Magnesium in PDB 4g6g: Crystal Structure of Ndh with Trt
Enzymatic activity of Crystal Structure of Ndh with Trt
All present enzymatic activity of Crystal Structure of Ndh with Trt:
1.6.5.9;
Protein crystallography data
The structure of Crystal Structure of Ndh with Trt, PDB code: 4g6g
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)
|
35.59 /
2.39
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
132.921,
230.598,
112.250,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
19.3 /
23.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Ndh with Trt
(pdb code 4g6g). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the
Crystal Structure of Ndh with Trt, PDB code: 4g6g:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 4g6g
Go back to
Magnesium Binding Sites List in 4g6g
Magnesium binding site 1 out
of 10 in the Crystal Structure of Ndh with Trt
 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 Trt within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg604
b:43.5
occ:1.00
|
O2P
|
A:FAD603
|
2.8
|
25.4
|
1.0
|
|
N
|
A:ASN384
|
2.8
|
24.3
|
1.0
|
|
O
|
A:ILE381
|
2.8
|
42.6
|
1.0
|
|
N
|
A:GLY177
|
2.9
|
20.3
|
1.0
|
|
CG
|
A:ASN384
|
3.0
|
24.8
|
1.0
|
|
OD1
|
A:ASN384
|
3.1
|
29.8
|
1.0
|
|
CA
|
A:GLY177
|
3.3
|
18.2
|
1.0
|
|
CA
|
A:ALA175
|
3.3
|
24.7
|
1.0
|
|
C
|
A:ALA175
|
3.3
|
26.5
|
1.0
|
|
N
|
A:ASP383
|
3.3
|
22.1
|
1.0
|
|
CB
|
A:ASN384
|
3.4
|
22.4
|
1.0
|
|
ND2
|
A:ASN384
|
3.5
|
21.6
|
1.0
|
|
N
|
A:VAL176
|
3.5
|
21.7
|
1.0
|
|
C
|
A:GLY382
|
3.5
|
28.4
|
1.0
|
|
CA
|
A:ASN384
|
3.6
|
25.0
|
1.0
|
|
CA
|
A:GLY382
|
3.6
|
12.3
|
1.0
|
|
O
|
A:ALA175
|
3.8
|
23.6
|
1.0
|
|
C
|
A:ASP383
|
3.8
|
34.2
|
1.0
|
|
C
|
A:ILE381
|
3.9
|
25.1
|
1.0
|
|
P
|
A:FAD603
|
4.0
|
24.1
|
1.0
|
|
CA
|
A:ASP383
|
4.0
|
26.2
|
1.0
|
|
CB
|
A:ALA175
|
4.0
|
23.7
|
1.0
|
|
C
|
A:VAL176
|
4.0
|
27.5
|
1.0
|
|
O
|
A:GLY382
|
4.2
|
33.5
|
1.0
|
|
C
|
A:GLY177
|
4.2
|
23.6
|
1.0
|
|
N
|
A:GLY382
|
4.2
|
28.6
|
1.0
|
|
O
|
A:GLY177
|
4.3
|
31.3
|
1.0
|
|
O1P
|
A:FAD603
|
4.4
|
20.9
|
1.0
|
|
O
|
A:SER174
|
4.4
|
30.2
|
1.0
|
|
CA
|
A:VAL176
|
4.4
|
25.1
|
1.0
|
|
N
|
A:ALA175
