Sodium in PDB 1mg2: Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin
Enzymatic activity of Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin
All present enzymatic activity of Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin:
1.4.99.3;
Protein crystallography data
The structure of Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin, PDB code: 1mg2
was solved by
D.Sun,
Z.W.Chen,
F.S.Mathews,
V.L.Davidson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.25
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.122,
188.201,
127.100,
90.00,
99.24,
90.00
|
R / Rfree (%)
|
17.3 /
21
|
Other elements in 1mg2:
The structure of Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin
(pdb code 1mg2). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin, PDB code: 1mg2:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 1mg2
Go back to
Sodium Binding Sites List in 1mg2
Sodium binding site 1 out
of 4 in the Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na604
b:22.3
occ:1.00
|
OD2
|
D:ASP75
|
2.4
|
25.7
|
1.0
|
O
|
D:HOH1409
|
2.5
|
23.3
|
1.0
|
O
|
D:TYR77
|
2.6
|
20.7
|
1.0
|
O
|
D:HOH1768
|
2.7
|
32.0
|
1.0
|
O
|
D:HOH1002
|
2.8
|
6.5
|
1.0
|
O
|
D:GLY72
|
3.1
|
19.4
|
1.0
|
CG
|
D:ASP75
|
3.2
|
24.6
|
1.0
|
OD1
|
D:ASP75
|
3.5
|
26.7
|
1.0
|
OE2
|
C:GLU31
|
3.6
|
25.4
|
1.0
|
C
|
D:GLY72
|
3.7
|
20.1
|
1.0
|
OE1
|
C:GLU31
|
3.7
|
25.2
|
1.0
|
C
|
D:TYR77
|
3.7
|
20.3
|
1.0
|
CD
|
C:GLU31
|
3.8
|
24.7
|
1.0
|
CD2
|
D:TYR77
|
4.1
|
17.4
|
1.0
|
N
|
D:ASP75
|
4.2
|
22.8
|
1.0
|
N
|
D:LEU73
|
4.2
|
19.0
|
1.0
|
O
|
D:ASP75
|
4.2
|
22.1
|
1.0
|
CA
|
D:LEU73
|
4.2
|
20.5
|
1.0
|
CB
|
D:TYR77
|
4.2
|
19.1
|
1.0
|
CA
|
D:TYR77
|
4.3
|
20.3
|
1.0
|
N
|
D:TYR77
|
4.4
|
20.9
|
1.0
|
CB
|
D:ASP75
|
4.4
|
24.3
|
1.0
|
C
|
D:LEU73
|
4.5
|
21.1
|
1.0
|
CA
|
D:GLY72
|
4.5
|
22.7
|
1.0
|
C
|
D:ASP75
|
4.5
|
22.1
|
1.0
|
CA
|
D:ASP75
|
4.5
|
21.6
|
1.0
|
CG
|
D:TYR77
|
4.6
|
17.7
|
1.0
|
N
|
D:ASN74
|
4.6
|
20.3
|
1.0
|
N
|
D:TRP78
|
4.8
|
20.4
|
1.0
|
CG
|
C:GLU31
|
4.8
|
20.3
|
1.0
|
NZ
|
C:LYS29
|
4.8
|
