Magnesium in PDB 1tu3: Crystal Structure of RAB5 Complex with RABAPTIN5 C-Terminal Domain
Protein crystallography data
The structure of Crystal Structure of RAB5 Complex with RABAPTIN5 C-Terminal Domain, PDB code: 1tu3
was solved by
G.Zhu,
P.Zhai,
J.Liu,
S.Terzyan,
G.Li,
X.C.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.72 /
2.31
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.400,
83.500,
144.900,
90.00,
102.20,
90.00
|
R / Rfree (%)
|
22.2 /
27.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of RAB5 Complex with RABAPTIN5 C-Terminal Domain
(pdb code 1tu3). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Crystal Structure of RAB5 Complex with RABAPTIN5 C-Terminal Domain, PDB code: 1tu3:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 1tu3
Go back to
Magnesium Binding Sites List in 1tu3
Magnesium binding site 1 out
of 5 in the Crystal Structure of RAB5 Complex with RABAPTIN5 C-Terminal Domain
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 RAB5 Complex with RABAPTIN5 C-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1201
b:28.0
occ:1.00
|
O2B
|
A:GNP1202
|
1.9
|
20.5
|
1.0
|
O
|
A:HOH404
|
2.0
|
33.5
|
1.0
|
O
|
A:HOH405
|
2.0
|
33.3
|
1.0
|
O2G
|
A:GNP1202
|
2.0
|
35.4
|
1.0
|
OG1
|
A:THR52
|
2.2
|
31.9
|
1.0
|
OG
|
A:SER34
|
2.3
|
34.7
|
1.0
|
CB
|
A:SER34
|
3.0
|
26.3
|
1.0
|
PG
|
A:GNP1202
|
3.1
|
37.6
|
1.0
|
PB
|
A:GNP1202
|
3.2
|
32.8
|
1.0
|
CB
|
A:THR52
|
3.3
|
32.0
|
1.0
|
N3B
|
A:GNP1202
|
3.3
|
32.8
|
1.0
|
N
|
A:SER34
|
3.7
|
29.3
|
1.0
|
O3G
|
A:GNP1202
|
3.8
|
38.0
|
1.0
|
N
|
A:THR52
|
3.8
|
41.9
|
1.0
|
CA
|
A:SER34
|
3.9
|
29.5
|
1.0
|
O2A
|
A:GNP1202
|
3.9
|
42.0
|
1.0
|
OD2
|
A:ASP75
|
4.0
|
41.6
|
1.0
|
CA
|
A:THR52
|
4.1
|
33.8
|
1.0
|
O3A
|
A:GNP1202
|
4.2
|
45.6
|
1.0
|
O1B
|
A:GNP1202
|
4.2
|
34.5
|
1.0
|
O1G
|
A:GNP1202
|
4.3
|
35.0
|
1.0
|
OD1
|
A:ASP75
|
4.4
|
40.4
|
1.0
|
PA
|
A:GNP1202
|
4.4
|
32.8
|
1.0
|
O1A
|
A:GNP1202
|
4.4
|
31.6
|
1.0
|
CG2
|
A:THR52
|
4.5
|
20.7
|
1.0
|
O
|
A:HOH407
|
4.5
|
32.5
|
1.0
|
CG
|
A:ASP75
|
4.6
|
37.9
|
1.0
|
O
|
A:GLU50
|
4.6
|
51.4
|
1.0
|
O
|
A:THR76
|
4.8
|
29.9
|
1.0
|
C
