Magnesium in PDB 5t5m: Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.
Enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.
All present enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.:
1.2.99.5;
Protein crystallography data
The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A., PDB code: 5t5m
was solved by
T.Wagner,
U.Ermler,
S.Shima,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.22 /
2.50
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.543,
105.543,
340.549,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
15.8 /
18.2
|
Other elements in 5t5m:
The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.
(pdb code 5t5m). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A., PDB code: 5t5m:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 5t5m
Go back to
Magnesium Binding Sites List in 5t5m
Magnesium binding site 1 out
of 3 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:65.6
occ:1.00
|
O
|
A:HOH738
|
2.5
|
58.4
|
1.0
|
OE2
|
B:GLU138
|
2.7
|
61.3
|
1.0
|
O
|
A:THR344
|
2.7
|
58.3
|
1.0
|
O
|
A:HOH729
|
3.1
|
53.8
|
1.0
|
O
|
A:VAL340
|
3.1
|
52.8
|
1.0
|
C
|
A:THR344
|
3.5
|
56.7
|
1.0
|
N
|
A:THR344
|
3.8
|
53.8
|
1.0
|
CD
|
B:GLU138
|
3.9
|
62.2
|
1.0
|
N
|
A:VAL340
|
3.9
|
49.3
|
1.0
|
NH1
|
B:ARG142
|
4.0
|
51.5
|
1.0
|
C
|
A:VAL340
|
4.0
|
52.3
|
1.0
|
CA
|
A:THR344
|
4.1
|
56.4
|
1.0
|
CB
|
A:ASP339
|
4.4
|
50.4
|
1.0
|
OD1
|
A:ASP339
|
4.4
|
53.0
|
1.0
|
N
|
A:GLY345
|
4.4
|
56.4
|
1.0
|
C
|
A:ASP339
|
4.5
|
48.9
|
1.0
|
CA
|
A:ASP339
|
4.5
|
49.9
|
1.0
|
OE1
|
A:GLU186
|
4.5
|
46.5
|
1.0
|
N
|
A:GLU343
|
4.6
|
55.2
|
1.0
|
CA
|
A:VAL340
|
4.6
|
49.6
|
1.0
|
C
|
A:GLU343
|
4.6
|
53.5
|
1.0
|
OE1
|
B:GLU138
|
4.7
|
64.7
|
1.0
|
N
|
A:LEU342
|
4.7
|
53.7
|
1.0
|
O
|
A:THR185
|
4.8
|
50.0
|
1.0
|
CA
|
A:GLY345
|
4.8
|
57.2
|
1.0
|
CG
|
B:GLU138
|
4.9
|
60.2
|
1.0
|
N
|
A:GLU341
|
4.9
|
53.1
|
1.0
|
CG
|
A:ASP339
|
4.9
|
50.0
|
1.0
|
CZ
|
B:ARG142
|
5.0
|
51.9
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 5t5m
Go back to
Magnesium Binding Sites List in 5t5m
Magnesium binding site 2 out
of 3 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg604
b:42.6
occ:1.00
|
OG
|
A:SER76
|
2.3
|
48.1
|
1.0
|
O
|
A:ARG69
|
2.4
|
52.1
|
1.0
|
O
|
A:HOH726
|
2.5
|
53.0
|
1.0
|
O
|
B:GLY305
|
2.6
|
46.5
|
1.0
|
O
|
A:HOH757
|
2.8
|
49.1
|
1.0
|
O
|
A:ARG72
|
3.3
|
49.2
|
1.0
|
C
|
A:ARG69
|
3.3
|
52.8
|
1.0
|
CB
|
A:SER76
|
3.5
|