44.4
|
1.0
|
N
|
D:GLY72
|
5.0
|
24.5
|
1.0
|
O
|
D:LEU73
|
5.0
|
19.1
|
1.0
|
|
Sodium binding site 2 out
of 4 in 1mg2
Go back to
Sodium Binding Sites List in 1mg2
Sodium binding site 2 out
of 4 in the Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na603
b:14.8
occ:1.00
|
OD2
|
H:ASP75
|
2.4
|
21.9
|
1.0
|
O
|
H:TYR77
|
2.7
|
29.7
|
1.0
|
O
|
H:GLY72
|
2.8
|
13.1
|
1.0
|
O
|
H:HOH1158
|
2.8
|
16.8
|
1.0
|
OE2
|
G:GLU31
|
3.1
|
15.6
|
1.0
|
CG
|
H:ASP75
|
3.4
|
22.8
|
1.0
|
C
|
H:GLY72
|
3.5
|
17.9
|
1.0
|
CD
|
G:GLU31
|
3.5
|
20.1
|
1.0
|
OE1
|
G:GLU31
|
3.7
|
20.0
|
1.0
|
OD1
|
H:ASP75
|
3.8
|
25.3
|
1.0
|
C
|
H:TYR77
|
3.9
|
28.4
|
1.0
|
N
|
H:LEU73
|
4.1
|
19.3
|
1.0
|
N
|
H:ASP75
|
4.2
|
21.1
|
1.0
|
CA
|
H:GLY72
|
4.3
|
18.6
|
1.0
|
O
|
H:ASP75
|
4.3
|
22.6
|
1.0
|
CA
|
H:LEU73
|
4.3
|
22.2
|
1.0
|
CG
|
G:GLU31
|
4.5
|
14.6
|
1.0
|
C
|
H:LEU73
|
4.5
|
23.6
|
1.0
|
N
|
H:ASN74
|
4.5
|
22.2
|
1.0
|
CB
|
H:ASP75
|
4.6
|
24.0
|
1.0
|
N
|
H:TYR77
|
4.6
|
30.2
|
1.0
|
CA
|
H:TYR77
|
4.6
|
30.3
|
1.0
|
N
|
H:GLY72
|
4.6
|
19.9
|
1.0
|
C
|
H:ASP75
|
4.6
|
23.9
|
1.0
|
CA
|
H:ASP75
|
4.6
|
21.0
|
1.0
|
CB
|
H:TYR77
|
4.7
|
31.6
|
1.0
|
CD2
|
H:TYR77
|
4.9
|
33.7
|
1.0
|
N
|
H:TRP78
|
5.0
|
26.7
|
1.0
|
|
Sodium binding site 3 out
of 4 in 1mg2
Go back to
Sodium Binding Sites List in 1mg2
Sodium binding site 3 out
of 4 in the Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Na601
b:13.8
occ:1.00
|
O
|
L:HOH1529
|
2.5
|
20.7
|
1.0
|
OD2
|
L:ASP75
|
2.5
|
23.9
|
1.0
|
O
|
L:HOH1273
|
2.6
|
10.8
|
1.0
|
O
|
L:TYR77
|
2.7
|
28.1
|
1.0
|
O
|
K:HOH1348
|
2.7
|
14.4
|
1.0
|
O
|
L:GLY72
|
2.8
|
16.3
|
1.0
|
OE2
|
K:GLU31
|
2.9
|
21.1
|
1.0
|
CG
|
L:ASP75
|
3.4
|
21.5
|
1.0
|
CD
|
K:GLU31
|
3.4
|
23.3
|
1.0
|
C
|
L:GLY72
|
3.5
|
15.7
|
1.0
|
OE1
|
K:GLU31
|
3.7
|
20.3
|
1.0
|
C
|
L:TYR77
|
3.7
|
25.6
|
1.0
|
OD1
|
L:ASP75
|
3.8
|
24.3
|
1.0
|
N
|
L:LEU73
|
4.2
|
13.6
|
1.0
|
CA
|
L:GLY72
|
4.3
|
15.5
|
1.0
|
CA
|
L:LEU73
|
4.3
|
14.6
|
1.0
|
N
|
L:ASP75
|
4.4
|
20.6
|
1.0
|
O
|
L:ASP75
|
4.5
|
22.2
|
1.0
|
CG
|
K:GLU31
|
