Magnesium in PDB 6vc8: Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion
Protein crystallography data
The structure of Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion, PDB code: 6vc8
was solved by
T.H.Tran,
D.R.Davies,
T.E.Edwards,
D.K.Simanshu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.91 /
2.50
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
69.21,
82.33,
88.14,
90,
112.92,
90
|
R / Rfree (%)
|
21.2 /
27.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion
(pdb code 6vc8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion, PDB code: 6vc8:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 6vc8
Go back to
Magnesium Binding Sites List in 6vc8
Magnesium binding site 1 out
of 3 in the Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion
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 Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1002
b:58.0
occ:1.00
|
O2B
|
A:GNP1001
|
2.1
|
47.9
|
1.0
|
O
|
A:HOH1103
|
2.1
|
63.4
|
1.0
|
O1G
|
A:GNP1001
|
2.1
|
53.2
|
1.0
|
OG
|
A:SER17
|
2.1
|
51.7
|
1.0
|
O
|
A:HOH1101
|
2.1
|
55.2
|
1.0
|
OG1
|
A:THR35
|
2.1
|
82.6
|
1.0
|
PG
|
A:GNP1001
|
3.0
|
59.0
|
1.0
|
N3B
|
A:GNP1001
|
3.0
|
58.2
|
1.0
|
CB
|
A:THR35
|
3.1
|
86.4
|
1.0
|
PB
|
A:GNP1001
|
3.1
|
55.8
|
1.0
|
CB
|
A:SER17
|
3.4
|
49.7
|
1.0
|
N
|
A:THR35
|
3.7
|
90.1
|
1.0
|
O2A
|
A:GNP1001
|
4.0
|
55.2
|
1.0
|
O2G
|
A:GNP1001
|
4.0
|
60.5
|
1.0
|
N
|
A:SER17
|
4.0
|
48.1
|
1.0
|
OD2
|
A:ASP57
|
4.0
|
62.2
|
1.0
|
O3G
|
A:GNP1001
|
4.0
|
59.7
|
1.0
|
CA
|
A:THR35
|
4.0
|
88.8
|
1.0
|
CG2
|
A:THR35
|
4.1
|
85.5
|
1.0
|
O3A
|
A:GNP1001
|
4.1
|
52.0
|
1.0
|
OD1
|
A:ASP57
|
4.3
|
60.0
|
1.0
|
O1B
|
A:GNP1001
|
4.3
|
51.5
|
1.0
|
CA
|
A:SER17
|
4.3
|
48.8
|
1.0
|
PA
|
A:GNP1001
|
4.5
|
54.2
|
1.0
|
CG
|
A:ASP57
|
4.5
|
59.2
|
1.0
|
O
|
A:THR58
|
4.5
|
63.3
|
1.0
|
C
|
A:PRO34
|
4.7
|
92.3
|
1.0
|
CB
|
A:LYS16
|
4.8
|
44.3
|
1.0
|
O1A
|
A:GNP1001
|
4.8
|
45.7
|
1.0
|
O
|
A:ASP33
|
4.8
|
84.4
|
1.0
|
NZ
|
A:LYS16
|
4.8
|
44.9
|
1.0
|
CE
|
A:LYS16
|
4.8
|
44.6
|
1.0
|
CA
|
A:PRO34
|
4.9
|
93.5
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 6vc8
Go back to
Magnesium Binding Sites List in 6vc8
Magnesium binding site 2 out
of 3 in the Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion
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 Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1002
b:54.5
occ:1.00
|
O
|
B:HOH1101
|
2.0
|
54.5
|
1.0
|
O2B
|
B:GNP1001
|
2.0
|
48.1
|
1.0
|
O
