Magnesium in PDB 6p24: Escherichia Coli Trna Synthetase
Enzymatic activity of Escherichia Coli Trna Synthetase
All present enzymatic activity of Escherichia Coli Trna Synthetase:
6.1.1.20;
Protein crystallography data
The structure of Escherichia Coli Trna Synthetase, PDB code: 6p24
was solved by
D.Kahne,
V.Baidin,
T.W.Owens,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
82.04 /
2.12
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.269,
173.583,
251.472,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.9 /
26.5
|
Other elements in 6p24:
The structure of Escherichia Coli Trna Synthetase also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
13;
Binding sites:
The binding sites of Magnesium atom in the Escherichia Coli Trna Synthetase
(pdb code 6p24). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the
Escherichia Coli Trna Synthetase, PDB code: 6p24:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 13 in 6p24
Go back to
Magnesium Binding Sites List in 6p24
Magnesium binding site 1 out
of 13 in the Escherichia Coli Trna Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:48.1
occ:1.00
|
OE2
|
A:GLU252
|
2.0
|
46.4
|
1.0
|
OE1
|
B:GLU463
|
2.1
|
39.5
|
1.0
|
CD
|
A:GLU252
|
3.0
|
46.8
|
1.0
|
CD
|
B:GLU463
|
3.2
|
40.8
|
1.0
|
OE1
|
A:GLU252
|
3.3
|
41.4
|
1.0
|
OE2
|
B:GLU463
|
4.0
|
35.0
|
1.0
|
O
|
B:HOH1005
|
4.0
|
41.6
|
1.0
|
CG
|
B:GLU463
|
4.0
|
40.0
|
1.0
|
CB
|
B:GLU463
|
4.0
|
37.0
|
1.0
|
OD1
|
B:ASP460
|
4.1
|
51.9
|
1.0
|
OD2
|
B:ASP454
|
4.2
|
48.9
|
1.0
|
ND2
|
B:ASN165
|
4.3
|
46.4
|
1.0
|
O
|
B:HOH924
|
4.3
|
38.2
|
1.0
|
OE2
|
B:GLU464
|
4.3
|
48.8
|
1.0
|
O
|
B:ASP454
|
4.3
|
46.2
|
1.0
|
CA
|
B:ASP460
|
4.3
|
39.7
|
1.0
|
O
|
B:ASP460
|
4.3
|
38.7
|
1.0
|
CG
|
A:GLU252
|
4.4
|
40.3
|
1.0
|
CB
|
B:ASP460
|
4.5
|
40.2
|
1.0
|
CG
|
B:ASP460
|
4.6
|
46.5
|
1.0
|
O
|
A:HOH535
|
4.8
|
55.4
|
1.0
|
C
|
B:ASP460
|
4.8
|
47.2
|
1.0
|
CB
|
B:ASP454
|
4.8
|
40.0
|
1.0
|
CG
|
B:ASP454
|
4.9
|
47.2
|
1.0
|
|
Magnesium binding site 2 out
of 13 in 6p24
Go back to
Magnesium Binding Sites List in 6p24
Magnesium binding site 2 out
