Magnesium in PDB 3wfr: Trna Processing Enzyme Complex 2
Enzymatic activity of Trna Processing Enzyme Complex 2
All present enzymatic activity of Trna Processing Enzyme Complex 2:
2.7.7.72;
Protein crystallography data
The structure of Trna Processing Enzyme Complex 2, PDB code: 3wfr
was solved by
S.Yamashita,
D.Takeshita,
K.Tomita,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.98 /
3.50
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
152.810,
154.590,
174.670,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
22.4 /
26.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Trna Processing Enzyme Complex 2
(pdb code 3wfr). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Trna Processing Enzyme Complex 2, PDB code: 3wfr:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 3wfr
Go back to
Magnesium Binding Sites List in 3wfr
Magnesium binding site 1 out
of 4 in the Trna Processing Enzyme Complex 2
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Trna Processing Enzyme Complex 2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg603
b:45.8
occ:1.00
|
O1
|
E:POP602
|
2.1
|
74.2
|
0.5
|
|
O2B
|
E:CTP601
|
2.1
|
74.5
|
0.5
|
|
OD2
|
E:ASP58
|
2.3
|
81.5
|
1.0
|
|
OD2
|
E:ASP60
|
2.3
|
97.5
|
1.0
|
|
OP1
|
A:C74
|
2.8
|
56.8
|
0.5
|
|
CG
|
E:ASP58
|
3.0
|
76.8
|
1.0
|
|
CG
|
E:ASP60
|
3.1
|
92.5
|
1.0
|
|
PB
|
E:CTP601
|
3.2
|
73.8
|
0.5
|
|
OD1
|
E:ASP60
|
3.2
|
95.3
|
1.0
|
|
O
|
E:ASP58
|
3.3
|
42.2
|
1.0
|
|
O4
|
E:POP602
|
3.4
|
0.1
|
0.5
|
|
O3A
|
E:CTP601
|
3.4
|
69.3
|
0.5
|
|
O1A
|
E:CTP601
|
3.5
|
43.3
|
0.5
|
|
P1
|
E:POP602
|
3.5
|
72.2
|
0.5
|
|
CB
|
E:ASP58
|
3.6
|
65.2
|
1.0
|
|
O1G
|
E:CTP601
|
3.7
|
0.8
|
0.5
|
|
OD1
|
E:ASP58
|
3.8
|
83.8
|
1.0
|
|
O3B
|
E:CTP601
|
3.8
|
80.1
|
0.5
|
|
C
|
E:ASP58
|
3.8
|
53.0
|
1.0
|
|
PA
|
E:CTP601
|
4.0
|
44.9
|
0.5
|
|
O2
|
E:POP602
|
4.0
|
73.5
|
0.5
|
|
C5'
|
E:CTP601
|
4.2
|
47.0
|
0.5
|
|
P
|
A:C74
|
4.2
|
58.6
|
0.5
|
|
C5'
|
A:C74
|
4.3
|
65.5
|
0.5
|
|
O5'
|
E:CTP601
|
4.3
|
46.1
|
0.5
|
|
PG
|
E:CTP601
|
4.3
|
0.8
|
0.5
|
|
CA
|
E:ASP58
|
4.4
|
56.2
|
1.0
|
|
N
|
E:GLY42
|
4.4
|
62.6
|
1.0
|
|
O
|
E:POP602
|
4.4
|
82.7
|
0.5
|
|
O3
|
E:POP602
|
4.4
|
77.5
|
0.5
|
|
O1B
|
E:CTP601
|
4.5
|
76.5
|
0.5
|
|
CA
|
E:GLY42
|
