Magnesium in PDB 8c49: Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
Enzymatic activity of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
All present enzymatic activity of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp:
6.1.1.26;
Protein crystallography data
The structure of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp, PDB code: 8c49
was solved by
F.J.Hardy,
C.W.Levy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
51.90 /
1.82
|
|
Space group
|
P 61
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.932,
59.932,
263.231,
90,
90,
120
|
|
R / Rfree (%)
|
19.5 /
20.9
|
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
(pdb code 8c49). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the
Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp, PDB code: 8c49:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 11 in 8c49
Go back to
Magnesium Binding Sites List in 8c49
Magnesium binding site 1 out
of 11 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
 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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg309
b:22.1
occ:1.00
|
O2B
|
A:ANP301
|
1.9
|
21.8
|
1.0
|
|
O2G
|
A:ANP301
|
2.0
|
22.8
|
1.0
|
|
O
|
A:HOH425
|
2.1
|
20.9
|
1.0
|
|
O
|
A:HOH454
|
2.1
|
20.4
|
1.0
|
|
O
|
A:HOH466
|
2.2
|
22.8
|
1.0
|
|
O
|
A:HOH414
|
2.2
|
21.8
|
1.0
|
|
HH11
|
A:ARG150
|
3.2
|
25.5
|
1.0
|
|
HE2
|
A:HIS158
|
3.3
|
27.4
|
1.0
|
|
PG
|
A:ANP301
|
3.3
|
21.4
|
1.0
|
|
PB
|
A:ANP301
|
3.3
|
23.4
|
1.0
|
|
HH12
|
A:ARG150
|
3.8
|
25.5
|
1.0
|
|
O1G
|
A:ANP301
|
3.8
|
22.9
|
1.0
|
|
NH1
|
A:ARG150
|
3.8
|
21.2
|
1.0
|
|
N3B
|
A:ANP301
|
3.8
|
22.9
|
1.0
|
|
O
|
A:HOH509
|
3.8
|
28.2
|
1.0
|
|
HE22
|
A:GLN107
|
3.8
|
29.4
|
1.0
|
|
NE2
|
A:HIS158
|
4.0
|
22.8
|
1.0
|
|
OE2
|
A:GLU152
|
4.1
|
20.5
|
1.0
|
|
HD2
|
A:HIS158
|
4.1
|
27.4
|
1.0
|
|
O3A
|
A:ANP301
|
4.1
|
21.6
|
1.0
|
|
OE1
|
A:GLN107
|
4.3
|
24.7
|
1.0
|
|
O1B
|
A:ANP301
|
4.4
|
19.7
|
1.0
|
|
HD3
|
A:ARG150
|
4.4
|
24.1
|
1.0
|
|
CD2
|
A:HIS158
|
4.4
|
22.8
|
1.0
|
|
N7
|
A:ANP301
|
4.5
|
22.1
|
1.0
|
|
OE1
|
A:GLU152
|
4.5
|
24.2
|
1.0
|
|
O
|
A:HOH482
|
4.5
|
32.5
|
1.0
|
|
O3G
|
A:ANP301
|
4.5
|
23.3
|
1.0
|
|
HNB1
|
A:ANP301
|
4.6
|
27.6
|
1.0
|
|
NE2
|
A:GLN107
|
4.6
|
24.4
|
1.0
|
|
CD
|
A:GLU152
|
4.7
|
23.8
|
1.0
|
|
H8
|
A:ANP301
|
4.8
|
24.8
|
1.0
|
|
HD2
|
A:ARG150
|
4.8
|
24.1
|