of 13 in the Escherichia Coli Trna Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:63.4
occ:1.00
|
OD1
|
A:ASN103
|
2.1
|
55.0
|
1.0
|
NZ
|
D:LYS505
|
2.9
|
40.9
|
1.0
|
O
|
B:ASP504
|
3.0
|
41.2
|
1.0
|
O
|
A:HOH516
|
3.0
|
49.1
|
1.0
|
CG
|
A:ASN103
|
3.2
|
69.0
|
1.0
|
O
|
A:ILE101
|
3.3
|
50.4
|
1.0
|
C
|
B:ASP504
|
3.3
|
42.3
|
1.0
|
CA
|
A:ASN103
|
3.4
|
52.9
|
1.0
|
O
|
A:GLU102
|
3.5
|
55.5
|
1.0
|
CA
|
B:ASP504
|
3.6
|
46.4
|
1.0
|
CE
|
D:LYS505
|
3.6
|
38.7
|
1.0
|
N
|
A:ASN103
|
3.6
|
52.1
|
1.0
|
O
|
B:ASN503
|
3.6
|
40.1
|
1.0
|
C
|
A:GLU102
|
3.7
|
54.9
|
1.0
|
CB
|
A:ASN103
|
3.9
|
56.7
|
1.0
|
N
|
B:GLY506
|
4.1
|
36.7
|
1.0
|
N
|
B:LYS505
|
4.2
|
46.8
|
1.0
|
C
|
A:ILE101
|
4.3
|
46.8
|
1.0
|
CG2
|
A:ILE101
|
4.3
|
41.6
|
1.0
|
ND2
|
A:ASN103
|
4.3
|
51.3
|
1.0
|
C
|
B:ASN503
|
4.5
|
37.7
|
1.0
|
N
|
B:ASP504
|
4.5
|
44.5
|
1.0
|
CB
|
B:ASP504
|
4.6
|
45.2
|
1.0
|
CA
|
B:LYS505
|
4.7
|
43.5
|
1.0
|
C
|
A:ASN103
|
4.7
|
47.0
|
1.0
|
C
|
B:LYS505
|
4.7
|
43.2
|
1.0
|
CA
|
B:GLY506
|
4.8
|
44.4
|
1.0
|
OG
|
D:SER623
|
4.8
|
41.0
|
1.0
|
CA
|
A:GLU102
|
4.8
|
53.2
|
1.0
|
N
|
A:GLY104
|
4.9
|
50.0
|
1.0
|
O
|
D:HOH985
|
4.9
|
45.4
|
1.0
|
OD1
|
B:ASP504
|
4.9
|
41.4
|
1.0
|
N
|
A:GLU102
|
4.9
|
48.2
|
1.0
|
|
Magnesium binding site 3 out
of 13 in 6p24
Go back to
Magnesium Binding Sites List in 6p24
Magnesium binding site 3 out
of 13 in the Escherichia Coli Trna Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:56.3
occ:1.00
|
OE1
|
A:GLU268
|
2.1
|
57.6
|
1.0
|
OE1
|
B:GLU31
|
2.3
|
67.4
|
1.0
|
OE1
|
A:GLU256
|
2.6
|
59.3
|
1.0
|
CD
|
A:GLU268
|
2.7
|
75.5
|
1.0
|
OE2
|
A:GLU268
|
2.8
|
60.9
|
1.0
|
OE2
|
A:GLU256
|
2.9
|
49.9
|
1.0
|
CD
|
A:GLU256
|
3.1
|
56.8
|
1.0
|
CD
|
B:GLU31
|
3.2
|
52.8
|
1.0
|
OE2
|
B:GLU31
|
3.5
|
74.3
|
1.0
|
O
|
B:HOH969
|
3.5
|
55.6
|
1.0
|
NH1
|
A:ARG244
|
4.0
|
43.3
|
1.0
|
CG
|
A:GLU268
|
4.2
|
66.7
|
1.0
|
CG
|
A:GLU256
|
4.5
|
43.7
|
1.0
|
CG
|
B:GLU31
|
4.6
|
55.3
|
1.0
|
NH2
|
A:ARG244
|
4.6
|
42.8
|
1.0
|
CZ
|
A:ARG244
|
4.8
|
46.1
|
1.0
|
CB
|
B:GLU31
|
4.9
|
42.8
|
1.0
|
CB
|
A:GLU268
|
4.9
|
60.7
|
1.0
|
|