|
4.4
|
21.2
|
1.0
|
|
O3P
|
A:FAD603
|
4.4
|
18.9
|
1.0
|
|
CB
|
A:ASP383
|
4.5
|
33.0
|
1.0
|
|
C
|
A:ASN384
|
4.6
|
20.9
|
1.0
|
|
N
|
A:ALA385
|
4.7
|
37.2
|
1.0
|
|
C
|
A:SER174
|
4.8
|
35.4
|
1.0
|
|
O
|
A:ASP383
|
4.9
|
22.5
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 4g6g
Go back to
Magnesium Binding Sites List in 4g6g
Magnesium binding site 2 out
of 10 in the Crystal Structure of Ndh with Trt
 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 Trt within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg605
b:40.5
occ:1.00
|
O1P
|
A:FAD603
|
2.7
|
20.9
|
1.0
|
|
O
|
A:ALA175
|
2.9
|
23.6
|
1.0
|
|
N
|
A:ALA65
|
2.9
|
23.7
|
1.0
|
|
N
|
A:GLY62
|
3.0
|
23.8
|
1.0
|
|
CA
|
A:GLY62
|
3.3
|
16.4
|
1.0
|
|
C
|
A:GLY62
|
3.3
|
21.7
|
1.0
|
|
CB
|
A:ALA65
|
3.4
|
18.9
|
1.0
|
|
O5B
|
A:FAD603
|
3.4
|
29.6
|
1.0
|
|
CB
|
A:ALA175
|
3.4
|
23.7
|
1.0
|
|
N
|
A:GLY64
|
3.5
|
29.8
|
1.0
|
|
O
|
A:GLY62
|
3.5
|
22.1
|
1.0
|
|
CA
|
A:ALA65
|
3.7
|
25.2
|
1.0
|
|
N
|
A:TRP63
|
3.8
|
19.3
|
1.0
|
|
C5B
|
A:FAD603
|
3.8
|
20.0
|
1.0
|
|
C
|
A:GLY64
|
3.8
|
20.4
|
1.0
|
|
CA
|
A:GLY64
|
3.8
|
23.7
|
1.0
|
|
C4B
|
A:FAD603
|
3.9
|
23.1
|
1.0
|
|
C
|
A:ALA175
|
3.9
|
26.5
|
1.0
|
|
P
|
A:FAD603
|
4.0
|
24.1
|
1.0
|
|
N
|
A:SER61
|
4.1
|
17.7
|
1.0
|
|
C
|
A:SER61
|
4.2
|
31.4
|
1.0
|
|
C
|
A:TRP63
|
4.3
|
22.1
|
1.0
|
|
O3P
|
A:FAD603
|
4.3
|
18.9
|
1.0
|
|
CA
|
A:ALA175
|
4.3
|
24.7
|
1.0
|
|
PA
|
A:FAD603
|
4.3
|
24.1
|
1.0
|
|
C
|
A:GLY60
|
4.3
|
24.5
|
1.0
|
|
CA
|
A:GLY60
|
4.5
|
20.1
|
1.0
|
|
O2A
|
A:FAD603
|
4.5
|
20.8
|
1.0
|
|
CA
|
A:SER61
|
4.6
|
26.4
|
1.0
|
|
CA
|
A:TRP63
|
4.6
|
22.4
|
1.0
|
|
O4B
|
A:FAD603
|
4.7
|
23.4
|
1.0
|
|
O
|
A:LEU59
|
4.7
|
25.3
|
1.0
|
|
O2P
|
A:FAD603
|
4.7
|
25.4
|
1.0
|
|
N
|
A:ILE66
|
4.8
|
27.6
|
1.0
|
|
C
|
A:ALA65
|
4.8
|
26.1
|
1.0
|
|
O
|
A:GLY60
|
4.9
|
19.3
|
1.0
|
|
O
|
A:GLY64
|
5.0
|
26.8
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 4g6g
Go back to
Magnesium Binding Sites List in 4g6g
Magnesium binding site 3 out
of 10 in the Crystal Structure of Ndh with Trt