1.0
|
|
HN61
|
A:ANP301
|
4.9
|
26.3
|
1.0
|
|
CD
|
A:GLN107
|
4.9
|
24.3
|
1.0
|
|
C8
|
A:ANP301
|
5.0
|
20.6
|
1.0
|
|
Magnesium binding site 2 out
of 11 in 8c49
Go back to
Magnesium Binding Sites List in 8c49
Magnesium binding site 2 out
of 11 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
 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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg310
b:19.1
occ:1.00
|
O2A
|
A:ANP301
|
1.9
|
21.6
|
1.0
|
|
OG
|
A:SER221
|
2.1
|
20.4
|
1.0
|
|
OE2
|
A:GLU218
|
2.1
|
21.3
|
1.0
|
|
O
|
A:HOH429
|
2.2
|
21.2
|
1.0
|
|
O1B
|
A:ANP301
|
2.2
|
19.7
|
1.0
|
|
O
|
A:HOH483
|
2.3
|
21.3
|
1.0
|
|
CD
|
A:GLU218
|
3.1
|
23.8
|
1.0
|
|
HB2
|
A:SER221
|
3.1
|
24.7
|
1.0
|
|
CB
|
A:SER221
|
3.1
|
20.5
|
1.0
|
|
HNB1
|
A:ANP301
|
3.2
|
27.6
|
1.0
|
|
HO3'
|
A:ANP301
|
3.2
|
27.6
|
1.0
|
|
PA
|
A:ANP301
|
3.2
|
20.4
|
1.0
|
|
PB
|
A:ANP301
|
3.2
|
23.4
|
1.0
|
|
OE1
|
A:GLU218
|
3.5
|
21.5
|
1.0
|
|
O3A
|
A:ANP301
|
3.5
|
21.6
|
1.0
|
|
HB3
|
A:SER221
|
3.5
|
24.7
|
1.0
|
|
N3B
|
A:ANP301
|
3.7
|
22.9
|
1.0
|
|
H3'
|
A:ANP301
|
3.8
|
26.0
|
1.0
|
|
O
|
A:HOH420
|
3.9
|
22.6
|
1.0
|
|
OD2
|
A:ASP211
|
4.0
|
24.4
|
1.0
|
|
O1A
|
A:ANP301
|
4.0
|
22.3
|
1.0
|
|
O
|
A:HOH493
|
4.0
|
26.9
|
1.0
|
|
H5'2
|
A:ANP301
|
4.0
|
26.8
|
1.0
|
|
O3'
|
A:ANP301
|
4.0
|
23.0
|
1.0
|
|
O
|
A:HOH479
|
4.1
|
28.6
|
1.0
|
|
HG1
|
A:THR209
|
4.2
|
27.7
|
1.0
|
|
OD1
|
A:ASP211
|
4.3
|
22.0
|
1.0
|
|
CG
|
A:GLU218
|
4.3
|
23.1
|
1.0
|
|
C3'
|
A:ANP301
|
4.3
|
21.6
|
1.0
|
|
CA
|
A:SER221
|
4.4
|
19.6
|
1.0
|
|
O5'
|
A:ANP301
|
4.4
|
23.3
|
1.0
|
|
HG3
|
A:GLU218
|
4.4
|
27.7
|
1.0
|
|
CG
|
A:ASP211
|
4.5
|
20.6
|
1.0
|
|
HA
|
A:SER221
|
4.5
|
23.6
|
1.0
|
|
O2B
|
A:ANP301
|
4.5
|
21.8
|
1.0
|
|
HG2
|
A:GLU218
|
4.5
|
27.7
|
1.0
|
|
C5'
|
A:ANP301
|
4.6
|
22.3
|
1.0
|
|
O
|
A:HOH441
|
4.7
|
34.1
|
1.0
|
|
N
|
A:SER221
|
4.7
|
19.7
|
1.0
|
|
HG21
|
A:THR209
|
4.8
|
28.9
|
1.0
|
|
MG
|
A:MG311
|
4.9
|
32.9
|
1.0
|
|
H
|
A:SER221
|
4.9
|
23.7
|
1.0
|
|
Magnesium binding site 3 out
of 11 in 8c49
Go back to
Magnesium Binding Sites List in 8c49
Magnesium binding site 3 out
of 11 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
 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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg311
b:32.9
occ:1.00
|
O
|
A:HOH493
|
2.1
|
26.9
|
1.0
|
|
O
|
A:HOH494
|
2.1
|
32.7