Magnesium binding site 4 out
of 13 in 6p24
Go back to
Magnesium Binding Sites List in 6p24
Magnesium binding site 4 out
of 13 in the Escherichia Coli Trna Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:68.9
occ:1.00
|
O
|
A:GLY308
|
3.5
|
52.9
|
1.0
|
OG1
|
A:THR310
|
3.6
|
66.8
|
1.0
|
N
|
A:THR310
|
3.7
|
52.0
|
1.0
|
O
|
A:HOH526
|
3.8
|
61.5
|
1.0
|
CG2
|
A:THR310
|
3.8
|
45.2
|
1.0
|
CB
|
D:ALA697
|
3.9
|
54.8
|
1.0
|
CA
|
A:VAL309
|
4.1
|
46.6
|
1.0
|
O
|
D:ALA697
|
4.2
|
51.7
|
1.0
|
CB
|
A:THR310
|
4.2
|
51.3
|
1.0
|
C
|
D:ALA697
|
4.3
|
53.0
|
1.0
|
O
|
D:ARG698
|
4.3
|
53.6
|
1.0
|
C
|
D:ARG698
|
4.3
|
64.0
|
1.0
|
C
|
A:VAL309
|
4.4
|
49.5
|
1.0
|
C
|
A:GLY308
|
4.5
|
50.9
|
1.0
|
N
|
D:GLU699
|
4.6
|
64.3
|
1.0
|
N
|
D:ARG698
|
4.6
|
54.5
|
1.0
|
CA
|
A:THR310
|
4.6
|
53.2
|
1.0
|
CA
|
D:ALA697
|
4.8
|
53.2
|
1.0
|
CA
|
D:GLU699
|
4.8
|
66.8
|
1.0
|
CA
|
D:ARG698
|
4.8
|
58.0
|
1.0
|
N
|
A:VAL309
|
4.8
|
48.2
|
1.0
|
O
|
D:HOH1110
|
5.0
|
62.9
|
1.0
|
|
Magnesium binding site 5 out
of 13 in 6p24
Go back to
Magnesium Binding Sites List in 6p24
Magnesium binding site 5 out
of 13 in the Escherichia Coli Trna Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:73.7
occ:1.00
|
O
|
D:HOH933
|
2.8
|
50.5
|
1.0
|
O
|
A:LYS327
|
2.8
|
76.6
|
1.0
|
O
|
D:LEU627
|
3.1
|
53.2
|
1.0
|
O
|
D:HOH1060
|
3.2
|
51.1
|
1.0
|
OXT
|
A:LYS327
|
3.3
|
78.5
|
1.0
|
C
|
A:LYS327
|
3.4
|
70.5
|
1.0
|
N
|
D:GLY629
|
3.8
|
53.4
|
1.0
|
C
|
D:LEU627
|
3.9
|
46.3
|
1.0
|
CA
|
D:GLY629
|
4.0
|
41.7
|
1.0
|
C
|
D:THR628
|
4.0
|
47.5
|
1.0
|
O
|
D:VAL693
|
4.1
|
59.8
|
1.0
|
CB
|
D:ARG692
|
4.3
|
42.3
|
1.0
|
O
|
D:THR628
|
4.3
|
46.7
|
1.0
|
CD
|
D:ARG692
|
4.3
|
40.8
|
1.0
|
O
|
D:ASP626
|
4.6
|
40.7
|
1.0
|
CA
|
D:THR628
|
4.6
|
54.5
|
1.0
|
N
|
D:THR628
|
4.7
|
54.9
|
1.0
|
CA
|
D:LEU627
|
4.8
|
50.2
|
1.0
|
CG
|
D:ARG692
|
4.8
|
52.4
|
1.0
|
CA
|
A:LYS327
|
4.8
|
65.0
|
1.0
|
N
|
D:VAL693
|
4.9
|
48.6
|
1.0
|
NH1
|
D:ARG692
|
4.9
|
55.1
|
1.0
|
|
Magnesium binding site 6 out
of 13 in 6p24
Go back to
Magnesium Binding Sites List in 6p24
Magnesium binding site 6 out
