Cobalt in PDB 1tu4: Crystal Structure of RAB5-Gdp Complex
Protein crystallography data
The structure of Crystal Structure of RAB5-Gdp Complex, PDB code: 1tu4
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)
|
29.61 /
2.20
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.900,
84.900,
199.900,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.7 /
27.4
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of RAB5-Gdp Complex
(pdb code 1tu4). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the
Crystal Structure of RAB5-Gdp Complex, PDB code: 1tu4:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
Cobalt binding site 1 out
of 6 in 1tu4
Go back to
Cobalt Binding Sites List in 1tu4
Cobalt binding site 1 out
of 6 in the Crystal Structure of RAB5-Gdp Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Crystal Structure of RAB5-Gdp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co1201
b:37.1
occ:1.00
|
O
|
A:HOH308
|
1.8
|
29.8
|
1.0
|
OG
|
A:SER34
|
2.0
|
25.6
|
1.0
|
O
|
A:HOH302
|
2.1
|
32.2
|
1.0
|
O
|
A:HOH301
|
2.1
|
30.8
|
1.0
|
O
|
D:HOH303
|
2.2
|
33.9
|
1.0
|
O1B
|
A:GDP1200
|
2.2
|
36.8
|
1.0
|
CB
|
A:SER34
|
3.1
|
28.6
|
1.0
|
PB
|
A:GDP1200
|
3.3
|
35.0
|
1.0
|
O3B
|
A:GDP1200
|
3.4
|
31.5
|
1.0
|
ND2
|
D:ASN16
|
3.8
|
61.0
|
1.0
|
N
|
A:SER34
|
3.9
|
28.7
|
1.0
|
CA
|
A:SER34
|
4.0
|
29.4
|
1.0
|
OD2
|
A:ASP75
|
4.0
|
32.4
|
1.0
|
OD1
|
A:ASP75
|
4.1
|
27.6
|
1.0
|
O
|
A:THR76
|
4.2
|
31.8
|
1.0
|
OD1
|
D:ASN16
|
4.2
|
61.3
|
1.0
|
O1A
|
A:GDP1200
|
4.2
|
35.0
|
1.0
|
OG1
|
A:THR76
|
4.3
|
32.0
|
1.0
|
O2B
|
A:GDP1200
|
4.4
|
37.0
|
1.0
|
O3A
|
A:GDP1200
|
4.4
|
33.4
|
1.0
|
CG
|
D:ASN16
|
4.4
|
63.4
|
1.0
|
CG
|
A:ASP75
|
4.5
|
32.0
|
1.0
|
OE1
|
A:GLU80
|
4.6
|
33.2
|
1.0
|
PA
|
A:GDP1200
|
4.7
|
34.2
|
1.0
|
NZ
|
A:LYS33
|
4.7
|
29.8
|
1.0
|
O2A
|
A:GDP1200
|
4.8
|
32.0
|
1.0
|
CB
|
A:LYS33
|
4.8
|
24.3
|
1.0
|
CE
|
A:LYS33
|
4.9
|
30.3
|
1.0
|
N
|
A:GLY78
|
5.0
|
32.8
|
1.0
|
C
|
A:LYS33
|
5.0
|
27.2
|
1.0
|
C
|
A:THR76
|
5.0
|
30.5
|
1.0
|
|
Cobalt binding site 2 out
of 6 in 1tu4
Go back to
Cobalt Binding Sites List in 1tu4
Cobalt binding site 2 out
of 6 in the Crystal Structure of RAB5-Gdp Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Crystal Structure of RAB5-Gdp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co2201
b:48.8
occ:1.00
|