|
1.0
|
|
O
|
A:HOH497
|
2.2
|
30.2
|
1.0
|
|
O1G
|
A:ANP301
|
2.2
|
22.9
|
1.0
|
|
OE1
|
A:GLU218
|
2.3
|
21.5
|
1.0
|
|
O
|
A:HOH515
|
2.4
|
32.2
|
1.0
|
|
HNB1
|
A:ANP301
|
3.1
|
27.6
|
1.0
|
|
PG
|
A:ANP301
|
3.3
|
21.4
|
1.0
|
|
CD
|
A:GLU218
|
3.5
|
23.8
|
1.0
|
|
N3B
|
A:ANP301
|
3.7
|
22.9
|
1.0
|
|
O3G
|
A:ANP301
|
3.7
|
23.3
|
1.0
|
|
HB2
|
A:GLU218
|
3.9
|
28.0
|
1.0
|
|
O
|
A:HOH429
|
3.9
|
21.2
|
1.0
|
|
HB3
|
A:GLU218
|
4.0
|
28.0
|
1.0
|
|
O
|
A:HOH465
|
4.1
|
25.3
|
1.0
|
|
CB
|
A:GLU218
|
4.3
|
23.3
|
1.0
|
|
OE2
|
A:GLU218
|
4.3
|
21.3
|
1.0
|
|
O
|
A:HOH482
|
4.4
|
32.5
|
1.0
|
|
O1B
|
A:ANP301
|
4.4
|
19.7
|
1.0
|
|
CG
|
A:GLU218
|
4.5
|
23.1
|
1.0
|
|
HH12
|
A:ARG248
|
4.6
|
26.1
|
1.0
|
|
PB
|
A:ANP301
|
4.6
|
23.4
|
1.0
|
|
O
|
A:HOH456
|
4.6
|
30.0
|
1.0
|
|
O
|
A:HOH479
|
4.7
|
28.6
|
1.0
|
|
O2G
|
A:ANP301
|
4.7
|
22.8
|
1.0
|
|
MG
|
A:MG310
|
4.9
|
19.1
|
1.0
|
|
OD2
|
A:ASP211
|
4.9
|
24.4
|
1.0
|
|
HG3
|
A:GLU218
|
4.9
|
27.7
|
1.0
|
|
Magnesium binding site 4 out
of 11 in 8c49
Go back to
Magnesium Binding Sites List in 8c49
Magnesium binding site 4 out
of 11 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
 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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg312
b:18.8
occ:1.00
|
H
|
A:LEU121
|
2.3
|
23.3
|
1.0
|
|
H
|
A:ALA122
|
2.7
|
26.0
|
1.0
|
|
HB2
|
A:MET120
|
2.7
|
26.9
|
1.0
|
|
H1
|
A:PGE305
|
2.8
|
34.4
|
1.0
|
|
HG2
|
A:MET164
|
2.9
|
27.8
|
1.0
|
|
N
|
A:LEU121
|
3.0
|
19.4
|
1.0
|
|
HB2
|
A:LEU121
|
3.1
|
23.3
|
1.0
|
|
HE3
|
A:MET164
|
3.1
|
26.7
|
1.0
|
|
OD1
|
A:ASN166
|
3.1
|
25.4
|
1.0
|
|
O1
|
A:PGE305
|
3.1
|
30.7
|
1.0
|
|
HB2
|
A:ASN166
|
3.2
|
24.9
|
1.0
|
|
N
|
A:ALA122
|
3.3
|
21.6
|
1.0
|
|
C1
|
A:PGE305
|
3.4
|
28.6
|
1.0
|
|
HO1
|
A:PGE305
|
3.4
|
36.9
|
1.0
|
|
H3
|
A:PGE305
|
3.4
|
36.7
|
1.0
|
|
HB2
|
A:ALA122
|
3.5
|
29.1
|
1.0
|
|
H22
|
A:PGE305
|
3.6
|
33.2
|
1.0
|
|
CB
|
A:MET120
|
3.6
|
22.4
|
1.0
|
|
CA
|
A:LEU121
|
3.7
|
19.2
|
1.0
|
|
HA
|
A:MET120
|
3.7
|
26.2
|
1.0
|
|
CG
|
A:MET164
|
3.8
|
23.1
|
1.0
|
|
CB
|
A:LEU121
|
3.8
|
19.3
|
1.0
|
|
HA3
|
A:GLY243
|
3.8
|
25.2
|
1.0
|
|
CG
|
A:ASN166
|
3.9
|
22.4
|
1.0
|
|
C
|
A:MET120
|
3.9
|
21.4
|
1.0
|
|
HB3
|
A:MET120
|
3.9
|
26.9
|
1.0
|
|
C
|
A:LEU121
|
3.9
|
22.2
|
1.0
|
|
HG3
|
A:MET164
|
3.9
|
27.8
|
1.0
|
|
CE
|
A:MET164
|
4.0
|
22.2
|
1.0
|
|
CA
|