4.5
|
62.9
|
1.0
|
|
P2
|
E:POP602
|
4.5
|
0.6
|
0.5
|
|
N
|
E:TRP43
|
4.5
|
55.3
|
1.0
|
|
N
|
E:VAL59
|
4.6
|
33.9
|
1.0
|
|
CB
|
E:ASP60
|
4.6
|
79.8
|
1.0
|
|
O5'
|
A:C74
|
4.6
|
66.8
|
0.5
|
|
N
|
E:ASP60
|
4.7
|
62.5
|
1.0
|
|
O2G
|
E:CTP601
|
4.7
|
0.0
|
0.5
|
|
C
|
E:VAL59
|
4.8
|
55.5
|
1.0
|
|
CA
|
E:VAL59
|
4.8
|
34.5
|
1.0
|
|
O3'
|
A:A73
|
4.8
|
70.3
|
0.5
|
|
O3'
|
A:A73
|
4.8
|
72.0
|
0.5
|
|
C
|
E:GLY42
|
4.9
|
63.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 3wfr
Go back to
Magnesium Binding Sites List in 3wfr
Magnesium binding site 2 out
of 4 in the Trna Processing Enzyme Complex 2
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Trna Processing Enzyme Complex 2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg603
b:81.2
occ:1.00
|
OP1
|
B:C74
|
2.0
|
83.2
|
0.5
|
|
OD2
|
F:ASP58
|
2.1
|
74.4
|
1.0
|
|
OD1
|
F:ASP60
|
2.3
|
78.9
|
1.0
|
|
O1
|
F:POP602
|
2.5
|
0.7
|
0.5
|
|
O2B
|
F:CTP601
|
2.5
|
0.7
|
0.5
|
|
O1A
|
F:CTP601
|
2.7
|
81.6
|
0.5
|
|
OD2
|
F:ASP60
|
2.7
|
92.6
|
1.0
|
|
CG
|
F:ASP60
|
2.8
|
83.8
|
1.0
|
|
CG
|
F:ASP58
|
2.9
|
81.2
|
1.0
|
|
O1G
|
F:CTP601
|
3.3
|
0.0
|
0.5
|
|
O4
|
F:POP602
|
3.4
|
0.1
|
0.5
|
|
P
|
B:C74
|
3.5
|
94.3
|
0.5
|
|
PB
|
F:CTP601
|
3.5
|
0.5
|
0.5
|
|
O
|
F:ASP58
|
3.5
|
70.8
|
1.0
|
|
PA
|
F:CTP601
|
3.6
|
93.5
|
0.5
|
|
CB
|
F:ASP58
|
3.6
|
79.7
|
1.0
|
|
P1
|
F:POP602
|
3.7
|
0.0
|
0.5
|
|
OD1
|
F:ASP58
|
3.7
|
88.4
|
1.0
|
|
O3A
|
F:CTP601
|
3.8
|
0.6
|
0.5
|
|
O3B
|
F:CTP601
|
3.8
|
0.2
|
0.5
|
|
C
|
F:ASP58
|
3.9
|
72.8
|
1.0
|
|
O2
|
F:POP602
|
3.9
|
0.2
|
0.5
|
|
O5'
|
F:CTP601
|
3.9
|
67.6
|
0.5
|
|
O3'
|
B:A73
|
4.0
|
95.8
|
0.5
|
|
C5'
|
F:CTP601
|
4.1
|
81.5
|
0.5
|
|
PG
|
F:CTP601
|
4.2
|
0.4
|
0.5
|
|
O5
|
F:POP602
|
4.2
|
0.2
|
0.5
|
|
C5'
|
B:C74
|
4.2
|
96.8
|
0.5
|
|
P2
|
F:POP602
|
4.2
|
0.8
|
0.5
|
|
O3'
|
B:A73
|
4.3
|
95.2
|
0.5
|
|
O5'
|
B:C74
|
4.3
|
84.1
|
0.5
|
|
CB
|
F:ASP60
|
4.3
|
81.2
|
1.0
|
|
CA
|
F:ASP58
|
4.4
|
76.9
|
1.0
|
|
N
|
F:VAL59
|
4.4
|
70.7
|
1.0
|
|
C
|
F:VAL59
|
4.4
|
75.6
|
1.0
|
|
O
|
F:POP602
|
4.5
|
0.3
|
0.5
|
|
O
|
F:VAL59
|
4.5
|
80.0
|
1.0
|
|
OP2
|
B:C74
|
4.5
|
82.1
|
0.5
|
|
OD2
|
F:ASP112
|
4.6
|
80.3
|
1.0
|
|
N
|
F:ASP60
|
4.7
|
77.0
|
1.0
|
|
CA
|
F:VAL59
|