O
|
B:HOH306
|
2.0
|
47.0
|
1.0
|
O3B
|
B:GDP2200
|
2.1
|
34.1
|
1.0
|
O
|
B:HOH304
|
2.2
|
34.0
|
1.0
|
O
|
B:HOH305
|
2.2
|
38.8
|
1.0
|
OG
|
B:SER34
|
2.3
|
23.3
|
1.0
|
O
|
B:HOH307
|
2.4
|
52.1
|
1.0
|
CB
|
B:SER34
|
3.3
|
28.3
|
1.0
|
PB
|
B:GDP2200
|
3.3
|
33.6
|
1.0
|
O2B
|
B:GDP2200
|
3.4
|
36.1
|
1.0
|
N
|
B:SER34
|
3.8
|
29.9
|
1.0
|
OD2
|
B:ASP75
|
3.9
|
37.0
|
1.0
|
O
|
B:HOH513
|
4.0
|
45.0
|
1.0
|
O1
|
B:SO4264
|
4.1
|
74.1
|
1.0
|
CA
|
B:SER34
|
4.1
|
28.2
|
1.0
|
OD1
|
B:ASP75
|
4.1
|
38.8
|
1.0
|
O4
|
B:SO4264
|
4.2
|
73.8
|
1.0
|
O1B
|
B:GDP2200
|
4.3
|
31.0
|
1.0
|
CG
|
B:ASP75
|
4.4
|
37.5
|
1.0
|
O
|
B:HOH317
|
4.4
|
42.6
|
1.0
|
O1A
|
B:GDP2200
|
4.4
|
34.6
|
1.0
|
O3A
|
B:GDP2200
|
4.4
|
30.8
|
1.0
|
O
|
B:THR76
|
4.8
|
33.9
|
1.0
|
CB
|
B:LYS33
|
4.8
|
29.8
|
1.0
|
CE
|
B:LYS33
|
4.8
|
31.0
|
1.0
|
S
|
B:SO4264
|
4.8
|
71.6
|
1.0
|
PA
|
B:GDP2200
|
4.8
|
33.4
|
1.0
|
C
|
B:LYS33
|
4.9
|
30.7
|
1.0
|
|
Cobalt binding site 3 out
of 6 in 1tu4
Go back to
Cobalt Binding Sites List in 1tu4
Cobalt binding site 3 out
of 6 in the Crystal Structure of RAB5-Gdp Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Crystal Structure of RAB5-Gdp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co251
b:32.5
occ:1.00
|
OE2
|
B:GLU80
|
1.9
|
36.4
|
1.0
|
OE1
|
B:GLU80
|
2.0
|
38.4
|
1.0
|
ND1
|
A:HIS83
|
2.1
|
26.0
|
1.0
|
O
|
B:HOH396
|
2.2
|
26.4
|
1.0
|
ND1
|
B:HIS83
|
2.2
|
28.0
|
1.0
|
CD
|
B:GLU80
|
2.2
|
40.8
|
1.0
|
O
|
A:HOH395
|
2.3
|
26.9
|
1.0
|
CE1
|
A:HIS83
|
2.9
|
25.9
|
1.0
|
CE1
|
B:HIS83
|
3.1
|
28.9
|
1.0
|
CG
|
B:HIS83
|
3.3
|
29.5
|
1.0
|
CG
|
A:HIS83
|
3.3
|
26.4
|
1.0
|
CB
|
B:HIS83
|
3.6
|
31.8
|
1.0
|
CG
|
B:GLU80
|
3.8
|
41.0
|
1.0
|
CB
|
A:HIS83
|
3.8
|
29.5
|
1.0
|
O
|
A:TYR82
|
3.9
|
29.4
|
1.0
|
NE2
|
A:HIS83
|
4.1
|
26.2
|
1.0
|
CA
|
A:HIS83
|
4.1
|
27.7
|
1.0
|
OE2
|
B:GLU28
|
4.2
|
32.2
|
1.0
|
NE2
|
B:HIS83
|
4.3
|
28.2
|
1.0
|
CD2
|
A:HIS83
|
4.3
|
25.1
|
1.0
|
CD2
|
B:HIS83
|
4.4
|
29.8
|
1.0
|
OE1
|
B:GLU28
|
4.5
|
33.4
|
1.0
|
O
|
A:HOH346
|
4.6
|
37.8
|
1.0
|
CZ2
|
B:TRP114
|
4.6
|
27.1
|
1.0
|
C
|
A:TYR82
|
4.6
|
29.7
|
1.0
|
O
|
B:HOH327
|
4.6
|
28.1
|
1.0
|
CB
|
B:GLU80
|
4.6
|
37.9
|
1.0
|
CA
|
B:GLU80
|
4.8
|
36.0
|
1.0
|
O
|
B:GLU80
|
4.8
|
36.5
|
1.0
|
CD
|
B:GLU28
|
4.8
|
30.7
|
1.0
|
N
|
A:HIS83
|
4.8
|
29.0
|
1.0
|
|