|
A:SER51
|
4.8
|
42.6
|
1.0
|
C
|
A:LYS33
|
4.9
|
28.3
|
1.0
|
CB
|
A:LYS33
|
4.9
|
21.6
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 1tu3
Go back to
Magnesium Binding Sites List in 1tu3
Magnesium binding site 2 out
of 5 in the Crystal Structure of RAB5 Complex with RABAPTIN5 C-Terminal Domain
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 RAB5 Complex with RABAPTIN5 C-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2201
b:40.5
occ:1.00
|
O2B
|
B:GNP2202
|
1.9
|
45.6
|
1.0
|
O
|
B:HOH421
|
1.9
|
36.6
|
1.0
|
OG1
|
B:THR52
|
2.0
|
40.2
|
1.0
|
O
|
B:HOH420
|
2.0
|
38.6
|
1.0
|
OG
|
B:SER34
|
2.0
|
41.5
|
1.0
|
O2G
|
B:GNP2202
|
2.1
|
45.5
|
1.0
|
PB
|
B:GNP2202
|
3.2
|
49.4
|
1.0
|
CB
|
B:THR52
|
3.2
|
48.5
|
1.0
|
PG
|
B:GNP2202
|
3.2
|
49.4
|
1.0
|
CB
|
B:SER34
|
3.2
|
45.5
|
1.0
|
N3B
|
B:GNP2202
|
3.5
|
43.5
|
1.0
|
OD2
|
B:ASP75
|
3.8
|
53.0
|
1.0
|
N
|
B:THR52
|
3.8
|
50.1
|
1.0
|
O3G
|
B:GNP2202
|
3.8
|
50.2
|
1.0
|
N
|
B:SER34
|
3.9
|
41.3
|
1.0
|
OD1
|
B:ASP75
|
4.0
|
49.2
|
1.0
|
CA
|
B:THR52
|
4.0
|
47.0
|
1.0
|
O
|
B:HOH423
|
4.1
|
51.1
|
1.0
|
CA
|
B:SER34
|
4.2
|
39.6
|
1.0
|
O1B
|
B:GNP2202
|
4.2
|
51.3
|
1.0
|
CG2
|
B:THR52
|
4.3
|
34.3
|
1.0
|
O3A
|
B:GNP2202
|
4.3
|
60.0
|
1.0
|
CG
|
B:ASP75
|
4.3
|
46.5
|
1.0
|
O2A
|
B:GNP2202
|
4.3
|
51.5
|
1.0
|
O1G
|
B:GNP2202
|
4.5
|
45.3
|
1.0
|
PA
|
B:GNP2202
|
4.6
|
53.4
|
1.0
|
O1A
|
B:GNP2202
|
4.6
|
47.7
|
1.0
|
O
|
B:THR76
|
4.7
|
37.0
|
1.0
|
CB
|
B:LYS33
|
4.8
|
43.2
|
1.0
|
C
|
B:SER51
|
4.8
|
50.5
|
1.0
|
CE
|
B:LYS33
|
4.9
|
38.8
|
1.0
|
O
|
B:GLU50
|
4.9
|
57.1
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 1tu3
Go back to
Magnesium Binding Sites List in 1tu3
Magnesium binding site 3 out
of 5 in the Crystal Structure of RAB5 Complex with RABAPTIN5 C-Terminal Domain
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 RAB5 Complex with RABAPTIN5 C-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg3201
b:45.8
occ:1.00
|
OG1
|
C:THR52
|
2.0
|
53.5
|
1.0
|
O2B
|
C:GNP3202
|
2.0
|
29.9
|
1.0
|
O2G
|
C:GNP3202
|
2.1
|
39.3
|
1.0
|
O
|
C:HOH432
|
2.2
|
46.0
|
1.0
|
OG
|
C:SER34
|
2.2
