Magnesium in PDB 7zyw: Crystal Structure of T2R-Ttl-PM534 Complex
Protein crystallography data
The structure of Crystal Structure of T2R-Ttl-PM534 Complex, PDB code: 7zyw
was solved by
M.A.Oliva,
J.F.Diaz,
C.Cuevas,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.66 /
2.45
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.803,
158.026,
181.08,
90,
90,
90
|
R / Rfree (%)
|
21.9 /
24.4
|
Other elements in 7zyw:
The structure of Crystal Structure of T2R-Ttl-PM534 Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-PM534 Complex
(pdb code 7zyw). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of T2R-Ttl-PM534 Complex, PDB code: 7zyw:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7zyw
Go back to
Magnesium Binding Sites List in 7zyw
Magnesium binding site 1 out
of 4 in the Crystal Structure of T2R-Ttl-PM534 Complex
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 T2R-Ttl-PM534 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg505
b:50.9
occ:1.00
|
O1G
|
A:GTP501
|
2.1
|
46.1
|
1.0
|
O
|
A:HOH603
|
2.1
|
50.1
|
1.0
|
O
|
A:HOH611
|
2.1
|
52.9
|
1.0
|
O
|
A:HOH614
|
2.1
|
46.8
|
1.0
|
O
|
A:HOH602
|
2.1
|
50.3
|
1.0
|
O1B
|
A:GTP501
|
2.3
|
44.8
|
1.0
|
HZ1
|
B:LYS254
|
3.3
|
83.4
|
1.0
|
PG
|
A:GTP501
|
3.4
|
50.5
|
1.0
|
HG2
|
A:GLU71
|
3.4
|
79.2
|
1.0
|
PB
|
A:GTP501
|
3.4
|
46.2
|
1.0
|
HB2
|
A:GLN11
|
3.5
|
60.8
|
1.0
|
O3B
|
A:GTP501
|
3.8
|
57.6
|
1.0
|
H
|
A:GLN11
|
3.8
|
57.0
|
1.0
|
O3A
|
A:GTP501
|
3.8
|
55.2
|
1.0
|
HB2
|
A:ASP98
|
3.8
|
58.0
|
1.0
|
OE2
|
A:GLU71
|
4.0
|
74.6
|
1.0
|
HG3
|
A:GLU71
|
4.0
|
79.2
|
1.0
|
HB3
|
A:ASP98
|
4.0
|
58.0
|
1.0
|
NZ
|
B:LYS254
|
4.1
|
83.9
|
1.0
|
O2G
|
A:GTP501
|
4.1
|
53.8
|
1.0
|
CG
|
A:GLU71
|
4.1
|
77.3
|
1.0
|
OD1
|
A:ASP69
|
4.1
|
50.9
|
1.0
|
HB3
|
A:GLN11
|
4.1
|
60.8
|
1.0
|
HE21
|
A:GLN11
|
4.2
|
69.1
|
1.0
|
HZ2
|
B:LYS254
|
4.2
|
83.4
|
1.0
|
HZ3
|
B:LYS254
|
4.2
|
83.4
|
1.0
|
CB
|
A:GLN11
|
4.3
|
60.6
|
1.0
|
CB
|
A:ASP98
|
4.3
|
59.1
|
1.0
|
OD2
|
A:ASP69
|
4.3
|
57.8
|
1.0
|
O3G
|
A:GTP501
|
4.5
|
48.0
|
1.0
|
N
|
A:GLN11
|
4.5
|
57.1
|
1.0
|
CD
|
A:GLU71
|
4.5
|
79.1
|
1.0
|
OD2
|
A:ASP98
|
4.6
|
72.4
|
1.0
|
NE2
|
A:GLN11
|
4.6
|
69.0
|
1.0
|
CG
|
A:ASP98
|
4.7
|
63.5
|
1.0
|
CG
|
A:ASP69
|
4.7
|
54.2
|
1.0
|
HG21
|
A:VAL74
|
4.7
|
74.9
|
1.0
|
O2B
|
A:GTP501
|
4.7
|
54.0
|
1.0
|
O1A
|
A:GTP501
|
4.8
|
52.6
|
1.0
|
HG23
|
A:VAL74