4.7
|
71.4
|
1.0
|
|
O2G
|
F:CTP601
|
4.8
|
0.1
|
0.5
|
|
N
|
F:GLY42
|
4.8
|
75.7
|
1.0
|
|
O3
|
F:POP602
|
4.9
|
0.6
|
0.5
|
|
O1B
|
F:CTP601
|
4.9
|
0.0
|
0.5
|
|
O2'
|
B:A73
|
5.0
|
97.9
|
0.5
|
|
Magnesium binding site 3 out
of 4 in 3wfr
Go back to
Magnesium Binding Sites List in 3wfr
Magnesium binding site 3 out
of 4 in the Trna Processing Enzyme Complex 2
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Trna Processing Enzyme Complex 2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg603
b:76.4
occ:1.00
|
OP1
|
C:C75
|
2.1
|
48.7
|
0.5
|
|
OD2
|
G:ASP58
|
2.1
|
0.6
|
1.0
|
|
O1A
|
G:CTP601
|
2.2
|
49.4
|
0.5
|
|
OD1
|
G:ASP60
|
2.4
|
85.5
|
1.0
|
|
OD2
|
G:ASP60
|
2.5
|
78.2
|
1.0
|
|
O2B
|
G:CTP601
|
2.7
|
81.6
|
0.5
|
|
CG
|
G:ASP60
|
2.8
|
78.9
|
1.0
|
|
O
|
G:POP602
|
2.8
|
90.2
|
0.5
|
|
O6
|
G:POP602
|
2.9
|
82.0
|
0.5
|
|
CG
|
G:ASP58
|
3.0
|
1.0
|
1.0
|
|
PA
|
G:CTP601
|
3.3
|
70.3
|
0.5
|
|
O1G
|
G:CTP601
|
3.3
|
98.1
|
0.5
|
|
P
|
C:C75
|
3.5
|
83.3
|
0.5
|
|
P2
|
G:POP602
|
3.5
|
79.1
|
0.5
|
|
C5'
|
C:C75
|
3.5
|
67.9
|
0.5
|
|
O5'
|
G:CTP601
|
3.5
|
67.8
|
0.5
|
|
PB
|
G:CTP601
|
3.5
|
79.9
|
0.5
|
|
O3A
|
G:CTP601
|
3.6
|
63.8
|
0.5
|
|
OD1
|
G:ASP58
|
3.7
|
0.3
|
1.0
|
|
C5'
|
G:CTP601
|
3.7
|
68.6
|
0.5
|
|
CB
|
G:ASP58
|
3.8
|
0.9
|
1.0
|
|
O3B
|
G:CTP601
|
3.8
|
85.8
|
0.5
|
|
O
|
G:ASP58
|
3.8
|
84.9
|
1.0
|
|
O5'
|
C:C75
|
3.9
|
69.0
|
0.5
|
|
O3'
|
C:C74
|
4.1
|
84.5
|
0.5
|
|
O3'
|
C:C74
|
4.1
|
84.6
|
0.5
|
|
PG
|
G:CTP601
|
4.1
|
97.9
|
0.5
|
|
P1
|
G:POP602
|
4.2
|
95.4
|
0.5
|
|
C
|
G:ASP58
|
4.2
|
86.0
|
1.0
|
|
O3
|
G:POP602
|
4.3
|
99.8
|
0.5
|
|
CB
|
G:ASP60
|
4.3
|
72.6
|
1.0
|
|
O5
|
G:POP602
|
4.4
|
74.3
|
0.5
|
|
OD2
|
G:ASP112
|
4.5
|
73.7
|
1.0
|
|
O4
|
G:POP602
|
4.6
|
83.4
|
0.5
|
|
O2A
|
G:CTP601
|
4.6
|
75.9
|
0.5
|
|
OP2
|
C:C75
|
4.6
|
80.9
|
0.5
|
|
CA
|
G:ASP58
|
4.7
|
90.3
|
1.0
|
|
O2G
|
G:CTP601
|
4.7
|
97.7
|
0.5
|
|
C4'
|
C:C75
|
4.8
|
65.2
|
0.5
|
|
N
|
G:VAL59
|
4.8
|
76.9
|
1.0
|
|
O1
|
G:POP602
|
4.9
|
97.6
|
0.5
|
|
C
|
G:VAL59
|
4.9
|
65.2
|
1.0
|
|
N
|
G:GLY42
|
4.9
|
79.5
|
1.0
|
|
N
|
G:ASP60
|
4.9
|
65.3
|
1.0
|
|
O1B
|
G:CTP601
|
5.0
|
82.4
|
0.5
|
|
Magnesium binding site 4 out
of 4 in 3wfr
Go back to
Magnesium Binding Sites List in 3wfr