|
B:HOH1104
|
2.0
|
56.3
|
1.0
|
O1G
|
B:GNP1001
|
2.0
|
60.3
|
1.0
|
OG
|
B:SER17
|
2.0
|
53.0
|
1.0
|
OG1
|
B:THR35
|
2.0
|
65.0
|
1.0
|
CB
|
B:SER17
|
3.0
|
51.2
|
1.0
|
PG
|
B:GNP1001
|
3.1
|
63.3
|
1.0
|
CB
|
B:THR35
|
3.2
|
63.7
|
1.0
|
PB
|
B:GNP1001
|
3.2
|
47.0
|
1.0
|
N3B
|
B:GNP1001
|
3.4
|
50.6
|
1.0
|
O2G
|
B:GNP1001
|
3.7
|
48.0
|
1.0
|
N
|
B:SER17
|
3.7
|
51.3
|
1.0
|
CA
|
B:SER17
|
3.8
|
53.1
|
1.0
|
N
|
B:THR35
|
3.9
|
70.3
|
1.0
|
O2A
|
B:GNP1001
|
4.1
|
35.0
|
1.0
|
CG2
|
B:THR35
|
4.1
|
63.0
|
1.0
|
OD2
|
B:ASP57
|
4.1
|
64.6
|
1.0
|
O1B
|
B:GNP1001
|
4.2
|
50.2
|
1.0
|
CA
|
B:THR35
|
4.2
|
68.8
|
1.0
|
O
|
B:ASP33
|
4.2
|
70.1
|
1.0
|
O3A
|
B:GNP1001
|
4.3
|
51.7
|
1.0
|
OD1
|
B:ASP57
|
4.3
|
61.6
|
1.0
|
O3G
|
B:GNP1001
|
4.4
|
61.0
|
1.0
|
O
|
B:THR58
|
4.4
|
56.9
|
1.0
|
PA
|
B:GNP1001
|
4.5
|
47.0
|
1.0
|
C
|
B:LYS16
|
4.6
|
53.2
|
1.0
|
CG
|
B:ASP57
|
4.6
|
62.7
|
1.0
|
CB
|
B:LYS16
|
4.6
|
47.1
|
1.0
|
O1A
|
B:GNP1001
|
4.6
|
50.1
|
1.0
|
CE
|
B:LYS16
|
4.8
|
41.6
|
1.0
|
NZ
|
B:LYS16
|
4.8
|
37.5
|
1.0
|
C
|
B:PRO34
|
5.0
|
67.7
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 6vc8
Go back to
Magnesium Binding Sites List in 6vc8
Magnesium binding site 3 out
of 3 in the Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion
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 Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1002
b:69.2
occ:1.00
|
O2B
|
C:GNP1001
|
2.0
|
62.6
|
1.0
|
O
|
C:HOH1101
|
2.0
|
67.7
|
1.0
|
O
|
C:HOH1103
|
2.0
|
71.8
|
1.0
|
O
|
C:HOH1106
|
2.0
|
76.2
|
1.0
|
O1G
|
C:GNP1001
|
2.0
|
84.8
|
1.0
|
OG
|
C:SER17
|
2.1
|
79.5
|
1.0
|
CB
|
C:SER17
|
3.1
|
74.7
|
1.0
|
PG
|
C:GNP1001
|
3.3
|
80.7
|
1.0
|
PB
|
C:GNP1001
|
3.3
|
67.1
|
1.0
|
N3B
|
C:GNP1001
|
3.6
|
72.2
|
1.0
|
N
|
C:SER17
|
3.6
|
64.8
|
1.0
|
OD2
|
C:ASP57
|
3.9
|
79.0
|
1.0
|
O2G
|
C:GNP1001
|
3.9
|
77.4
|
1.0
|
O2A
|
C:GNP1001
|
3.9
|
65.1
|
1.0
|
CA
|
C:SER17
|
4.0
|
68.2
|
1.0
|
O1B
|
C:GNP1001
|
4.2
|
65.0
|
1.0
|
OD1
|
C:ASP57
|
4.2
|
76.3
|
1.0
|
O3A
|
C:GNP1001
|
4.4
|
70.5
|
1.0
|
O3G
|
C:GNP1001
|
4.4
|
77.5
|
1.0
|
PA
|
C:GNP1001
|
4.4
|
67.3
|
1.0
|
CG
|
C:ASP57
|
4.5
|
77.2
|
1.0
|
O1A
|
C:GNP1001
|
4.6
|
66.7
|
1.0
|
CB
|
C:LYS16
|
4.6
|
61.5
|
1.0
|
C
|
C:LYS16
|
4.7
|
66.4
|
1.0
|
NZ
|
C:LYS16
|
4.9
|
60.5
|
1.0
|
CE
|
C:LYS16
|
4.9
|
61.8
|
1.0
|
|
Reference:
T.H.Tran,
D.K.Simanshu.
Lipid Dependent Dynamics of the Ras Signaling Protein To Be Published.
Page generated: Tue Oct 1 21:27:22 2024
|