of 13 in the Escherichia Coli Trna Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg801
b:69.4
occ:1.00
|
OE2
|
B:GLU31
|
3.4
|
74.3
|
1.0
|
NH2
|
A:ARG244
|
3.8
|
42.8
|
1.0
|
CD
|
B:GLU31
|
4.1
|
52.8
|
1.0
|
CZ
|
A:ARG244
|
4.2
|
46.1
|
1.0
|
CG
|
B:GLU31
|
4.2
|
55.3
|
1.0
|
O
|
A:TRP266
|
4.4
|
55.7
|
1.0
|
NH2
|
A:ARG242
|
4.4
|
47.3
|
1.0
|
OD2
|
A:ASP258
|
4.5
|
52.7
|
1.0
|
NE
|
A:ARG244
|
4.6
|
51.1
|
1.0
|
NH1
|
A:ARG244
|
4.7
|
43.3
|
1.0
|
CG2
|
B:THR26
|
4.8
|
43.0
|
1.0
|
OE1
|
A:GLU268
|
4.9
|
57.6
|
1.0
|
CG
|
A:ASP258
|
4.9
|
54.9
|
1.0
|
OD1
|
A:ASP258
|
4.9
|
50.0
|
1.0
|
CB
|
A:GLU268
|
5.0
|
60.7
|
1.0
|
|
Magnesium binding site 7 out
of 13 in 6p24
Go back to
Magnesium Binding Sites List in 6p24
Magnesium binding site 7 out
of 13 in the Escherichia Coli Trna Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg802
b:58.8
occ:1.00
|
O
|
A:HOH518
|
2.6
|
39.3
|
1.0
|
O
|
A:HOH545
|
2.7
|
50.9
|
1.0
|
OE2
|
B:GLU459
|
3.0
|
53.1
|
1.0
|
CG
|
B:GLU459
|
3.5
|
43.1
|
1.0
|
CD1
|
B:LEU416
|
3.5
|
58.6
|
1.0
|
CD
|
B:GLU459
|
3.6
|
50.0
|
1.0
|
O
|
A:HOH536
|
3.8
|
42.2
|
1.0
|
NZ
|
B:LYS412
|
3.8
|
69.7
|
1.0
|
CD
|
A:PRO277
|
4.0
|
51.5
|
1.0
|
CD2
|
B:LEU416
|
4.0
|
52.0
|
1.0
|
O
|
A:VAL275
|
4.0
|
46.6
|
1.0
|
CG
|
B:LEU416
|
4.2
|
59.7
|
1.0
|
CB
|
A:PRO277
|
4.2
|
44.9
|
1.0
|
N
|
A:PRO277
|
4.3
|
49.5
|
1.0
|
CG
|
A:PRO277
|
4.3
|
41.5
|
1.0
|
CA
|
A:PRO277
|
4.5
|
51.8
|
1.0
|
CB
|
A:PRO287
|
4.5
|
57.4
|
1.0
|
CE
|
B:LYS412
|
4.7
|
61.9
|
1.0
|
O
|
A:PRO287
|
4.8
|
53.5
|
1.0
|
CD
|
B:LYS412
|
4.8
|
53.0
|
1.0
|
OE1
|
B:GLU459
|
4.8
|
51.5
|
1.0
|
CB
|
B:GLU459
|
4.9
|
40.3
|
1.0
|
|
Magnesium binding site 8 out
of 13 in 6p24
Go back to
Magnesium Binding Sites List in 6p24
Magnesium binding site 8 out
of 13 in the Escherichia Coli Trna Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg803
b:62.5
occ:1.00
|
OG1
|
B:THR253
|
2.6
|
58.7
|
1.0
|
O
|
B:HOH929
|
2.8
|
55.3
|
1.0
|
OD1
|
B:ASN254
|
2.8
|
50.8
|
1.0
|
O
|
B:MET264
|
3.2
|
65.5
|
1.0
|
CB
|
B:THR253
|
3.3
|
57.6
|
1.0
|
CG
|
B:ASN254
|
3.7
|
48.9
|
1.0
|
C
|
B:THR253
|
3.8
|
55.1
|
1.0
|
N
|