A:MET120
|
4.0
|
21.8
|
1.0
|
|
CB
|
A:ASN166
|
4.0
|
20.7
|
1.0
|
|
C2
|
A:PGE305
|
4.0
|
27.7
|
1.0
|
|
HG
|
A:LEU121
|
4.0
|
23.1
|
1.0
|
|
CB
|
A:ALA122
|
4.2
|
24.2
|
1.0
|
|
CA
|
A:ALA122
|
4.2
|
22.4
|
1.0
|
|
C3
|
A:PGE305
|
4.3
|
30.6
|
1.0
|
|
H32
|
A:PGE305
|
4.3
|
36.7
|
1.0
|
|
HA
|
A:ALA122
|
4.3
|
26.9
|
1.0
|
|
H12
|
A:PGE305
|
4.3
|
34.4
|
1.0
|
|
HE2
|
A:MET164
|
4.3
|
26.7
|
1.0
|
|
HB3
|
A:ALA122
|
4.4
|
29.1
|
1.0
|
|
SD
|
A:MET164
|
4.4
|
27.4
|
1.0
|
|
CG
|
A:LEU121
|
4.4
|
19.2
|
1.0
|
|
HD12
|
A:LEU121
|
4.4
|
23.4
|
1.0
|
|
H52
|
A:PGE305
|
4.5
|
29.8
|
1.0
|
|
HG
|
A:CYS148
|
4.5
|
22.9
|
1.0
|
|
HB3
|
A:ASN166
|
4.5
|
24.9
|
1.0
|
|
HA2
|
A:GLY243
|
4.5
|
25.2
|
1.0
|
|
HB3
|
A:LEU121
|
4.6
|
23.3
|
1.0
|
|
HA
|
A:LEU121
|
4.6
|
23.1
|
1.0
|
|
HE1
|
A:MET164
|
4.6
|
26.7
|
1.0
|
|
CA
|
A:GLY243
|
4.6
|
21.0
|
1.0
|
|
O2
|
A:PGE305
|
4.6
|
31.3
|
1.0
|
|
CG
|
A:MET120
|
4.7
|
24.6
|
1.0
|
|
HB3
|
A:MET164
|
4.9
|
25.0
|
1.0
|
|
HG3
|
A:MET120
|
4.9
|
29.5
|
1.0
|
|
H5'1
|
A:ANP301
|
4.9
|
26.8
|
1.0
|
|
H2
|
A:PGE305
|
4.9
|
33.2
|
1.0
|
|
CB
|
A:MET164
|
4.9
|
20.8
|
1.0
|
|
SD
|
A:MET120
|
5.0
|
29.6
|
1.0
|
|
CD1
|
A:LEU121
|
5.0
|
19.4
|
1.0
|
|
Magnesium binding site 5 out
of 11 in 8c49
Go back to
Magnesium Binding Sites List in 8c49
Magnesium binding site 5 out
of 11 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
 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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg313
b:32.0
occ:1.00
|
H
|
A:ARG173
|
2.3
|
31.2
|
1.0
|
|
O
|
A:HOH462
|
2.7
|
27.9
|
1.0
|
|
O
|
A:HOH471
|
2.9
|
33.9
|
1.0
|
|
OD2
|
A:ASP169
|
3.0
|
21.9
|
1.0
|
|
HB2
|
A:ARG173
|
3.0
|
33.7
|
1.0
|
|
N
|
A:ARG173
|
3.1
|
26.0
|
1.0
|
|
HA
|
A:PRO172
|
3.2
|
28.6
|
1.0
|
|
HD3
|
A:LYS141
|
3.2
|
32.5
|
1.0
|
|
HZ3
|
A:LYS141
|
3.3
|
36.9
|
1.0
|
|
HG3
|
A:PRO139
|
3.3
|
34.4
|
1.0
|
|
HG3
|
A:ARG173
|
3.5
|
34.4
|
1.0
|
|
CB
|
A:ARG173
|
3.7
|
28.1
|
1.0
|
|
HE2
|
A:TYR183
|
3.8
|
33.0
|
1.0
|
|
HG11
|
A:VAL179
|
3.8
|
26.8
|
1.0
|
|
CG
|
A:ASP169
|
3.9
|
21.3
|
1.0
|
|
CA
|
A:PRO172
|
3.9
|
23.8
|
1.0
|
|
HB3
|
A:PRO139
|
3.9
|
29.0
|
1.0
|
|
OD1
|
A:ASP169
|
3.9
|
22.6
|
1.0
|
|
CA
|
A:ARG173
|
3.9
|
25.7
|
1.0
|
|
C
|
A:PRO172
|
4.0
|
23.3
|
1.0
|
|
OH
|
A:TYR183
|
4.1
|
34.7
|
1.0
|
|
CG
|
A:ARG173
|
4.1
|
28.6
|
1.0
|
|
HB2
|
A:PRO172
|
4.1
|
27.8
|
1.0
|
|
NZ
|
A:LYS141