 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 Trt within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg606
b:36.2
occ:1.00
|
O
|
A:HOH704
|
2.6
|
24.5
|
1.0
|
|
O
|
A:LEU89
|
2.9
|
24.5
|
1.0
|
|
O2A
|
A:FAD603
|
2.9
|
20.8
|
1.0
|
|
NH2
|
A:ARG85
|
3.0
|
21.7
|
1.0
|
|
CA
|
A:GLY62
|
3.4
|
16.4
|
1.0
|
|
N
|
A:TRP63
|
3.8
|
19.3
|
1.0
|
|
N
|
A:LEU89
|
3.8
|
18.4
|
1.0
|
|
CB
|
A:LEU89
|
3.8
|
16.5
|
1.0
|
|
C
|
A:LEU89
|
3.8
|
28.1
|
1.0
|
|
CD1
|
A:TRP63
|
3.9
|
22.5
|
1.0
|
|
CZ
|
A:ARG85
|
3.9
|
29.6
|
1.0
|
|
PA
|
A:FAD603
|
3.9
|
24.1
|
1.0
|
|
NH1
|
A:ARG85
|
3.9
|
15.0
|
1.0
|
|
C
|
A:GLY62
|
4.0
|
21.7
|
1.0
|
|
CG2
|
A:THR91
|
4.0
|
18.7
|
1.0
|
|
CE1
|
A:PHE88
|
4.0
|
29.2
|
1.0
|
|
CA
|
A:LEU89
|
4.0
|
16.4
|
1.0
|
|
CD1
|
A:PHE88
|
4.2
|
21.4
|
1.0
|
|
O5B
|
A:FAD603
|
4.2
|
29.6
|
1.0
|
|
O1A
|
A:FAD603
|
4.3
|
15.5
|
1.0
|
|
NE1
|
A:TRP63
|
4.4
|
20.4
|
1.0
|
|
CG
|
A:LEU89
|
4.4
|
22.4
|
1.0
|
|
O4'
|
A:FAD603
|
4.6
|
33.0
|
1.0
|
|
CG
|
A:TRP63
|
4.6
|
26.5
|
1.0
|
|
N
|
A:GLY62
|
4.6
|
23.8
|
1.0
|
|
O
|
A:SER61
|
4.7
|
17.4
|
1.0
|
|
CZ
|
A:PHE88
|
4.8
|
17.0
|
1.0
|
|
CA
|
A:TRP63
|
4.9
|
22.4
|
1.0
|
|
CD2
|
A:LEU89
|
4.9
|
15.7
|
1.0
|
|
C
|
A:PHE88
|
4.9
|
25.4
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 4g6g
Go back to
Magnesium Binding Sites List in 4g6g
Magnesium binding site 4 out
of 10 in the Crystal Structure of Ndh with Trt
 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 Trt within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:54.7
occ:1.00
|
NZ
|
A:LYS196
|
2.9
|
43.2
|
1.0
|
|
O1A
|
A:FAD603
|
3.0
|
15.5
|
1.0
|
|
N
|
A:ALA178
|
3.0
|
26.6
|
1.0
|
|
OD2
|
A:ASP383
|
3.0
|
49.4
|
1.0
|
|
O
|
A:ALA178
|
3.3
|
36.0
|
1.0
|
|
O
|
A:HOH755
|
3.5
|
31.8
|
1.0
|
|
O3P
|
A:FAD603
|
3.5
|
18.9
|
1.0
|
|
CA
|
A:GLY177
|
3.5
|
18.2
|
1.0
|
|
CE
|
A:LYS196
|
3.6
|
24.3
|
1.0
|
|
C
|
A:GLY177
|
3.7
|
23.6
|
1.0
|
|
CA
|
A:ALA178
|
3.9
|
26.2
|
1.0
|
|
PA
|
A:FAD603
|
3.9
|
24.1
|
1.0
|
|
CG
|
A:ASP383
|
3.9
|
51.1
|
1.0
|
|
C
|
A:ALA178
|
4.0
|
20.5
|
1.0
|
|
O4'
|
A:FAD603
|
4.0
|
33.0
|
1.0
|
|
CB
|
A:ASP383
|
4.0
|
33.0
|
1.0
|
|
O
|
A:HOH752
|
4.1
|
40.2
|
1.0
|
|
O
|