B:ASN254
|
3.8
|
51.9
|
1.0
|
O
|
B:THR253
|
4.1
|
57.2
|
1.0
|
CG2
|
B:VAL250
|
4.1
|
55.7
|
1.0
|
CA
|
B:THR253
|
4.1
|
57.4
|
1.0
|
O
|
B:VAL250
|
4.2
|
63.7
|
1.0
|
CA
|
B:ASN254
|
4.2
|
52.7
|
1.0
|
C
|
B:MET264
|
4.3
|
65.5
|
1.0
|
CG2
|
B:THR253
|
4.5
|
62.0
|
1.0
|
ND2
|
B:ASN254
|
4.5
|
43.9
|
1.0
|
CB
|
B:ASN254
|
4.6
|
54.4
|
1.0
|
N
|
B:MET264
|
4.9
|
56.2
|
1.0
|
|
Magnesium binding site 9 out
of 13 in 6p24
Go back to
Magnesium Binding Sites List in 6p24
Magnesium binding site 9 out
of 13 in the Escherichia Coli Trna Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg804
b:78.3
occ:1.00
|
O
|
C:HOH526
|
3.4
|
39.7
|
1.0
|
ND1
|
B:HIS488
|
3.5
|
65.4
|
1.0
|
OG
|
C:SER118
|
3.5
|
60.0
|
1.0
|
CE1
|
C:PHE119
|
4.1
|
52.5
|
1.0
|
CG
|
B:HIS488
|
4.4
|
61.2
|
1.0
|
CE1
|
B:HIS488
|
4.4
|
48.9
|
1.0
|
O
|
B:HOH1029
|
4.4
|
53.5
|
1.0
|
CB
|
B:HIS488
|
4.4
|
50.0
|
1.0
|
CB
|
C:SER118
|
4.5
|
42.5
|
1.0
|
CD1
|
C:PHE119
|
4.7
|
51.2
|
1.0
|
CZ
|
C:PHE119
|
4.9
|
54.7
|
1.0
|
CA
|
C:ARG115
|
4.9
|
46.4
|
1.0
|
O
|
C:ARG115
|
5.0
|
43.9
|
1.0
|
|
Magnesium binding site 10 out
of 13 in 6p24
Go back to
Magnesium Binding Sites List in 6p24
Magnesium binding site 10 out
of 13 in the Escherichia Coli Trna Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg401
b:73.3
occ:1.00
|
OE2
|
C:GLU268
|
2.1
|
67.2
|
1.0
|
OE2
|
D:GLU31
|
2.4
|
70.1
|
1.0
|
O2
|
C:EDO406
|
2.6
|
76.4
|
1.0
|
O
|
C:HOH543
|
2.8
|
70.7
|
1.0
|
CD
|
C:GLU268
|
3.0
|
78.8
|
1.0
|
CD
|
D:GLU31
|
3.1
|
55.4
|
1.0
|
OE1
|
D:GLU31
|
3.2
|
66.8
|
1.0
|
OE1
|
C:GLU268
|
3.2
|
74.4
|
1.0
|
OE2
|
C:GLU256
|
3.5
|
68.0
|
1.0
|
C2
|
C:EDO406
|
3.6
|
77.7
|
1.0
|
OE1
|
C:GLU256
|
4.0
|
63.3
|
1.0
|
O
|
D:HOH1065
|
4.1
|
59.5
|
1.0
|
CD
|
C:GLU256
|
4.1
|
62.4
|
1.0
|
NH1
|
C:ARG244
|
4.3
|
58.4
|
1.0
|
CG
|
C:GLU268
|
4.4
|
67.2
|
1.0
|
CG
|
D:GLU31
|
4.6
|
49.4
|
1.0
|
NH2
|
C:ARG244
|
4.8
|
44.9
|
1.0
|
C1
|
C:EDO406
|
4.9
|
67.9
|
1.0
|
CB
|
C:GLU268
|
5.0
|
55.6
|
1.0
|
|
Reference:
D.Kahne,
V.Baidin,
T.W.Owens.
Escherichia Coli Trna Synthetase To Be Published.
Page generated: Tue Oct 1 13:50:42 2024
|