4.5
|
20.6
|
1.0
|
CA
|
L:TYR77
|
4.5
|
26.9
|
1.0
|
CB
|
L:TYR77
|
4.5
|
23.3
|
1.0
|
CD2
|
L:TYR77
|
4.5
|
20.7
|
1.0
|
N
|
L:TYR77
|
4.6
|
27.8
|
1.0
|
N
|
L:GLY72
|
4.6
|
20.0
|
1.0
|
CB
|
L:ASP75
|
4.6
|
21.2
|
1.0
|
N
|
L:ASN74
|
4.6
|
19.9
|
1.0
|
C
|
L:LEU73
|
4.7
|
18.1
|
1.0
|
N
|
L:TRP78
|
4.7
|
22.1
|
1.0
|
C
|
L:ASP75
|
4.8
|
22.6
|
1.0
|
CA
|
L:ASP75
|
4.8
|
21.0
|
1.0
|
CA
|
L:TRP78
|
4.9
|
21.1
|
1.0
|
CB
|
K:GLU31
|
4.9
|
17.0
|
1.0
|
|
Sodium binding site 4 out
of 4 in 1mg2
Go back to
Sodium Binding Sites List in 1mg2
Sodium binding site 4 out
of 4 in the Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Na602
b:8.7
occ:1.00
|
OD2
|
P:ASP75
|
2.4
|
31.7
|
1.0
|
O
|
O:HOH1352
|
2.6
|
11.2
|
1.0
|
O
|
P:TYR77
|
2.7
|
29.6
|
1.0
|
O
|
P:HOH2639
|
2.8
|
38.0
|
1.0
|
O
|
P:HOH1276
|
2.8
|
21.2
|
1.0
|
O
|
P:GLY72
|
2.9
|
19.5
|
1.0
|
OE2
|
O:GLU31
|
3.0
|
21.8
|
1.0
|
CG
|
P:ASP75
|
3.3
|
31.3
|
1.0
|
CD
|
O:GLU31
|
3.5
|
21.8
|
1.0
|
C
|
P:GLY72
|
3.5
|
19.2
|
1.0
|
OD1
|
P:ASP75
|
3.6
|
30.0
|
1.0
|
OE1
|
O:GLU31
|
3.7
|
19.1
|
1.0
|
C
|
P:TYR77
|
3.8
|
28.8
|
1.0
|
N
|
P:LEU73
|
4.2
|
20.1
|
1.0
|
CA
|
P:GLY72
|
4.3
|
20.4
|
1.0
|
CA
|
P:LEU73
|
4.3
|
19.7
|
1.0
|
N
|
P:ASP75
|
4.3
|
25.9
|
1.0
|
O
|
P:ASP75
|
4.4
|
35.7
|
1.0
|
CD2
|
P:TYR77
|
4.4
|
19.9
|
1.0
|
CB
|
P:TYR77
|
4.4
|
27.0
|
1.0
|
CA
|
P:TYR77
|
4.5
|
27.7
|
1.0
|
CG
|
O:GLU31
|
4.5
|
22.9
|
1.0
|
CB
|
P:ASP75
|
4.6
|
28.3
|
1.0
|
N
|
P:TYR77
|
4.6
|
29.2
|
1.0
|
N
|
P:GLY72
|
4.6
|
20.2
|
1.0
|
N
|
P:ASN74
|
4.6
|
20.6
|
1.0
|
C
|
P:LEU73
|
4.7
|
21.7
|
1.0
|
N
|
P:TRP78
|
4.8
|
27.5
|
1.0
|
C
|
P:ASP75
|
4.8
|
32.6
|
1.0
|
CA
|
P:ASP75
|
4.8
|
30.6
|
1.0
|
O2A
|
P:HEM200
|
4.8
|
22.6
|
1.0
|
CG
|
P:TYR77
|
4.9
|
22.7
|
1.0
|
CA
|
P:TRP78
|
4.9
|
28.0
|
1.0
|
|
Reference:
D.Sun,
Z.W.Chen,
F.S.Mathews,
V.L.Davidson.
Mutation of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction with Amicyanin Biochemistry V. 41 13926 2002.
ISSN: ISSN 0006-2960
PubMed: 12437349
DOI: 10.1021/BI026654X
Page generated: Sun Oct 6 20:31:32 2024
|