Magnesium in PDB 7s0z: Structures of Tcdb in Complex with R-Ras
Protein crystallography data
The structure of Structures of Tcdb in Complex with R-Ras, PDB code: 7s0z
was solved by
L.Zheng,
J.Rongsheng,
C.Peng,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
76.02 /
2.34
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.308,
112.112,
101.571,
90,
95.89,
90
|
R / Rfree (%)
|
20.1 /
24.1
|
Other elements in 7s0z:
The structure of Structures of Tcdb in Complex with R-Ras also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structures of Tcdb in Complex with R-Ras
(pdb code 7s0z). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Structures of Tcdb in Complex with R-Ras, PDB code: 7s0z:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 7s0z
Go back to
Magnesium Binding Sites List in 7s0z
Magnesium binding site 1 out
of 5 in the Structures of Tcdb in Complex with R-Ras
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structures of Tcdb in Complex with R-Ras within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg619
b:39.3
occ:1.00
|
O
|
A:HOH904
|
2.7
|
33.1
|
1.0
|
O1A
|
A:UDP601
|
2.7
|
27.7
|
1.0
|
O3'
|
A:UDP601
|
2.8
|
30.1
|
1.0
|
CG
|
A:ASP288
|
3.1
|
29.1
|
1.0
|
OD2
|
A:ASP288
|
3.2
|
29.0
|
1.0
|
C3'
|
A:UDP601
|
3.3
|
30.1
|
1.0
|
OD1
|
A:ASP288
|
3.4
|
28.8
|
1.0
|
CG2
|
A:VAL287
|
3.4
|
30.9
|
1.0
|
N
|
A:ASP288
|
3.4
|
27.9
|
1.0
|
CB
|
A:ASP288
|
3.5
|
28.7
|
1.0
|
O5'
|
A:UDP601
|
3.6
|
29.0
|
1.0
|
PA
|
A:UDP601
|
3.6
|
28.7
|
1.0
|
MG
|
A:MG620
|
3.6
|
39.7
|
1.0
|
N
|
A:VAL287
|
3.8
|
29.3
|
1.0
|
CB
|
A:ASP286
|
3.8
|
29.6
|
1.0
|
C5'
|
A:UDP601
|
4.0
|
29.5
|
1.0
|
CA
|
A:ASP288
|
4.1
|
27.8
|
1.0
|
MN
|
A:MN618
|
4.2
|
29.4
|
1.0
|
O
|
A:HOH755
|
4.2
|
28.7
|
1.0
|
CG
|
A:ASP286
|
4.2
|
30.1
|
1.0
|
C
|
A:VAL287
|
4.2
|
28.6
|
1.0
|
C4'
|
A:UDP601
|
4.2
|
30.0
|
1.0
|
O2A
|
A:UDP601
|
4.2
|
29.2
|
1.0
|
CA
|
A:VAL287
|
4.3
|
29.4
|
1.0
|
C
|
A:ASP286
|
4.3
|
29.0
|
1.0
|
OD2
|
A:ASP286
|
4.5
|
30.3
|
1.0
|
CB
|
A:VAL287
|
4.5
|
29.9
|
1.0
|
CA
|
A:ASP286
|
4.5
|
29.2
|
1.0
|
CD1
|
A:LEU520
|
4.6
|
36.0
|
1.0
|
C2'
|
A:UDP601
|
4.7
|
30.2
|
1.0
|
OD1
|
A:ASP286
|
4.7
|
30.3
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 7s0z
Go back to
Magnesium Binding Sites List in 7s0z
Magnesium binding site 2 out
of 5 in the Structures of Tcdb in Complex with R-Ras
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structures of Tcdb in Complex with R-Ras within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg620
b:39.7
occ:1.00
|
O
|
A:HOH904
|
2.6
|
33.1
|
1.0
|
O
|
A:ASN518
|
2.8
|
32.5
|
1.0
|
O2A
|
A:UDP601
|
2.8
|
29.2
|
1.0
|
O
|
A:GLN515
|
3.0
|
33.5
|
1.0
|
O
|
A:HOH727
|
3.1
|
36.2
|
1.0
|
OD2
|
A:ASP288
|
3.1
|
29.0
|
1.0
|
O1A
|
A:UDP601
|
3.2
|
27.7
|
1.0
|
PA
|
A:UDP601
|
3.5
|
28.7
|
1.0
|
MG
|
A:MG619
|
3.6
|
39.3
|
1.0
|
C
|
A:ASN518
|
3.8
|
33.7
|
1.0
|
MN
|
A:MN618
|
3.9
|
29.4
|
1.0
|
CG
|
A:LEU520
|
3.9
|
34.7
|
1.0
|
CG
|
A:ASP288
|
3.9
|
29.1
|
1.0
|
C
|
A:GLN515
|
3.9
|
32.5
|
1.0
|
CD1
|
A:LEU520
|
4.1
|
36.0
|
1.0
|
CB
|
A:ASP288
|
4.1
|
28.7
|
1.0
|
CA
|
A:SER519
|
4.2
|
32.7
|
1.0
|
N
|
A:LEU520
|
4.3
|
32.6
|
1.0
|
N
|
A:SER519
|
4.3
|
32.9
|
1.0
|
C
|
A:SER519
|
4.5
|
33.1
|
1.0
|
O5'
|
A:UDP601
|
4.5
|
29.0
|
1.0
|
CA
|
A:GLU516
|
4.6