|
53.9
|
1.0
|
O
|
C:HOH431
|
2.5
|
51.5
|
1.0
|
CB
|
C:SER34
|
3.1
|
60.2
|
1.0
|
CB
|
C:THR52
|
3.2
|
66.8
|
1.0
|
PG
|
C:GNP3202
|
3.2
|
56.6
|
1.0
|
PB
|
C:GNP3202
|
3.3
|
59.3
|
1.0
|
N3B
|
C:GNP3202
|
3.5
|
53.8
|
1.0
|
N
|
C:THR52
|
3.5
|
73.8
|
1.0
|
N
|
C:SER34
|
3.7
|
51.4
|
1.0
|
OD2
|
C:ASP75
|
3.9
|
59.1
|
1.0
|
CA
|
C:THR52
|
3.9
|
70.2
|
1.0
|
O3G
|
C:GNP3202
|
3.9
|
49.2
|
1.0
|
CA
|
C:SER34
|
4.0
|
55.8
|
1.0
|
OD1
|
C:ASP75
|
4.0
|
55.8
|
1.0
|
O2A
|
C:GNP3202
|
4.2
|
64.2
|
1.0
|
CG2
|
C:THR52
|
4.3
|
48.5
|
1.0
|
O1B
|
C:GNP3202
|
4.3
|
54.3
|
1.0
|
O3A
|
C:GNP3202
|
4.3
|
60.6
|
1.0
|
CG
|
C:ASP75
|
4.4
|
56.9
|
1.0
|
O1G
|
C:GNP3202
|
4.4
|
70.5
|
1.0
|
C
|
C:SER51
|
4.6
|
79.4
|
1.0
|
CB
|
C:LYS33
|
4.6
|
55.3
|
1.0
|
PA
|
C:GNP3202
|
4.6
|
69.7
|
1.0
|
O
|
C:GLU50
|
4.8
|
82.5
|
1.0
|
O
|
C:THR76
|
4.8
|
44.6
|
1.0
|
CA
|
C:SER51
|
4.8
|
79.7
|
1.0
|
O1A
|
C:GNP3202
|
4.8
|
76.3
|
1.0
|
C
|
C:LYS33
|
4.9
|
54.4
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 1tu3
Go back to
Magnesium Binding Sites List in 1tu3
Magnesium binding site 4 out
of 5 in the Crystal Structure of RAB5 Complex with RABAPTIN5 C-Terminal Domain
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 RAB5 Complex with RABAPTIN5 C-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg4201
b:51.9
occ:1.00
|
O2B
|
D:GNP4202
|
1.9
|
42.8
|
1.0
|
O2G
|
D:GNP4202
|
2.0
|
57.4
|
1.0
|
O
|
D:HOH440
|
2.1
|
39.5
|
1.0
|
OG
|
D:SER34
|
2.1
|
68.2
|
1.0
|
O
|
D:HOH441
|
2.2
|
58.8
|
1.0
|
OG1
|
D:THR52
|
2.4
|
73.3
|
1.0
|
PG
|
D:GNP4202
|
3.0
|
67.4
|
1.0
|
PB
|
D:GNP4202
|
3.1
|
62.6
|
1.0
|
N3B
|
D:GNP4202
|
3.1
|
63.5
|
1.0
|
CB
|
D:THR52
|
3.2
|
65.5
|
1.0
|
CB
|
D:SER34
|
3.2
|
65.5
|
1.0
|
N
|
D:THR52
|
3.8
|
69.6
|
1.0
|
N
|
D:SER34
|
3.8
|
62.0
|
1.0
|
OD2
|
D:ASP75
|
3.9
|
55.6
|
1.0
|
O3G
|
D:GNP4202
|
3.9
|
57.7
|
1.0
|
CA
|
D:SER34
|
4.0
|
65.4
|
1.0
|
CA
|
D:THR52
|
4.1
|
70.1
|
1.0
|
OD1
|
D:ASP75
|
4.1
|
54.6
|
1.0
|
O1B
|
D:GNP4202
|
4.1
|
45.2
|
1.0
|
O1G
|
D:GNP4202
|
4.1
|
73.0
|
1.0
|
O2A
|
D:GNP4202
|
4.1
|
68.0
|
1.0
|
O3A
|
D:GNP4202
|
4.2
|
59.6
|
1.0
|
CG2
|
D:THR52