|
4.8
|
74.9
|
1.0
|
HG1
|
A:THR145
|
4.8
|
61.8
|
1.0
|
PA
|
A:GTP501
|
4.9
|
50.5
|
1.0
|
HE22
|
A:GLN11
|
4.9
|
69.1
|
1.0
|
HA2
|
A:GLY10
|
4.9
|
51.6
|
1.0
|
CA
|
A:GLN11
|
5.0
|
59.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7zyw
Go back to
Magnesium Binding Sites List in 7zyw
Magnesium binding site 2 out
of 4 in the Crystal Structure of T2R-Ttl-PM534 Complex
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 T2R-Ttl-PM534 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg505
b:37.9
occ:1.00
|
O
|
B:HOH617
|
2.1
|
46.5
|
1.0
|
OE1
|
B:GLN11
|
2.1
|
54.6
|
1.0
|
O
|
B:HOH619
|
2.1
|
47.2
|
1.0
|
O
|
B:HOH601
|
2.1
|
55.6
|
1.0
|
O
|
B:HOH621
|
2.1
|
49.3
|
1.0
|
O1A
|
B:GDP501
|
2.2
|
43.7
|
1.0
|
CD
|
B:GLN11
|
3.3
|
64.0
|
1.0
|
HB3
|
B:GLN11
|
3.5
|
44.8
|
1.0
|
PA
|
B:GDP501
|
3.5
|
39.6
|
1.0
|
O3A
|
B:GDP501
|
3.8
|
49.0
|
1.0
|
H8
|
B:GDP501
|
3.8
|
45.5
|
1.0
|
OD2
|
B:ASP179
|
3.9
|
53.0
|
1.0
|
HB2
|
B:GLN11
|
3.9
|
44.8
|
1.0
|
CB
|
B:GLN11
|
4.0
|
44.9
|
1.0
|
CG
|
B:GLN11
|
4.2
|
59.0
|
1.0
|
HE22
|
B:GLN11
|
4.2
|
74.8
|
1.0
|
NE2
|
B:GLN11
|
4.2
|
75.8
|
1.0
|
OD1
|
B:ASN101
|
4.3
|
45.5
|
1.0
|
O1B
|
B:GDP501
|
4.3
|
45.3
|
1.0
|
C5'
|
B:GDP501
|
4.4
|
44.8
|
1.0
|
O5'
|
B:GDP501
|
4.5
|
42.2
|
1.0
|
HG2
|
B:GLN11
|
4.5
|
58.5
|
1.0
|
HD21
|
B:ASN101
|
4.6
|
51.3
|
1.0
|
O2A
|
B:GDP501
|
4.6
|
40.3
|
1.0
|
PB
|
B:GDP501
|
4.7
|
43.5
|
1.0
|
OE1
|
C:GLU254
|
4.7
|
67.7
|
1.0
|
C8
|
B:GDP501
|
4.8
|
45.5
|
1.0
|
CG
|
B:ASP179
|
5.0
|
55.7
|
1.0
|
HG3
|
B:GLN11
|
5.0
|
58.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7zyw
Go back to
Magnesium Binding Sites List in 7zyw
Magnesium binding site 3 out
of 4 in the Crystal Structure of T2R-Ttl-PM534 Complex
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 T2R-Ttl-PM534 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg504
b:46.5
occ:1.00
|
O
|
C:HOH607
|
2.1
|
41.7
|
1.0
|
O
|
C:HOH646
|
2.1
|
50.1
|
1.0
|
O
|
C:HOH618
|
2.1
|
47.8
|
1.0
|
O
|
C:HOH632
|
2.1
|
45.6
|
1.0
|
O1G
|
C:GTP501
|
2.2
|
45.9
|
1.0
|
O1B
|
C:GTP501
|
2.3
|
42.4
|
1.0
|
PG
|
C:GTP501
|
3.3
|
48.7
|
1.0
|
HZ1
|
D:LYS254
|
3.3
|
58.8
|
1.0
|
PB
|
C:GTP501
|
3.3
|
41.8
|
1.0
|
HB2
|
C:GLN11
|
3.6
|
47.9
|
1.0
|
O2G
|
C:GTP501
|
3.6
|
49.9
|
1.0
|
HG2
|
C:GLU71
|
3.6
|
62.7
|
1.0
|
O3B
|
C:GTP501
|
3.7
|
52.2
|
1.0
|
H
|
C:GLN11
|
3.7
|
36.8
|
1.0
|
O3A
|
