|
3.3
|
38.7
|
1.0
|
|
CA
|
B:ALA175
|
3.3
|
29.4
|
1.0
|
|
C
|
B:ALA175
|
3.4
|
31.1
|
1.0
|
|
CB
|
B:ASN384
|
3.4
|
27.0
|
1.0
|
|
C
|
B:GLY382
|
3.5
|
41.5
|
1.0
|
|
N
|
B:VAL176
|
3.6
|
25.1
|
1.0
|
|
CA
|
B:ASN384
|
3.7
|
32.2
|
1.0
|
|
OD1
|
B:ASN384
|
3.7
|
30.7
|
1.0
|
|
CA
|
B:GLY382
|
3.8
|
30.0
|
1.0
|
|
O
|
B:ALA175
|
3.9
|
28.8
|
1.0
|
|
P
|
B:FAD606
|
3.9
|
31.9
|
1.0
|
|
C
|
B:ASP383
|
3.9
|
36.6
|
1.0
|
|
C
|
B:ILE381
|
3.9
|
35.8
|
1.0
|
|
CA
|
B:ASP383
|
4.1
|
33.4
|
1.0
|
|
C
|
B:VAL176
|
4.1
|
35.1
|
1.0
|
|
O
|
B:GLY382
|
4.1
|
33.9
|
1.0
|
|
CB
|
B:ALA175
|
4.1
|
27.8
|
1.0
|
|
C
|
B:GLY177
|
4.2
|
34.0
|
1.0
|
|
O3P
|
B:FAD606
|
4.2
|
37.7
|
1.0
|
|
N
|
B:GLY382
|
4.3
|
35.7
|
1.0
|
|
O
|
B:GLY177
|
4.3
|
37.3
|
1.0
|
|
O
|
B:SER174
|
4.4
|
36.5
|
1.0
|
|
N
|
B:ALA175
|
4.4
|
35.1
|
1.0
|
|
CA
|
B:VAL176
|
4.4
|
28.5
|
1.0
|
|
C
|
B:ASN384
|
4.6
|
40.5
|
1.0
|
|
CB
|
B:ASP383
|
4.7
|
36.7
|
1.0
|
|
N
|
B:ALA385
|
4.7
|
34.9
|
1.0
|
|
O5'
|
B:FAD606
|
4.8
|
40.0
|
1.0
|
|
C
|
B:SER174
|
4.8
|
31.8
|
1.0
|
|
O2P
|
B:FAD606
|
4.9
|
29.5
|
1.0
|
|
Magnesium binding site 9 out
of 11 in 4g73
Go back to
Magnesium Binding Sites List in 4g73
Magnesium binding site 9 out
of 11 in the Crystal Structure of Ndh with Nadh and Quinone
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of Ndh with Nadh and Quinone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg608
b:45.9
occ:1.00
|
O
|
B:ALA175
|
2.8
|
28.8
|
1.0
|
|
N
|
B:ALA65
|
2.8
|
27.9
|
1.0
|
|
N
|
B:GLY62
|
3.1
|
29.4
|
1.0
|
|
C
|
B:GLY62
|
3.2
|
26.2
|
1.0
|
|
CB
|
B:ALA65
|
3.3
|
23.8
|
1.0
|
|
O2P
|
B:FAD606
|
3.3
|
29.5
|
1.0
|
|
N
|
B:GLY64
|
3.3
|
30.9
|
1.0
|
|
CB
|
B:ALA175
|
3.3
|
27.8
|
1.0
|
|
CA
|
B:GLY62
|
3.4
|
25.7
|
1.0
|
|
O
|
B:GLY62
|
3.4
|
29.5
|
1.0
|
|
CA
|
B:ALA65
|
3.6
|
29.3
|
1.0
|
|
N
|
B:TRP63
|
3.7
|
25.1
|
1.0
|
|
C5B
|
B:FAD606
|
3.7
|
25.6
|
1.0
|
|
C
|
B:GLY64
|
3.8
|
33.5
|
1.0
|
|
CA
|
B:GLY64
|
3.8
|
30.7
|
1.0
|
|
C
|
B:ALA175
|
3.9
|
31.1
|
1.0
|
|
O5B
|
B:FAD606
|
3.9
|
32.8
|
1.0
|
|
C4B
|
B:FAD606
|
4.0
|
35.2
|
1.0
|
|
P
|
B:FAD606
|
4.0
|
31.9
|
1.0
|
|
O3P
|
B:FAD606
|
4.0
|
37.7
|
1.0
|
|
C
|
B:TRP63
|
4.2
|
27.6
|
1.0
|
|
CA
|
B:ALA175
|
4.2
|
29.4
|
1.0
|
|
N
|
B:SER61
|
4.2
|
31.3
|
1.0
|
|
C
|
B:SER61
|
4.3
|
30.6
|
1.0
|
|
O1P
|
B:FAD606
|
4.3
|
40.1