A:HOH835
|
4.2
|
44.9
|
1.0
|
|
CB
|
A:ALA178
|
4.2
|
16.3
|
1.0
|
|
C5'
|
A:FAD603
|
4.6
|
22.5
|
1.0
|
|
NH1
|
A:ARG344
|
4.6
|
36.2
|
1.0
|
|
C4'
|
A:FAD603
|
4.8
|
34.3
|
1.0
|
|
P
|
A:FAD603
|
4.8
|
24.1
|
1.0
|
|
C3'
|
A:FAD603
|
4.9
|
41.1
|
1.0
|
|
N
|
A:GLY177
|
4.9
|
20.3
|
1.0
|
|
O2P
|
A:FAD603
|
4.9
|
25.4
|
1.0
|
|
C5B
|
A:FAD603
|
4.9
|
20.0
|
1.0
|
|
CD
|
A:LYS196
|
4.9
|
37.8
|
1.0
|
|
O
|
A:HOH706
|
4.9
|
23.8
|
1.0
|
|
O
|
A:GLY177
|
4.9
|
31.3
|
1.0
|
|
O5B
|
A:FAD603
|
5.0
|
29.6
|
1.0
|
|
O2A
|
A:FAD603
|
5.0
|
20.8
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 4g6g
Go back to
Magnesium Binding Sites List in 4g6g
Magnesium binding site 5 out
of 10 in the Crystal Structure of Ndh with Trt
 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 Trt within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:15.7
occ:1.00
|
O
|
B:GLY333
|
2.6
|
25.0
|
1.0
|
|
O
|
B:HOH812
|
2.6
|
39.9
|
1.0
|
|
O
|
B:HOH785
|
2.7
|
36.0
|
1.0
|
|
O
|
B:HOH820
|
2.9
|
45.6
|
1.0
|
|
O
|
B:HOH722
|
2.9
|
29.1
|
1.0
|
|
O
|
B:HOH717
|
3.6
|
38.2
|
1.0
|
|
C
|
B:GLY333
|
3.7
|
35.1
|
1.0
|
|
O
|
B:HOH902
|
4.1
|
45.1
|
1.0
|
|
O
|
B:HOH818
|
4.1
|
43.9
|
1.0
|
|
CG2
|
B:THR207
|
4.2
|
27.9
|
1.0
|
|
CE1
|
B:TYR332
|
4.4
|
26.4
|
1.0
|
|
O
|
B:GLU311
|
4.4
|
42.9
|
1.0
|
|
CA
|
B:GLY333
|
4.4
|
27.2
|
1.0
|
|
O
|
B:TYR191
|
4.6
|
27.4
|
1.0
|
|
N
|
B:THR334
|
4.6
|
21.3
|
1.0
|
|
CA
|
B:THR334
|
4.7
|
25.5
|
1.0
|
|
O
|
B:HOH865
|
4.8
|
47.0
|
1.0
|
|
ND2
|
B:ASN211
|
4.8
|
18.3
|
1.0
|
|
CD1
|
B:TYR332
|
4.9
|
19.4
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 4g6g
Go back to
Magnesium Binding Sites List in 4g6g
Magnesium binding site 6 out
of 10 in the Crystal Structure of Ndh with Trt
 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 Trt within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:67.8
occ:1.00
|
O
|
B:HOH736
|
2.6
|
40.4
|
1.0
|
|
O
|
B:LEU116
|
2.8
|
59.5
|
1.0
|
|
O
|
B:LYS118
|
2.9
|
66.2
|
1.0
|
|
C
|
B:LEU116
|
3.8
|
47.0
|
1.0
|
|
C
|
B:LYS118
|
4.1
|
46.6
|
1.0
|
|
CA
|
B:LEU116
|
4.3
|
40.9
|
1.0
|
|
N
|
B:LYS118
|
4.6
|
53.4
|
1.0
|
|
O
|
