Magnesium in PDB 8t75: Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)
Enzymatic activity of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)
All present enzymatic activity of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd):
2.7.11.1;
3.6.5.2;
Protein crystallography data
The structure of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd), PDB code: 8t75
was solved by
M.J.Whitley,
D.K.Simanshu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.45 /
2.65
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.409,
199.509,
113.428,
90,
112.28,
90
|
R / Rfree (%)
|
17.8 /
21.9
|
Other elements in 8t75:
The structure of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)
(pdb code 8t75). 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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd), PDB code: 8t75:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8t75
Go back to
Magnesium Binding Sites List in 8t75
Magnesium binding site 1 out
of 4 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)
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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg202
b:61.3
occ:1.00
|
OG1
|
A:THR35
|
1.9
|
63.8
|
1.0
|
O2B
|
A:GNP201
|
1.9
|
61.2
|
1.0
|
O
|
A:HOH303
|
2.0
|
58.1
|
1.0
|
O1G
|
A:GNP201
|
2.0
|
68.7
|
1.0
|
O
|
A:HOH302
|
2.1
|
54.6
|
1.0
|
OG
|
A:SER17
|
2.1
|
64.5
|
1.0
|
PG
|
A:GNP201
|
3.0
|
60.6
|
1.0
|
CB
|
A:THR35
|
3.1
|
58.5
|
1.0
|
PB
|
A:GNP201
|
3.2
|
49.1
|
1.0
|
CB
|
A:SER17
|
3.3
|
60.4
|
1.0
|
N3B
|
A:GNP201
|
3.3
|
52.9
|
1.0
|
OD2
|
A:ASP57
|
3.7
|
99.7
|
1.0
|
O3G
|
A:GNP201
|
3.7
|
48.0
|
1.0
|
N
|
A:THR35
|
3.7
|
60.4
|
1.0
|
N
|
A:SER17
|
3.9
|
68.5
|
1.0
|
CA
|
A:THR35
|
4.0
|
53.8
|
1.0
|
O2A
|
A:GNP201
|
4.1
|
59.8
|
1.0
|
O1B
|
A:GNP201
|
4.1
|
60.2
|
1.0
|
CA
|
A:SER17
|
4.1
|
57.6
|
1.0
|
CG2
|
A:THR35
|
4.2
|
60.5
|
1.0
|
O3A
|
A:GNP201
|
4.2
|
68.0
|
1.0
|
OD1
|
A:ASP57
|
4.2
|
103.4
|
1.0
|
O
|
A:ASP33
|
4.2
|
75.4
|
1.0
|
CG
|
A:ASP57
|
4.3
|
93.9
|
1.0
|
O
|
A:THR58
|
4.4
|
70.2
|
1.0
|
O2G
|
A:GNP201
|
4.4
|
61.1
|
1.0
|
PA
|
A:GNP201
|
4.5
|
57.5
|
1.0
|
O1A
|
A:GNP201
|
4.7
|
66.1
|
1.0
|
NZ
|
A:LYS16
|
4.7
|
53.8
|
1.0
|
C
|
A:PRO34
|
4.7
|
64.5
|
1.0
|
CB
|
A:LYS16
|
4.8
|
56.5
|
1.0
|
CE
|
A:LYS16
|
4.8
|
58.5
|
1.0
|
C
|
A:LYS16
|
4.9
|
67.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8t75
Go back to
Magnesium Binding Sites List in 8t75
Magnesium binding site 2 out
of 4 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)
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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg202
b:44.1
occ:1.00
|
OG
|
C:SER17
|
2.0
|
46.9
|
1.0
|
O
|
C:HOH306
|
2.0
|
39.3
|
1.0
|
O3G
|
C:GNP201
|
2.0
|
49.2
|
1.0
|
O
|
C:HOH302
|
2.0
|
33.0
|
1.0
|
OG1
|
C:THR35
|
2.3
|
58.8
|
1.0
|
CG2
|
C:THR35
|
2.4
|
68.2
|
1.0
|
O2B
|
C:GNP201
|
2.6
|
49.7
|
1.0
|
CB
|
C:THR35
|
2.9
|
62.4
|
1.0
|
CB
|
C:SER17
|
3.3
|
44.5
|
1.0
|
OD2
|
C:ASP57
|
3.4
|
93.0
|
1.0
|
N
|
C:THR35
|
3.4
|
58.6
|
1.0
|
PG
|
C:GNP201
|
3.5
|
56.3
|
1.0
|
CA
|
C:THR35
|
3.7
|
66.7
|
1.0
|
N3B
|
C:GNP201
|
3.8
|
50.1
|
1.0
|
PB
|
C:GNP201
|
3.8
|
50.6
|
1.0
|
O
|
C:ASP33
|
4.0
|
63.3
|
1.0
|
CG
|
C:ASP57
|
4.1
|
88.0
|
1.0
|
OD1
|
C:ASP57
|
4.2
|
94.7
|
1.0
|
N
|
C:SER17
|
4.2
|
40.9
|
1.0
|
O1G
|
C:GNP201
|
4.3
|
51.6
|
1.0
|
CA
|
C:SER17
|
4.3
|
45.7
|
1.0
|
O2A
|
C:GNP201
|
4.4
|
47.4