|
1.0
|
|
O2A
|
B:FAD606
|
4.4
|
26.8
|
1.0
|
|
C
|
B:GLY60
|
4.4
|
31.9
|
1.0
|
|
PA
|
B:FAD606
|
4.4
|
25.4
|
1.0
|
|
CA
|
B:TRP63
|
4.5
|
30.3
|
1.0
|
|
CA
|
B:GLY60
|
4.5
|
27.3
|
1.0
|
|
O4B
|
B:FAD606
|
4.7
|
30.8
|
1.0
|
|
O
|
B:LEU59
|
4.7
|
28.4
|
1.0
|
|
CA
|
B:SER61
|
4.7
|
27.3
|
1.0
|
|
N
|
B:ILE66
|
4.7
|
32.4
|
1.0
|
|
C
|
B:ALA65
|
4.8
|
32.9
|
1.0
|
|
O
|
B:GLY60
|
4.9
|
26.1
|
1.0
|
|
O
|
B:GLY64
|
4.9
|
31.7
|
1.0
|
|
Magnesium binding site 10 out
of 11 in 4g73
Go back to
Magnesium Binding Sites List in 4g73
Magnesium binding site 10 out
of 11 in the Crystal Structure of Ndh with Nadh and Quinone
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of Ndh with Nadh and Quinone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg609
b:46.8
occ:1.00
|
O
|
B:LEU89
|
2.9
|
26.5
|
1.0
|
|
NH2
|
B:ARG85
|
3.0
|
22.7
|
1.0
|
|
O
|
B:HOH704
|
3.2
|
35.4
|
1.0
|
|
O2A
|
B:FAD606
|
3.2
|
26.8
|
1.0
|
|
CA
|
B:GLY62
|
3.2
|
25.7
|
1.0
|
|
N
|
B:LEU89
|
3.7
|
26.1
|
1.0
|
|
CB
|
B:LEU89
|
3.7
|
24.3
|
1.0
|
|
N
|
B:TRP63
|
3.7
|
25.1
|
1.0
|
|
C
|
B:LEU89
|
3.8
|
31.1
|
1.0
|
|
CZ
|
B:ARG85
|
3.8
|
26.0
|
1.0
|
|
C
|
B:GLY62
|
3.9
|
26.2
|
1.0
|
|
CE1
|
B:PHE88
|
3.9
|
26.3
|
1.0
|
|
NH1
|
B:ARG85
|
3.9
|
28.9
|
1.0
|
|
CA
|
B:LEU89
|
3.9
|
24.8
|
1.0
|
|
CG2
|
B:THR91
|
3.9
|
27.3
|
1.0
|
|
CD1
|
B:TRP63
|
3.9
|
24.7
|
1.0
|
|
CD1
|
B:PHE88
|
4.0
|
22.7
|
1.0
|
|
PA
|
B:FAD606
|
4.1
|
25.4
|
1.0
|
|
O5B
|
B:FAD606
|
4.2
|
32.8
|
1.0
|
|
NE1
|
B:TRP63
|
4.4
|
23.4
|
1.0
|
|
N
|
B:GLY62
|
4.5
|
29.4
|
1.0
|
|
CG
|
B:LEU89
|
4.5
|
25.8
|
1.0
|
|
O4'
|
B:FAD606
|
4.6
|
36.7
|
1.0
|
|
O
|
B:SER61
|
4.6
|
31.3
|
1.0
|
|
O1A
|
B:FAD606
|
4.6
|
24.5
|
1.0
|
|
CG
|
B:TRP63
|
4.7
|
33.8
|
1.0
|
|
CZ
|
B:PHE88
|
4.7
|
24.2
|
1.0
|
|
CA
|
B:TRP63
|
4.8
|
30.3
|
1.0
|
|
C
|
B:PHE88
|
4.8
|
25.1
|
1.0
|
|
CG
|
B:PHE88
|
4.9
|
23.4
|
1.0
|
|
O
|
B:GLY62
|
4.9
|
29.5
|
1.0
|
|
CD2
|
B:LEU89
|
5.0
|
24.1
|
1.0
|
|
N
|
B:THR91
|
5.0
|
24.5
|
1.0
|
|
C
|
B:SER61
|
5.0
|
30.6
|
1.0
|
|
Reference:
Y.Feng,
W.Li,
J.Li,
J.Wang,
J.Ge,
D.Xu,
Y.Liu,
K.Wu,
Q.Zeng,
J.W.Wu,
C.Tian,
B.Zhou,
M.Yang.
Structural Insight Into the Type-II Mitochondrial Nadh Dehydrogenases. Nature V. 491 478 2012.
ISSN: ISSN 0028-0836
PubMed: 23086143
DOI: 10.1038/NATURE11541
Page generated: Mon Aug 11 13:09:38 2025
|