|
29.9
|
1.0
|
N
|
A:GLU516
|
4.7
|
30.4
|
1.0
|
CB
|
A:GLN515
|
4.7
|
34.7
|
1.0
|
CB
|
A:LEU520
|
4.8
|
32.4
|
1.0
|
O2B
|
A:UDP601
|
4.8
|
28.7
|
1.0
|
CA
|
A:ASN518
|
4.8
|
35.4
|
1.0
|
O
|
A:GLU516
|
4.8
|
29.3
|
1.0
|
CA
|
A:GLN515
|
4.8
|
33.9
|
1.0
|
O3A
|
A:UDP601
|
4.8
|
28.6
|
1.0
|
CD2
|
A:LEU520
|
4.9
|
35.0
|
1.0
|
C
|
A:GLU516
|
4.9
|
29.6
|
1.0
|
N
|
A:ASN518
|
4.9
|
34.6
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 7s0z
Go back to
Magnesium Binding Sites List in 7s0z
Magnesium binding site 3 out
of 5 in the Structures of Tcdb in Complex with R-Ras
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structures of Tcdb in Complex with R-Ras within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg621
b:51.0
occ:1.00
|
O
|
A:HOH814
|
3.0
|
32.9
|
1.0
|
O
|
A:HOH904
|
3.1
|
33.1
|
1.0
|
CG
|
A:GLN515
|
4.0
|
35.7
|
1.0
|
CG2
|
A:VAL287
|
4.1
|
30.9
|
1.0
|
OE1
|
A:GLN515
|
4.2
|
40.6
|
1.0
|
CG2
|
A:THR110
|
4.3
|
38.1
|
1.0
|
CB
|
A:GLN515
|
4.4
|
34.7
|
1.0
|
N
|
A:ALA111
|
4.4
|
35.6
|
1.0
|
CB
|
A:ALA111
|
4.4
|
34.5
|
1.0
|
CD
|
A:GLN515
|
4.5
|
38.1
|
1.0
|
CA
|
A:ALA111
|
4.5
|
35.4
|
1.0
|
OD1
|
A:ASN108
|
4.5
|
42.5
|
1.0
|
CB
|
A:THR110
|
4.7
|
38.2
|
1.0
|
CZ3
|
A:TRP102
|
4.8
|
37.6
|
1.0
|
CD1
|
A:LEU520
|
4.9
|
36.0
|
1.0
|
C
|
A:THR110
|
4.9
|
36.8
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 7s0z
Go back to
Magnesium Binding Sites List in 7s0z
Magnesium binding site 4 out
of 5 in the Structures of Tcdb in Complex with R-Ras
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structures of Tcdb in Complex with R-Ras within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg624
b:66.0
occ:1.00
|
O2A
|
C:GDP305
|
3.1
|
34.5
|
1.0
|
O2B
|
C:GDP305
|
3.1
|
35.3
|
1.0
|
OE2
|
A:GLU462
|
3.2
|
51.1
|
1.0
|
O3B
|
C:GDP305
|
3.3
|
34.4
|
1.0
|
OG
|
C:SER43
|
3.3
|
35.9
|
1.0
|
PB
|
C:GDP305
|
3.7
|
35.2
|
1.0
|
O
|
C:HOH448
|
3.9
|
49.3
|
1.0
|
CD
|
A:GLU462
|
3.9
|
45.9
|
1.0
|
CB
|
C:SER43
|
4.1
|
33.5
|
1.0
|
OE1
|
A:GLU462
|
4.1
|
48.4
|
1.0
|
PA
|
C:GDP305
|
4.2
|
35.2
|
1.0
|
O
|
C:HOH406
|
4.2
|
48.3
|
1.0
|
OD2
|
C:ASP59
|
4.2
|
37.5
|
0.4
|
O3A
|
C:GDP305
|
4.4
|
34.5
|
1.0
|
O1A
|
C:GDP305
|
4.9
|
34.4
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 7s0z
Go back to
Magnesium Binding Sites List in 7s0z
Magnesium binding site 5 out
of 5 in the Structures of Tcdb in Complex with R-Ras
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structures of Tcdb in Complex with R-Ras within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg2303
b:60.9
occ:1.00
|
OG
|
D:SER43
|
2.7
|
38.4
|
1.0
|
O
|
D:HOH2407
|
2.7
|
45.1
|
1.0
|
O2B
|
D:GDP2302
|
2.9
|
37.5
|
1.0
|
CB
|
D:SER43
|
3.7
|
36.5
|
1.0
|
OE1
|
B:GLU462
|
3.8
|
55.5
|
1.0
|
O1A
|
D:GDP2302
|
4.0
|
35.6
|
1.0
|
O1B
|
D:GDP2302
|
4.0
|
38.1
|
1.0
|
PB
|
D:GDP2302
|
4.0
|
37.9
|
1.0
|
CA
|
D:SER43
|
4.8
|
35.4
|
1.0
|
CD
|
B:GLU462
|
4.8
|
52.7
|
1.0
|
N
|
D:SER43
|
4.8
|
35.2
|
1.0
|
O
|
D:HOH2415
|
4.9
|
40.4
|
1.0
|
PA
|
D:GDP2302
|
4.9
|
38.8
|
1.0
|
O
|
D:HOH2457
|
4.9
|
50.6
|
1.0
|
OD1
|
B:ASN464
|
5.0
|
43.7
|
1.0
|
O3A
|
D:GDP2302
|
5.0
|
38.2
|
1.0
|
|
Reference:
L.Zheng,
J.Rongsheng,
C.Peng.
Structures of Tcdb in Complex with R-Ras To Be Published.
Page generated: Thu Oct 3 08:10:02 2024
|