B:ALA115
|
4.7
|
47.6
|
1.0
|
|
CD2
|
B:LEU116
|
4.9
|
38.1
|
1.0
|
|
N
|
B:LYS117
|
4.9
|
47.8
|
1.0
|
|
CA
|
B:LYS119
|
4.9
|
50.8
|
1.0
|
|
CA
|
B:LYS118
|
5.0
|
42.9
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 4g6g
Go back to
Magnesium Binding Sites List in 4g6g
Magnesium binding site 7 out
of 10 in the Crystal Structure of Ndh with Trt
 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 Trt within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg608
b:56.0
occ:1.00
|
O2P
|
B:FAD607
|
2.8
|
40.4
|
1.0
|
|
O
|
B:ILE381
|
2.8
|
47.3
|
1.0
|
|
N
|
B:ASN384
|
2.9
|
33.5
|
1.0
|
|
N
|
B:GLY177
|
2.9
|
29.1
|
1.0
|
|
CG
|
B:ASN384
|
3.1
|
40.5
|
1.0
|
|
OD1
|
B:ASN384
|
3.2
|
38.6
|
1.0
|
|
CA
|
B:ALA175
|
3.3
|
38.9
|
1.0
|
|
C
|
B:ALA175
|
3.3
|
38.7
|
1.0
|
|
CA
|
B:GLY177
|
3.3
|
22.5
|
1.0
|
|
N
|
B:ASP383
|
3.3
|
44.8
|
1.0
|
|
CB
|
B:ASN384
|
3.4
|
35.5
|
1.0
|
|
N
|
B:VAL176
|
3.5
|
39.3
|
1.0
|
|
ND2
|
B:ASN384
|
3.5
|
40.6
|
1.0
|
|
C
|
B:GLY382
|
3.6
|
40.5
|
1.0
|
|
CA
|
B:ASN384
|
3.6
|
33.4
|
1.0
|
|
CA
|
B:GLY382
|
3.7
|
32.2
|
1.0
|
|
O
|
B:ALA175
|
3.8
|
35.9
|
1.0
|
|
C
|
B:ASP383
|
3.9
|
39.4
|
1.0
|
|
C
|
B:ILE381
|
3.9
|
31.8
|
1.0
|
|
P
|
B:FAD607
|
3.9
|
30.7
|
1.0
|
|
CB
|
B:ALA175
|
4.0
|
29.8
|
1.0
|
|
CA
|
B:ASP383
|
4.0
|
39.2
|
1.0
|
|
C
|
B:VAL176
|
4.1
|
40.6
|
1.0
|
|
O
|
B:GLY382
|
4.2
|
37.0
|
1.0
|
|
C
|
B:GLY177
|
4.2
|
35.5
|
1.0
|
|
N
|
B:GLY382
|
4.3
|
34.3
|
1.0
|
|
O1P
|
B:FAD607
|
4.3
|
38.3
|
1.0
|
|
O
|
B:GLY177
|
4.3
|
39.4
|
1.0
|
|
O3P
|
B:FAD607
|
4.4
|
24.8
|
1.0
|
|
O
|
B:SER174
|
4.4
|
49.4
|
1.0
|
|
N
|
B:ALA175
|
4.4
|
37.4
|
1.0
|
|
CA
|
B:VAL176
|
4.4
|
23.0
|
1.0
|
|
CB
|
B:ASP383
|
4.6
|
43.5
|
1.0
|
|
C
|
B:ASN384
|
4.6
|
32.0
|
1.0
|
|
N
|
B:ALA385
|
4.8
|
47.3
|
1.0
|
|
C
|
B:SER174
|
4.8
|
35.1
|
1.0
|
|
O
|
B:ASP383
|
5.0
|
44.6
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 4g6g
Go back to
Magnesium Binding Sites List in 4g6g
Magnesium binding site 8 out
of 10 in the Crystal Structure of Ndh with Trt
 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 Trt within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg609