C:GTP501
|
3.7
|
48.4
|
1.0
|
HB2
|
C:ASP98
|
3.8
|
48.6
|
1.0
|
HG3
|
C:GLU71
|
4.0
|
62.7
|
1.0
|
OE2
|
C:GLU71
|
4.0
|
67.7
|
1.0
|
OD1
|
C:ASP69
|
4.0
|
47.4
|
1.0
|
NZ
|
D:LYS254
|
4.0
|
58.1
|
1.0
|
HZ3
|
D:LYS254
|
4.1
|
58.8
|
1.0
|
OD2
|
C:ASP69
|
4.2
|
46.8
|
1.0
|
CG
|
C:GLU71
|
4.2
|
63.1
|
1.0
|
HB3
|
C:GLN11
|
4.2
|
47.9
|
1.0
|
HZ2
|
D:LYS254
|
4.2
|
58.8
|
1.0
|
HB3
|
C:ASP98
|
4.3
|
48.6
|
1.0
|
CB
|
C:GLN11
|
4.3
|
48.0
|
1.0
|
N
|
C:GLN11
|
4.5
|
36.8
|
1.0
|
CB
|
C:ASP98
|
4.5
|
48.5
|
1.0
|
CG
|
C:ASP69
|
4.5
|
45.3
|
1.0
|
O3G
|
C:GTP501
|
4.5
|
43.5
|
1.0
|
CD
|
C:GLU71
|
4.6
|
65.1
|
1.0
|
OD2
|
C:ASP98
|
4.6
|
62.0
|
1.0
|
OE1
|
C:GLN11
|
4.6
|
75.9
|
1.0
|
O2B
|
C:GTP501
|
4.6
|
44.9
|
1.0
|
HG1
|
C:THR145
|
4.7
|
54.6
|
1.0
|
HA2
|
C:GLY10
|
4.8
|
42.6
|
1.0
|
HG21
|
C:VAL74
|
4.8
|
53.8
|
1.0
|
O1A
|
C:GTP501
|
4.8
|
50.1
|
1.0
|
PA
|
C:GTP501
|
4.9
|
43.5
|
1.0
|
HB
|
C:THR145
|
4.9
|
46.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7zyw
Go back to
Magnesium Binding Sites List in 7zyw
Magnesium binding site 4 out
of 4 in the Crystal Structure of T2R-Ttl-PM534 Complex
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 T2R-Ttl-PM534 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:85.2
occ:1.00
|
O
|
D:HOH602
|
2.1
|
91.2
|
1.0
|
O
|
D:HOH601
|
2.1
|
83.7
|
1.0
|
OE1
|
D:GLN11
|
2.1
|
125.0
|
1.0
|
O1A
|
D:GDP501
|
2.6
|
88.6
|
1.0
|
CD
|
D:GLN11
|
3.3
|
134.6
|
1.0
|
HD21
|
D:ASN101
|
3.5
|
99.9
|
1.0
|
HB3
|
D:GLN11
|
3.7
|
106.7
|
1.0
|
PA
|
D:GDP501
|
3.7
|
77.7
|
1.0
|
O3A
|
D:GDP501
|
3.7
|
82.6
|
1.0
|
OD1
|
D:ASN101
|
3.8
|
101.0
|
1.0
|
HB2
|
D:GLN11
|
3.9
|
106.7
|
1.0
|
H8
|
D:GDP501
|
4.1
|
81.2
|
1.0
|
HE22
|
D:GLN11
|
4.1
|
151.6
|
1.0
|
O1B
|
D:GDP501
|
4.1
|
81.3
|
1.0
|
CB
|
D:GLN11
|
4.1
|
108.1
|
1.0
|
NE2
|
D:GLN11
|
4.2
|
156.5
|
1.0
|
ND2
|
D:ASN101
|
4.2
|
101.6
|
1.0
|
C5'
|
D:GDP501
|
4.3
|
82.7
|
1.0
|
OD2
|
D:ASP179
|
4.3
|
127.7
|
1.0
|
CG
|
D:GLN11
|
4.3
|
127.1
|
1.0
|
O5'
|
D:GDP501
|
4.4
|
76.7
|
1.0
|
CG
|
D:ASN101
|
4.5
|
92.4
|
1.0
|
PB
|
D:GDP501
|
4.6
|
76.8
|
1.0
|
HB3
|
D:ASP179
|
4.6
|
141.9
|
1.0
|
HG2
|
D:GLN11
|
4.8
|
124.4
|
1.0
|
O2A
|
D:GDP501
|
4.9
|
72.3
|
1.0
|
HD22
|
D:ASN101
|
5.0
|
99.9
|
1.0
|
|
Reference:
M.A.Oliva,
J.F.Diaz,
C.Cuevas.
Structure of T2R-Ttl-PM534 Complex To Be Published.
Page generated: Thu Oct 3 17:07:11 2024
|