|
1.0
|
O
|
C:THR58
|
4.4
|
62.4
|
1.0
|
O2G
|
C:GNP201
|
4.4
|
63.6
|
1.0
|
C
|
C:PRO34
|
4.5
|
58.8
|
1.0
|
C
|
C:THR35
|
4.8
|
60.1
|
1.0
|
O3A
|
C:GNP201
|
4.8
|
45.5
|
1.0
|
O1B
|
C:GNP201
|
4.8
|
50.7
|
1.0
|
CA
|
C:PRO34
|
4.8
|
63.5
|
1.0
|
O
|
C:THR35
|
4.9
|
60.0
|
1.0
|
PA
|
C:GNP201
|
5.0
|
43.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8t75
Go back to
Magnesium Binding Sites List in 8t75
Magnesium binding site 3 out
of 4 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)
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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg202
b:53.4
occ:1.00
|
O
|
E:HOH302
|
2.0
|
63.2
|
1.0
|
OG
|
E:SER17
|
2.0
|
51.0
|
1.0
|
O2B
|
E:GNP201
|
2.0
|
49.6
|
1.0
|
O2G
|
E:GNP201
|
2.0
|
58.2
|
1.0
|
O
|
E:HOH305
|
2.2
|
47.8
|
1.0
|
OG1
|
E:THR35
|
2.6
|
63.2
|
1.0
|
CB
|
E:THR35
|
3.0
|
55.4
|
1.0
|
CB
|
E:SER17
|
3.2
|
45.5
|
1.0
|
PG
|
E:GNP201
|
3.2
|
60.5
|
1.0
|
OD2
|
E:ASP57
|
3.3
|
98.5
|
1.0
|
PB
|
E:GNP201
|
3.4
|
55.7
|
1.0
|
N3B
|
E:GNP201
|
3.6
|
61.2
|
1.0
|
O3G
|
E:GNP201
|
3.7
|
43.0
|
1.0
|
N
|
E:SER17
|
3.8
|
50.0
|
1.0
|
N
|
E:THR35
|
3.8
|
57.7
|
1.0
|
OD1
|
E:ASP57
|
3.9
|
90.8
|
1.0
|
CG
|
E:ASP57
|
4.0
|
98.8
|
1.0
|
CA
|
E:THR35
|
4.0
|
53.4
|
1.0
|
CG2
|
E:THR35
|
4.1
|
50.0
|
1.0
|
CA
|
E:SER17
|
4.1
|
52.0
|
1.0
|
O1B
|
E:GNP201
|
4.2
|
59.9
|
1.0
|
O
|
E:THR58
|
4.3
|
74.4
|
1.0
|
O2A
|
E:GNP201
|
4.3
|
64.6
|
1.0
|
O
|
E:ASP33
|
4.4
|
75.9
|
1.0
|
O3A
|
E:GNP201
|
4.4
|
53.8
|
1.0
|
O1G
|
E:GNP201
|
4.5
|
75.6
|
1.0
|
O1A
|
E:GNP201
|
4.7
|
56.9
|
1.0
|
PA
|
E:GNP201
|
4.7
|
57.3
|
1.0
|
CB
|
E:LYS16
|
4.7
|
35.8
|
1.0
|
C
|
E:LYS16
|
4.8
|
51.6
|
1.0
|
CE
|
E:LYS16
|
4.8
|
43.2
|
1.0
|
C
|
E:PRO34
|
5.0
|
56.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8t75
Go back to
Magnesium Binding Sites List in 8t75
Magnesium binding site 4 out
of 4 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)
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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg202
b:57.4
occ:1.00
|
OG
|
G:SER17
|
2.0
|
77.4
|
1.0
|
O3G
|
G:GNP201
|
2.0
|
95.6
|
1.0
|
OG1
|
G:THR35
|
2.2
|
90.3
|
1.0
|
O2B
|
G:GNP201
|
2.3
|
85.4
|
1.0
|
O
|
G:HOH301
|
2.3
|
56.3
|
1.0
|
CB
|
G:SER17
|
3.1
|
60.4
|
1.0
|
CB
|
G:THR35
|
3.2
|
72.8
|
1.0
|
PG
|
G:GNP201
|
3.2
|
77.6
|
1.0
|
O
|
G:ASP33
|
3.3
|
92.4
|
1.0
|
N3B
|
G:GNP201
|
3.3
|
71.8
|
1.0
|
PB
|
G:GNP201
|
3.4
|
82.6
|
1.0
|
N
|
G:THR35
|
3.4
|
79.4
|
1.0
|
O2A
|
G:GNP201
|
3.5
|
91.0
|
1.0
|
CA
|
G:THR35
|
3.9
|
73.8
|
1.0
|
N
|
G:SER17
|
4.1
|
86.3
|
1.0
|
O3A
|
G:GNP201
|
4.1
|
73.8
|
1.0
|
OD2
|
G:ASP57
|
4.2
|
103.2
|
1.0
|
CA
|
G:SER17
|
4.2
|
72.7
|
1.0
|
O2G
|
G:GNP201
|
4.2
|
82.2
|
1.0
|
PA
|
G:GNP201
|
4.2
|
83.2
|
1.0
|
O1G
|
G:GNP201
|
4.3
|
68.5
|
1.0
|
C
|
G:PRO34
|
4.4
|
87.7
|
1.0
|
CG2
|
G:THR35
|
4.4
|
90.0
|
1.0
|
C
|
G:ASP33
|
4.4
|
100.7
|
1.0
|
O1A
|
G:GNP201
|
4.5
|
91.5
|
1.0
|
O1B
|
G:GNP201
|
4.5
|
77.2
|
1.0
|
CA
|
G:PRO34
|
4.6
|
93.5
|
1.0
|
OD1
|
G:ASP57
|
4.9
|
103.2
|
1.0
|
CG
|
G:ASP57
|
4.9
|
96.5
|
1.0
|
|
Reference:
M.J.Whitley,
T.H.Tran,
M.Yi,
S.Dharmaiah,
G.Cornilescu,
D.K.Simanshu.
Comparative Analysis of KRAS4A and KRAS4B Splice Variants Reveals Distinctive Structural and Functional Properties Sci Adv 2024.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ADJ4137
Page generated: Fri Oct 4 20:31:29 2024
|