b:54.7
occ:1.00
|
O1P
|
B:FAD607
|
2.6
|
38.3
|
1.0
|
|
O
|
B:ALA175
|
2.8
|
35.9
|
1.0
|
|
N
|
B:ALA65
|
2.9
|
32.0
|
1.0
|
|
N
|
B:GLY62
|
3.0
|
31.2
|
1.0
|
|
CA
|
B:GLY62
|
3.3
|
23.5
|
1.0
|
|
C
|
B:GLY62
|
3.3
|
34.4
|
1.0
|
|
CB
|
B:ALA65
|
3.4
|
39.4
|
1.0
|
|
O5B
|
B:FAD607
|
3.4
|
31.8
|
1.0
|
|
CB
|
B:ALA175
|
3.4
|
29.8
|
1.0
|
|
N
|
B:GLY64
|
3.5
|
32.5
|
1.0
|
|
O
|
B:GLY62
|
3.5
|
29.7
|
1.0
|
|
CA
|
B:ALA65
|
3.7
|
39.0
|
1.0
|
|
N
|
B:TRP63
|
3.8
|
30.9
|
1.0
|
|
C5B
|
B:FAD607
|
3.8
|
29.2
|
1.0
|
|
C
|
B:GLY64
|
3.9
|
38.1
|
1.0
|
|
CA
|
B:GLY64
|
3.9
|
28.4
|
1.0
|
|
C4B
|
B:FAD607
|
3.9
|
38.9
|
1.0
|
|
C
|
B:ALA175
|
3.9
|
38.7
|
1.0
|
|
P
|
B:FAD607
|
3.9
|
30.7
|
1.0
|
|
N
|
B:SER61
|
4.1
|
27.5
|
1.0
|
|
O3P
|
B:FAD607
|
4.2
|
24.8
|
1.0
|
|
C
|
B:SER61
|
4.2
|
39.9
|
1.0
|
|
CA
|
B:ALA175
|
4.3
|
38.9
|
1.0
|
|
C
|
B:TRP63
|
4.3
|
27.8
|
1.0
|
|
PA
|
B:FAD607
|
4.3
|
28.8
|
1.0
|
|
C
|
B:GLY60
|
4.3
|
36.2
|
1.0
|
|
CA
|
B:GLY60
|
4.5
|
22.0
|
1.0
|
|
O2A
|
B:FAD607
|
4.6
|
23.6
|
1.0
|
|
CA
|
B:SER61
|
4.6
|
35.2
|
1.0
|
|
CA
|
B:TRP63
|
4.6
|
32.5
|
1.0
|
|
O4B
|
B:FAD607
|
4.6
|
22.8
|
1.0
|
|
O
|
B:LEU59
|
4.7
|
36.6
|
1.0
|
|
O2P
|
B:FAD607
|
4.7
|
40.4
|
1.0
|
|
N
|
B:ILE66
|
4.8
|
30.2
|
1.0
|
|
C
|
B:ALA65
|
4.8
|
32.9
|
1.0
|
|
O
|
B:GLY60
|
4.9
|
37.2
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 4g6g
Go back to
Magnesium Binding Sites List in 4g6g
Magnesium binding site 9 out
of 10 in the Crystal Structure of Ndh with Trt
 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 Trt within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg610
b:57.2
occ:1.00
|
O
|
B:HOH727
|
2.5
|
38.8
|
1.0
|
|
O
|
B:LEU89
|
2.9
|
25.9
|
1.0
|
|
O2A
|
B:FAD607
|
2.9
|
23.6
|
1.0
|
|
NH2
|
B:ARG85
|
3.1
|
30.8
|
1.0
|
|
CA
|
B:GLY62
|
3.4
|
23.5
|
1.0
|
|
N
|
B:LEU89
|
3.8
|
21.7
|
1.0
|
|
N
|
B:TRP63
|
3.8
|
30.9
|
1.0
|
|
C
|
B:LEU89
|
3.8
|
28.7
|
1.0
|
|
CB
|
B:LEU89
|
3.8
|
29.0
|
1.0
|
|
CD1
|
B:TRP63
|
3.9
|
29.4
|
1.0
|
|
NH1
|
B:ARG85
|
3.9
|
25.0
|
1.0
|
|
CZ
|
B:ARG85
|
3.9
|
33.8
|
1.0
|
|
CG2
|
B:THR91
|
3.9
|
23.0
|
1.0
|
|