|
4.1
|
30.7
|
1.0
|
|
CG
|
A:PRO139
|
4.1
|
28.6
|
1.0
|
|
HB3
|
A:PRO172
|
4.1
|
27.8
|
1.0
|
|
HH11
|
A:ARG173
|
4.2
|
40.0
|
1.0
|
|
HB2
|
A:PRO139
|
4.2
|
29.0
|
1.0
|
|
CD
|
A:LYS141
|
4.2
|
27.0
|
1.0
|
|
HZ2
|
A:LYS141
|
4.2
|
36.9
|
1.0
|
|
CB
|
A:PRO139
|
4.3
|
24.1
|
1.0
|
|
CB
|
A:PRO172
|
4.3
|
23.1
|
1.0
|
|
HG2
|
A:PRO139
|
4.3
|
34.4
|
1.0
|
|
HD2
|
A:ARG173
|
4.4
|
38.7
|
1.0
|
|
O
|
A:ARG173
|
4.4
|
25.4
|
1.0
|
|
HG13
|
A:VAL179
|
4.5
|
26.8
|
1.0
|
|
C
|
A:ARG173
|
4.6
|
28.8
|
1.0
|
|
CE2
|
A:TYR183
|
4.6
|
27.4
|
1.0
|
|
HB3
|
A:ARG173
|
4.6
|
33.7
|
1.0
|
|
CG1
|
A:VAL179
|
4.6
|
22.3
|
1.0
|
|
CE
|
A:LYS141
|
4.7
|
27.8
|
1.0
|
|
HG21
|
A:VAL179
|
4.7
|
27.2
|
1.0
|
|
HD2
|
A:LYS141
|
4.7
|
32.5
|
1.0
|
|
HH
|
A:TYR183
|
4.7
|
41.7
|
1.0
|
|
HZ1
|
A:LYS141
|
4.7
|
36.9
|
1.0
|
|
HA
|
A:ARG173
|
4.8
|
30.9
|
1.0
|
|
HE2
|
A:LYS141
|
4.8
|
33.4
|
1.0
|
|
CZ
|
A:TYR183
|
4.8
|
29.8
|
1.0
|
|
CD
|
A:ARG173
|
4.8
|
32.2
|
1.0
|
|
HG2
|
A:ARG173
|
4.8
|
34.4
|
1.0
|
|
NH1
|
A:ARG173
|
4.9
|
33.3
|
1.0
|
|
HG2
|
A:LYS141
|
4.9
|
28.4
|
1.0
|
|
HG22
|
A:VAL179
|
4.9
|
27.2
|
1.0
|
|
Magnesium binding site 6 out
of 11 in 8c49
Go back to
Magnesium Binding Sites List in 8c49
Magnesium binding site 6 out
of 11 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
 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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg309
b:20.9
occ:1.00
|
O2G
|
B:ANP302
|
1.9
|
20.7
|
1.0
|
|
O
|
B:HOH475
|
2.0
|
24.1
|
1.0
|
|
O
|
B:HOH406
|
2.0
|
20.8
|
1.0
|
|
O2B
|
B:ANP302
|
2.0
|
18.0
|
1.0
|
|
O
|
B:HOH483
|
2.1
|
19.4
|
1.0
|
|
O
|
B:HOH456
|
2.2
|
23.7
|
1.0
|
|
PG
|
B:ANP302
|
3.2
|
24.8
|
1.0
|
|
HE2
|
B:HIS158
|
3.2
|
29.2
|
1.0
|
|
HH11
|
B:ARG150
|
3.3
|
24.4
|
1.0
|
|
PB
|
B:ANP302
|
3.4
|
20.2
|
1.0
|
|
N3B
|
B:ANP302
|
3.7
|
22.7
|
1.0
|
|
HH12
|
B:ARG150
|
3.8
|
24.4
|
1.0
|
|
O1G
|
B:ANP302
|
3.8
|
25.4
|
1.0
|
|
NH1
|
B:ARG150
|
3.9
|
20.2
|
1.0
|
|
NE2
|
B:HIS158
|
4.0
|
24.3
|
1.0
|
|
OE2
|
B:GLU152
|
4.0
|
24.2
|
1.0
|
|
HD2
|
B:HIS158
|
4.2
|
28.1
|
1.0
|
|
O3A
|
B:ANP302
|
4.2
|
19.9
|
1.0
|
|
O1B
|
B:ANP302
|
4.4
|
20.8
|
1.0
|
|
OE1
|
B:GLU152
|
4.4
|
27.1
|
1.0
|
|
O3G
|
B:ANP302
|
4.5
|
24.4
|
1.0
|
|
CD2
|
B:HIS158
|
4.5
|
23.4
|
1.0
|
|
HD3
|
B:ARG150
|
4.5
|
26.2
|
1.0
|
|
HNB1
|
B:ANP302
|
4.5
|
27.3
|
1.0
|
|
N7
|
B:ANP302
|
4.6
|
20.5
|
1.0
|
|
CD
|