51.1
|
1.0
|
CA
|
A:ARG69
|
3.6
|
51.6
|
1.0
|
C
|
B:GLY305
|
3.7
|
51.4
|
1.0
|
O
|
A:HOH771
|
3.7
|
56.6
|
1.0
|
CA
|
B:GLY305
|
4.0
|
54.0
|
1.0
|
C
|
A:ARG72
|
4.0
|
51.0
|
1.0
|
CB
|
A:ARG69
|
4.1
|
54.2
|
1.0
|
N
|
A:SER76
|
4.2
|
51.0
|
1.0
|
CA
|
A:SER76
|
4.3
|
52.6
|
1.0
|
N
|
A:MET70
|
4.5
|
53.6
|
1.0
|
CA
|
A:PRO73
|
4.6
|
54.7
|
1.0
|
N
|
A:PRO73
|
4.6
|
53.2
|
1.0
|
O
|
A:GLY68
|
4.7
|
55.1
|
1.0
|
O
|
A:VAL94
|
4.7
|
53.4
|
1.0
|
OG
|
A:SER90
|
4.8
|
52.5
|
1.0
|
N
|
B:TYR306
|
4.9
|
52.1
|
1.0
|
N
|
A:ARG69
|
4.9
|
51.1
|
1.0
|
OD2
|
A:ASP75
|
4.9
|
57.5
|
1.0
|
CG
|
A:ARG69
|
4.9
|
56.4
|
1.0
|
CA
|
A:ARG72
|
4.9
|
51.3
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 5t5m
Go back to
Magnesium Binding Sites List in 5t5m
Magnesium binding site 3 out
of 3 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg301
b:63.0
occ:1.00
|
O
|
C:ASP143
|
2.3
|
49.6
|
1.0
|
O
|
B:HOH654
|
2.4
|
66.9
|
1.0
|
OG
|
C:SER139
|
2.4
|
52.9
|
1.0
|
O
|
B:HOH609
|
2.5
|
55.2
|
1.0
|
O
|
C:TYR140
|
2.5
|
47.1
|
1.0
|
C
|
C:ASP143
|
3.3
|
48.5
|
1.0
|
N
|
C:ASP143
|
3.4
|
47.2
|
1.0
|
C
|
C:TYR140
|
3.5
|
45.7
|
1.0
|
CB
|
C:SER139
|
3.5
|
52.6
|
1.0
|
OD1
|
B:ASP128
|
3.6
|
58.3
|
1.0
|
N
|
C:GLY142
|
3.6
|
51.4
|
1.0
|
CD2
|
C:TYR165
|
3.7
|
48.1
|
1.0
|
CA
|
C:ASP143
|
3.8
|
49.2
|
1.0
|
C
|
C:GLY142
|
3.9
|
49.1
|
1.0
|
CE2
|
C:TYR165
|
4.0
|
48.3
|
1.0
|
OE1
|
C:GLU164
|
4.0
|
62.2
|
1.0
|
C
|
C:ARG141
|
4.0
|
50.3
|
1.0
|
CA
|
C:ARG141
|
4.2
|
48.9
|
1.0
|
N
|
C:TYR140
|
4.2
|
46.1
|
1.0
|
N
|
C:ARG141
|
4.2
|
47.0
|
1.0
|
CG
|
B:ASP128
|
4.3
|
56.2
|
1.0
|
CA
|
C:GLY142
|
4.3
|
52.5
|
1.0
|
N
|
C:TRP144
|
4.4
|
47.0
|
1.0
|
CG
|
C:TYR165
|
4.4
|
48.0
|
1.0
|
C
|
C:SER139
|
4.4
|
48.5
|
1.0
|
CB
|
C:ASP143
|
4.4
|
53.0
|
1.0
|
OD2
|
B:ASP128
|
4.4
|
56.2
|
1.0
|
CD
|
C:GLU164
|
4.5
|
61.4
|
1.0
|
CA
|
C:TYR140
|
4.5
|
44.2
|
1.0
|
OE2
|
C:GLU164
|
4.5
|
65.9
|
1.0
|
CA
|
C:SER139
|
4.6
|
52.3
|
1.0
|
O
|
C:GLY142
|
4.7
|
47.7
|
1.0
|
CA
|
C:TRP144
|
4.8
|
47.0
|
1.0
|
O
|
C:ARG141
|
4.8
|
51.0
|
1.0
|
CB
|
C:TYR165
|
4.8
|
49.8
|
1.0
|
CZ
|
C:TYR165
|
4.8
|
49.7
|
1.0
|
O
|
C:SER139
|
4.9
|
47.4
|
1.0
|
|
Reference:
T.Wagner,
U.Ermler,
S.Shima.
The Methanogenic CO2 Reducing-and-Fixing Enzyme Is Bifunctional and Contains 46 [4FE-4S] Clusters. Science V. 354 114 2016.
ISSN: ESSN 1095-9203
PubMed: 27846502
DOI: 10.1126/SCIENCE.AAF9284
Page generated: Mon Dec 14 21:11:23 2020
|