CE1
|
B:PHE88
|
4.0
|
28.2
|
1.0
|
|
PA
|
B:FAD607
|
4.0
|
28.8
|
1.0
|
|
CA
|
B:LEU89
|
4.0
|
25.2
|
1.0
|
|
C
|
B:GLY62
|
4.0
|
34.4
|
1.0
|
|
CD1
|
B:PHE88
|
4.2
|
26.9
|
1.0
|
|
O5B
|
B:FAD607
|
4.3
|
31.8
|
1.0
|
|
NE1
|
B:TRP63
|
4.4
|
16.1
|
1.0
|
|
O1A
|
B:FAD607
|
4.4
|
25.9
|
1.0
|
|
CG
|
B:LEU89
|
4.4
|
27.3
|
1.0
|
|
O4'
|
B:FAD607
|
4.6
|
37.0
|
1.0
|
|
CG
|
B:TRP63
|
4.7
|
26.1
|
1.0
|
|
N
|
B:GLY62
|
4.7
|
31.2
|
1.0
|
|
O
|
B:SER61
|
4.7
|
37.2
|
1.0
|
|
CZ
|
B:PHE88
|
4.8
|
24.4
|
1.0
|
|
CD2
|
B:LEU89
|
4.8
|
25.2
|
1.0
|
|
CA
|
B:TRP63
|
4.9
|
32.5
|
1.0
|
|
C
|
B:PHE88
|
5.0
|
34.2
|
1.0
|
|
N
|
B:THR91
|
5.0
|
22.5
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 4g6g
Go back to
Magnesium Binding Sites List in 4g6g
Magnesium binding site 10 out
of 10 in the Crystal Structure of Ndh with Trt
 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 Trt within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg611
b:62.6
occ:1.00
|
NZ
|
B:LYS196
|
2.2
|
56.2
|
1.0
|
|
O1A
|
B:FAD607
|
2.9
|
25.9
|
1.0
|
|
N
|
B:ALA178
|
2.9
|
38.3
|
1.0
|
|
OD2
|
B:ASP383
|
3.0
|
51.1
|
1.0
|
|
O
|
B:ALA178
|
3.2
|
43.8
|
1.0
|
|
CE
|
B:LYS196
|
3.4
|
31.8
|
1.0
|
|
CA
|
B:GLY177
|
3.5
|
22.5
|
1.0
|
|
O3P
|
B:FAD607
|
3.5
|
24.8
|
1.0
|
|
O
|
B:HOH793
|
3.6
|
31.0
|
1.0
|
|
C
|
B:GLY177
|
3.7
|
35.5
|
1.0
|
|
CG
|
B:ASP383
|
3.9
|
51.4
|
1.0
|
|
PA
|
B:FAD607
|
3.9
|
28.8
|
1.0
|
|
CA
|
B:ALA178
|
3.9
|
38.6
|
1.0
|
|
C
|
B:ALA178
|
4.0
|
32.7
|
1.0
|
|
CB
|
B:ASP383
|
4.0
|
43.5
|
1.0
|
|
O4'
|
B:FAD607
|
4.0
|
37.0
|
1.0
|
|
CB
|
B:ALA178
|
4.2
|
27.0
|
1.0
|
|
C5'
|
B:FAD607
|
4.5
|
34.1
|
1.0
|
|
NH1
|
B:ARG344
|
4.6
|
53.8
|
1.0
|
|
CD
|
B:LYS196
|
4.6
|
38.3
|
1.0
|
|
C4'
|
B:FAD607
|
4.7
|
42.8
|
1.0
|
|
P
|
B:FAD607
|
4.7
|
30.7
|
1.0
|
|
C3'
|
B:FAD607
|
4.8
|
44.5
|
1.0
|
|
O2A
|
B:FAD607
|
4.9
|
23.6
|
1.0
|
|
O2P
|
B:FAD607
|
4.9
|
40.4
|
1.0
|
|
N
|
B:GLY177
|
4.9
|
29.1
|
1.0
|
|
O
|
B:GLY177
|
4.9
|
39.4
|
1.0
|
|
C5B
|
B:FAD607
|
4.9
|
29.2
|
1.0
|
|
O5B
|
B:FAD607
|
5.0
|
31.8
|
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: Fri Aug 16 15:23:28 2024
|