B:GLU152
|
4.7
|
24.5
|
1.0
|
|
H8
|
B:ANP302
|
4.8
|
24.4
|
1.0
|
|
HD2
|
B:ARG150
|
5.0
|
26.2
|
1.0
|
|
Magnesium binding site 7 out
of 11 in 8c49
Go back to
Magnesium Binding Sites List in 8c49
Magnesium binding site 7 out
of 11 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
 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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg310
b:19.2
occ:1.00
|
O2A
|
B:ANP302
|
1.9
|
22.0
|
1.0
|
|
O1B
|
B:ANP302
|
2.0
|
20.8
|
1.0
|
|
OG
|
B:SER221
|
2.1
|
20.2
|
1.0
|
|
O
|
B:HOH465
|
2.1
|
20.3
|
1.0
|
|
OE2
|
B:GLU218
|
2.1
|
21.7
|
1.0
|
|
O
|
B:HOH405
|
2.1
|
20.7
|
1.0
|
|
CD
|
B:GLU218
|
3.1
|
22.5
|
1.0
|
|
PB
|
B:ANP302
|
3.2
|
20.2
|
1.0
|
|
PA
|
B:ANP302
|
3.2
|
20.5
|
1.0
|
|
CB
|
B:SER221
|
3.2
|
22.1
|
1.0
|
|
HB2
|
B:SER221
|
3.2
|
26.6
|
1.0
|
|
HNB1
|
B:ANP302
|
3.4
|
27.3
|
1.0
|
|
O3A
|
B:ANP302
|
3.4
|
19.9
|
1.0
|
|
OE1
|
B:GLU218
|
3.5
|
22.1
|
1.0
|
|
HB3
|
B:SER221
|
3.6
|
26.6
|
1.0
|
|
O
|
B:HOH429
|
3.8
|
25.5
|
1.0
|
|
H3'
|
B:ANP302
|
3.8
|
25.9
|
1.0
|
|
O
|
B:HOH403
|
3.8
|
26.9
|
1.0
|
|
N3B
|
B:ANP302
|
3.8
|
22.7
|
1.0
|
|
O1A
|
B:ANP302
|
3.9
|
21.1
|
1.0
|
|
OD2
|
B:ASP211
|
4.0
|
23.9
|
1.0
|
|
HG1
|
B:THR209
|
4.0
|
28.3
|
1.0
|
|
H5'2
|
B:ANP302
|
4.0
|
24.9
|
1.0
|
|
O3'
|
B:ANP302
|
4.1
|
22.6
|
1.0
|
|
OD1
|
B:ASP211
|
4.2
|
21.3
|
1.0
|
|
O
|
B:HOH459
|
4.3
|
35.9
|
1.0
|
|
CG
|
B:GLU218
|
4.4
|
21.4
|
1.0
|
|
O5'
|
B:ANP302
|
4.4
|
19.0
|
1.0
|
|
CA
|
B:SER221
|
4.4
|
20.7
|
1.0
|
|
C3'
|
B:ANP302
|
4.4
|
21.5
|
1.0
|
|
O2B
|
B:ANP302
|
4.4
|
18.0
|
1.0
|
|
CG
|
B:ASP211
|
4.5
|
23.6
|
1.0
|
|
HG3
|
B:GLU218
|
4.5
|
25.8
|
1.0
|
|
HG2
|
B:GLU218
|
4.6
|
25.8
|
1.0
|
|
HA
|
B:SER221
|
4.6
|
24.9
|
1.0
|
|
H12
|
B:PGE308
|
4.6
|
40.1
|
1.0
|
|
C5'
|
B:ANP302
|
4.6
|
20.7
|
1.0
|
|
HG21
|
B:THR209
|
4.7
|
33.0
|
1.0
|
|
N
|
B:SER221
|
4.7
|
21.1
|
1.0
|
|
OG1
|
B:THR209
|
4.8
|
23.5
|
1.0
|
|
HO3'
|
B:ANP302
|
4.9
|
27.1
|
1.0
|
|
H
|
B:SER221
|
4.9
|
25.4
|
1.0
|
|
MG
|
B:MG311
|
4.9
|
29.8
|
1.0
|
|
O1G
|
B:ANP302
|
5.0
|
25.4
|
1.0
|
|
Magnesium binding site 8 out
of 11 in 8c49
Go back to
Magnesium Binding Sites List in 8c49
Magnesium binding site 8 out
of 11 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
 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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg311
b:29.8
occ:1.00