Magnesium binding site 4 out
of 4 in the Trna Processing Enzyme Complex 2
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Trna Processing Enzyme Complex 2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg603
b:55.3
occ:1.00
|
O2B
|
H:CTP601
|
2.0
|
80.2
|
0.5
|
|
OD2
|
H:ASP58
|
2.1
|
59.2
|
1.0
|
|
OP1
|
D:C75
|
2.1
|
63.2
|
0.5
|
|
OD1
|
H:ASP60
|
2.3
|
70.1
|
1.0
|
|
O1A
|
H:CTP601
|
2.3
|
47.1
|
0.5
|
|
O1
|
H:POP602
|
2.3
|
80.8
|
0.5
|
|
OD2
|
H:ASP60
|
2.9
|
58.8
|
1.0
|
|
CG
|
H:ASP60
|
3.0
|
63.3
|
1.0
|
|
CG
|
H:ASP58
|
3.0
|
66.8
|
1.0
|
|
PB
|
H:CTP601
|
3.2
|
80.6
|
0.5
|
|
PA
|
H:CTP601
|
3.3
|
48.5
|
0.5
|
|
O4
|
H:POP602
|
3.4
|
0.9
|
0.5
|
|
O1G
|
H:CTP601
|
3.4
|
0.5
|
0.5
|
|
O5'
|
H:CTP601
|
3.5
|
52.9
|
0.5
|
|
P
|
D:C75
|
3.5
|
66.8
|
0.5
|
|
O3A
|
H:CTP601
|
3.6
|
66.1
|
0.5
|
|
P1
|
H:POP602
|
3.7
|
82.1
|
0.5
|
|
O3B
|
H:CTP601
|
3.7
|
36.1
|
0.5
|
|
C5'
|
H:CTP601
|
3.7
|
53.9
|
0.5
|
|
CB
|
H:ASP58
|
3.8
|
67.4
|
1.0
|
|
OD1
|
H:ASP58
|
3.8
|
76.7
|
1.0
|
|
C5'
|
D:C75
|
3.8
|
74.4
|
0.5
|
|
O
|
H:ASP58
|
3.9
|
69.6
|
1.0
|
|
O5
|
H:POP602
|
4.0
|
0.8
|
0.5
|
|
O2
|
H:POP602
|
4.0
|
75.9
|
0.5
|
|
PG
|
H:CTP601
|
4.0
|
0.1
|
0.5
|
|
O3'
|
D:C74
|
4.1
|
62.1
|
0.5
|
|
P2
|
H:POP602
|
4.1
|
0.5
|
0.5
|
|
O5'
|
D:C75
|
4.2
|
73.0
|
0.5
|
|
C
|
H:ASP58
|
4.2
|
62.0
|
1.0
|
|
O2G
|
H:CTP601
|
4.3
|
0.8
|
0.5
|
|
O
|
H:POP602
|
4.4
|
37.0
|
0.5
|
|
CB
|
H:ASP60
|
4.4
|
59.4
|
1.0
|
|
N
|
H:GLY42
|
4.5
|
61.4
|
1.0
|
|
O1B
|
H:CTP601
|
4.5
|
85.4
|
0.5
|
|
O3'
|
D:C74
|
4.6
|
63.7
|
0.5
|
|
OP2
|
D:C75
|
4.6
|
67.8
|
0.5
|
|
OD2
|
H:ASP112
|
4.6
|
0.6
|
1.0
|
|
CA
|
H:ASP58
|
4.6
|
62.1
|
1.0
|
|
CA
|
H:GLY42
|
4.7
|
59.1
|
1.0
|
|
O2A
|
H:CTP601
|
4.7
|
48.5
|
0.5
|
|
O3
|
H:POP602
|
4.7
|
86.8
|
0.5
|
|
N
|
H:VAL59
|
4.8
|
56.8
|
1.0
|
|
O2'
|
D:C74
|
4.8
|
81.6
|
0.5
|
|
N
|
H:ASP60
|
4.9
|
70.3
|
1.0
|
|
Reference:
S.Yamashita,
D.Takeshita,
K.Tomita.
Translocation and Rotation of Trna During Template-Independent Rna Polymerization By Trna Nucleotidyltransferase Structure V. 22 315 2014.
ISSN: ISSN 0969-2126
PubMed: 24389024
DOI: 10.1016/J.STR.2013.12.002
Page generated: Mon Dec 14 09:00:53 2020
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