|
4.3
|
55.4
|
1.0
|
CG
|
D:ASP75
|
4.4
|
59.4
|
1.0
|
O
|
D:THR76
|
4.5
|
46.9
|
1.0
|
PA
|
D:GNP4202
|
4.5
|
78.6
|
1.0
|
O1A
|
D:GNP4202
|
4.7
|
74.7
|
1.0
|
NZ
|
D:LYS33
|
4.8
|
52.5
|
1.0
|
O
|
D:HOH439
|
4.8
|
45.7
|
1.0
|
C
|
D:SER51
|
4.8
|
74.5
|
1.0
|
C
|
D:LYS33
|
4.9
|
54.3
|
1.0
|
CB
|
D:LYS33
|
5.0
|
56.7
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 1tu3
Go back to
Magnesium Binding Sites List in 1tu3
Magnesium binding site 5 out
of 5 in the Crystal Structure of RAB5 Complex with RABAPTIN5 C-Terminal Domain
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 RAB5 Complex with RABAPTIN5 C-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg5201
b:39.6
occ:1.00
|
OG
|
E:SER34
|
1.7
|
38.4
|
1.0
|
O2B
|
E:GNP5202
|
2.0
|
32.0
|
1.0
|
OG1
|
E:THR52
|
2.1
|
40.6
|
1.0
|
O
|
E:HOH450
|
2.1
|
28.1
|
1.0
|
O2G
|
E:GNP5202
|
2.1
|
43.1
|
1.0
|
O
|
E:HOH451
|
2.4
|
37.6
|
1.0
|
CB
|
E:SER34
|
3.0
|
41.1
|
1.0
|
CB
|
E:THR52
|
3.2
|
40.0
|
1.0
|
PG
|
E:GNP5202
|
3.2
|
41.8
|
1.0
|
PB
|
E:GNP5202
|
3.3
|
36.9
|
1.0
|
N3B
|
E:GNP5202
|
3.6
|
26.2
|
1.0
|
N
|
E:SER34
|
3.7
|
30.8
|
1.0
|
O3G
|
E:GNP5202
|
3.7
|
50.7
|
1.0
|
N
|
E:THR52
|
3.8
|
45.6
|
1.0
|
OD2
|
E:ASP75
|
3.8
|
47.9
|
1.0
|
CA
|
E:SER34
|
3.9
|
39.0
|
1.0
|
CA
|
E:THR52
|
4.0
|
40.4
|
1.0
|
OD1
|
E:ASP75
|
4.1
|
52.7
|
1.0
|
O2A
|
E:GNP5202
|
4.2
|
31.1
|
1.0
|
CG2
|
E:THR52
|
4.3
|
35.5
|
1.0
|
O1B
|
E:GNP5202
|
4.4
|
39.2
|
1.0
|
CG
|
E:ASP75
|
4.4
|
50.0
|
1.0
|
O3A
|
E:GNP5202
|
4.4
|
49.7
|
1.0
|
O1G
|
E:GNP5202
|
4.5
|
40.4
|
1.0
|
PA
|
E:GNP5202
|
4.6
|
41.8
|
1.0
|
O
|
E:HOH595
|
4.7
|
46.7
|
1.0
|
O
|
E:THR76
|
4.7
|
26.4
|
1.0
|
CB
|
E:LYS33
|
4.8
|
31.7
|
1.0
|
O1A
|
E:GNP5202
|
4.8
|
33.5
|
1.0
|
C
|
E:LYS33
|
4.8
|
31.8
|
1.0
|
O
|
E:GLU50
|
4.9
|
50.6
|
1.0
|
C
|
E:SER51
|
4.9
|
46.6
|
1.0
|
O
|
E:HOH454
|
4.9
|
47.9
|
1.0
|
|
Reference:
G.Zhu,
P.Zhai,
J.Liu,
S.Terzyan,
G.Li,
X.C.Zhang.
Structural Basis of RAB5-RABAPTIN5 Interaction in Endocytosis Nat.Struct.Mol.Biol. V. 11 975 2004.
ISSN: ISSN 1545-9993
PubMed: 15378032
DOI: 10.1038/NSMB832
Page generated: Tue Aug 13 14:38:04 2024
|