|
O
|
B:HOH449
|
1.8
|
31.7
|
1.0
|
|
O
|
B:HOH492
|
1.9
|
30.2
|
1.0
|
|
O
|
B:HOH429
|
2.0
|
25.5
|
1.0
|
|
O1G
|
B:ANP302
|
2.1
|
25.4
|
1.0
|
|
OE1
|
B:GLU218
|
2.1
|
22.1
|
1.0
|
|
O
|
B:HOH455
|
2.2
|
31.0
|
1.0
|
|
PG
|
B:ANP302
|
3.2
|
24.8
|
1.0
|
|
HNB1
|
B:ANP302
|
3.3
|
27.3
|
1.0
|
|
CD
|
B:GLU218
|
3.4
|
22.5
|
1.0
|
|
O3G
|
B:ANP302
|
3.6
|
24.4
|
1.0
|
|
HB2
|
B:GLU218
|
3.7
|
28.0
|
1.0
|
|
HB3
|
B:GLU218
|
3.8
|
28.0
|
1.0
|
|
N3B
|
B:ANP302
|
3.8
|
22.7
|
1.0
|
|
O
|
B:HOH440
|
3.8
|
24.4
|
1.0
|
|
O
|
B:HOH405
|
4.1
|
20.7
|
1.0
|
|
CB
|
B:GLU218
|
4.1
|
23.3
|
1.0
|
|
OE2
|
B:GLU218
|
4.2
|
21.7
|
1.0
|
|
O1B
|
B:ANP302
|
4.3
|
20.8
|
1.0
|
|
CG
|
B:GLU218
|
4.3
|
21.4
|
1.0
|
|
HG2
|
B:GLU201
|
4.4
|
37.7
|
1.0
|
|
HH12
|
B:ARG248
|
4.5
|
29.4
|
1.0
|
|
O2G
|
B:ANP302
|
4.6
|
20.7
|
1.0
|
|
PB
|
B:ANP302
|
4.7
|
20.2
|
1.0
|
|
OE1
|
B:GLU201
|
4.7
|
38.2
|
1.0
|
|
HG3
|
B:GLU218
|
4.8
|
25.8
|
1.0
|
|
OD2
|
B:ASP211
|
4.9
|
23.9
|
1.0
|
|
MG
|
B:MG310
|
4.9
|
19.2
|
1.0
|
|
Magnesium binding site 9 out
of 11 in 8c49
Go back to
Magnesium Binding Sites List in 8c49
Magnesium binding site 9 out
of 11 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
 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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg312
b:40.5
occ:1.00
|
OD1
|
B:ASP69
|
2.1
|
29.5
|
1.0
|
|
O
|
B:HOH490
|
2.1
|
31.3
|
1.0
|
|
O
|
B:HOH497
|
2.3
|
33.2
|
1.0
|
|
O
|
B:HOH531
|
2.5
|
37.2
|
1.0
|
|
O
|
B:HOH401
|
2.6
|
34.3
|
1.0
|
|
CG
|
B:ASP69
|
3.2
|
25.3
|
1.0
|
|
OD2
|
B:ASP69
|
3.7
|
27.4
|
1.0
|
|
HA
|
B:ASP69
|
4.0
|
26.5
|
1.0
|
|
CB
|
B:ASP69
|
4.4
|
23.3
|
1.0
|
|
O
|
B:GLN65
|
4.4
|
22.8
|
1.0
|
|
HB3
|
B:ASN68
|
4.5
|
27.9
|
1.0
|
|
CA
|
B:ASP69
|
4.5
|
22.0
|
1.0
|
|
H
|
B:ASP69
|
4.5
|
26.9
|
1.0
|
|
N
|
B:ASP69
|
4.6
|
22.4
|
1.0
|
|
HB3
|
B:GLN65
|
4.7
|
31.2
|
1.0
|
|
HB2
|
B:ASN68
|
4.7
|
27.9
|
1.0
|
|
O
|
B:HOH507
|
4.8
|
25.4
|
1.0
|
|
HB3
|
B:ASP69
|
5.0
|
28.0
|
1.0
|
|
HE21
|
B:GLN65
|
5.0
|
48.9
|
1.0
|
|
HA
|
B:GLN65
|
5.0
|
28.4
|
1.0
|
|
HB2
|
B:ASP69
|
5.0
|
28.0
|
1.0
|
|
Magnesium binding site 10 out
of 11 in 8c49
Go back to
Magnesium Binding Sites List in 8c49
Magnesium binding site 10 out
of 11 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp
 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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For 3-Methyl-L-Histidine, Bound to Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg313
b:34.3
occ:1.00
|
H
|
B:TYR21
|
2.3
|
40.7
|
1.0
|
|
HE
|
B:ARG14
|
2.3
|
47.6
|
1.0
|
|
HH21
|
B:ARG14
|
2.3
|
51.9
|
1.0
|
|
HG2
|
B:GLU22
|
2.6
|
50.4
|
1.0
|
|
H
|
B:GLU22
|
2.7
|
44.6
|
1.0
|
|
O
|
B:HOH474
|
2.8
|
38.6
|
1.0
|
|
NE
|
B:ARG14
|
3.1
|
39.6
|
1.0
|
|
NH2
|
B:ARG14
|
3.1
|
43.2
|
1.0
|
|
N
|
B:TYR21
|
3.1
|
33.9
|
1.0
|
|
HA
|
B:THR20
|
3.2
|
44.8
|
1.0
|
|
HD2
|
B:TYR21
|
3.3
|
39.1
|
1.0
|
|
N
|
B:GLU22
|
3.4
|
37.1
|
1.0
|
|
HB2
|
B:TYR21
|
3.5
|
39.9
|
1.0
|
|
CZ
|
B:ARG14
|
3.5
|
42.7
|
1.0
|
|
HG23
|
B:ILE10
|
3.6
|
43.2
|
1.0
|
|
CG
|
B:GLU22
|
3.6
|
41.9
|
1.0
|
|
HG23
|
B:THR20
|
3.6
|
47.6
|
1.0
|
|
HB3
|
B:GLU22
|
3.7
|
48.0
|
1.0
|
|
HH22
|
B:ARG14
|
3.8
|
51.9
|
1.0
|
|
CA
|
B:TYR21
|
3.9
|
37.1
|
1.0
|
|
HG2
|
B:ARG14
|
3.9
|
40.7
|
1.0
|
|
CD2
|
B:TYR21
|
4.0
|
32.6
|
1.0
|
|
HD12
|
B:ILE10
|
4.0
|
42.6
|
1.0
|
|
CB
|
B:GLU22
|
4.0
|
40.0
|
1.0
|
|
CA
|
B:THR20
|
4.0
|
37.3
|
1.0
|
|
HG22
|
B:THR20
|
4.0
|
47.6
|
1.0
|
|
C
|
B:THR20
|
4.1
|
37.8
|
1.0
|
|
CB
|
B:TYR21
|
4.1
|
33.2
|
1.0
|
|
HG3
|
B:GLU22
|
4.1
|
50.4
|
1.0
|
|
C
|
B:TYR21
|
4.1
|
35.9
|
1.0
|
|
HG21
|
B:ILE10
|
4.1
|
43.2
|
1.0
|
|
HG3
|
B:ARG14
|
4.2
|
40.7
|
1.0
|
|
CG2
|
B:ILE10
|
4.3
|
36.0
|
1.0
|
|
CG2
|
B:THR20
|
4.3
|
39.6
|
1.0
|
|
CD
|
B:ARG14
|
4.3
|
36.3
|
1.0
|
|
CA
|
B:GLU22
|
4.3
|
38.9
|
1.0
|
|
CG
|
B:ARG14
|
4.3
|
33.9
|
1.0
|
|
CD
|
B:GLU22
|
4.4
|
49.6
|
1.0
|
|
CG
|
B:TYR21
|
4.4
|
33.0
|
1.0
|
|
O
|
B:GLY19
|
4.5
|
36.1
|
1.0
|
|
HG22
|
B:ILE10
|
4.6
|
43.2
|
1.0
|
|
HD13
|
B:ILE10
|
4.6
|
42.6
|
1.0
|
|
OE1
|
B:GLU22
|
4.7
|
50.4
|
1.0
|
|
HD3
|
B:ARG14
|
4.7
|
43.6
|
1.0
|
|
CD1
|
B:ILE10
|
4.7
|
35.5
|
1.0
|
|
HA
|
B:GLU22
|
4.8
|
46.7
|
1.0
|
|
CB
|
B:THR20
|
4.8
|
40.4
|
1.0
|
|
HA
|
B:TYR21
|
4.8
|
44.6
|
1.0
|
|
NH1
|
B:ARG14
|
4.9
|
40.1
|
1.0
|
|
HD2
|
B:ARG14
|
4.9
|
43.6
|
1.0
|
|
HB2
|
B:GLU22
|
4.9
|
48.0
|
1.0
|
|
HB3
|
B:TYR21
|
5.0
|
39.9
|
1.0
|
|
CE2
|
B:TYR21
|
5.0
|
34.3
|
1.0
|
|
Reference:
C.J.Taylor,
F.J.Hardy,
A.J.Burke,
R.M.Bednar,
R.A.Mehl,
A.P.Green,
S.L.Lovelock.
Engineering Mutually Orthogonal Pylrs/Trna Pairs For Dual Encoding of Functional Histidine Analogues. Protein Sci. V. 32 E4640 2023.
ISSN: ESSN 1469-896X
PubMed: 37051694
DOI: 10.1002/PRO.4640
Page generated: Thu Oct 3 20:05:59 2024
|