Cobalt binding site 4 out
of 6 in 1tu4
Go back to
Cobalt Binding Sites List in 1tu4
Cobalt binding site 4 out
of 6 in the Crystal Structure of RAB5-Gdp Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Crystal Structure of RAB5-Gdp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co3201
b:47.1
occ:1.00
|
OG
|
C:SER34
|
2.1
|
42.1
|
1.0
|
O
|
C:HOH309
|
2.1
|
33.8
|
1.0
|
O
|
C:HOH311
|
2.1
|
34.5
|
1.0
|
O
|
C:HOH310
|
2.2
|
35.2
|
1.0
|
O3B
|
C:GDP3200
|
2.2
|
51.2
|
1.0
|
O
|
C:HOH312
|
2.5
|
46.9
|
1.0
|
CB
|
C:SER34
|
3.3
|
39.3
|
1.0
|
O2B
|
C:GDP3200
|
3.3
|
49.6
|
1.0
|
PB
|
C:GDP3200
|
3.3
|
51.8
|
1.0
|
N
|
C:SER34
|
4.0
|
38.1
|
1.0
|
O1A
|
C:GDP3200
|
4.1
|
51.4
|
1.0
|
CA
|
C:SER34
|
4.2
|
40.3
|
1.0
|
OD1
|
C:ASP75
|
4.2
|
41.9
|
1.0
|
O
|
C:THR76
|
4.2
|
41.3
|
1.0
|
O
|
C:HOH330
|
4.3
|
49.4
|
1.0
|
OD2
|
C:ASP75
|
4.3
|
39.1
|
1.0
|
O1B
|
C:GDP3200
|
4.3
|
49.1
|
1.0
|
OG1
|
C:THR76
|
4.4
|
39.3
|
1.0
|
O3A
|
C:GDP3200
|
4.4
|
47.2
|
1.0
|
OE2
|
C:GLU80
|
4.4
|
48.2
|
1.0
|
PA
|
C:GDP3200
|
4.6
|
48.7
|
1.0
|
CG
|
C:ASP75
|
4.7
|
38.1
|
1.0
|
O
|
D:HOH564
|
4.7
|
55.9
|
1.0
|
O2A
|
C:GDP3200
|
4.8
|
49.2
|
1.0
|
CB
|
C:LYS33
|
4.9
|
40.4
|
1.0
|
N
|
C:GLY78
|
4.9
|
46.4
|
1.0
|
C
|
C:THR76
|
5.0
|
41.0
|
1.0
|
|
Cobalt binding site 5 out
of 6 in 1tu4
Go back to
Cobalt Binding Sites List in 1tu4
Cobalt binding site 5 out
of 6 in the Crystal Structure of RAB5-Gdp Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Crystal Structure of RAB5-Gdp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co4201
b:63.3
occ:1.00
|
O
|
D:HOH313
|
2.0
|
52.5
|
1.0
|
O2B
|
D:GDP4200
|
2.2
|
47.3
|
1.0
|
O
|
D:HOH314
|
2.3
|
48.8
|
1.0
|
OG
|
D:SER34
|
2.4
|
49.9
|
1.0
|
O
|
D:HOH315
|
2.4
|
51.6
|
1.0
|
O
|
D:HOH316
|
2.5
|
65.0
|
1.0
|
PB
|
D:GDP4200
|
3.3
|
47.1
|
1.0
|
CB
|
D:SER34
|
3.3
|
48.5
|
1.0
|
O1B
|
D:GDP4200
|
3.3
|
46.9
|
1.0
|
OD2
|
D:ASP75
|
4.0
|
42.4
|
1.0
|
N
|
D:SER34
|
4.0
|
49.9
|
1.0
|
O2
|
D:SO4262
|
4.2
|
88.0
|
1.0
|
CA
|
D:SER34
|
4.2
|
49.3
|
1.0
|
O3B
|
D:GDP4200
|
4.3
|
43.4
|
1.0
|
OD1
|
D:ASP75
|
4.4
|
44.7
|
1.0
|
O3A
|
D:GDP4200
|
4.4
|
51.5
|
1.0
|
O1A
|
D:GDP4200
|
4.5
|
50.8
|
1.0
|
O4
|
D:SO4262
|
4.5
|
88.4
|
1.0
|
O
|
D:THR76
|
4.6
|
44.1
|
1.0
|
CG
|
D:ASP75
|
4.6
|
42.9
|
1.0
|
S
|
D:SO4262
|
4.8
|
89.2
|
1.0
|
O1
|
D:SO4262
|
4.8
|
88.4
|
1.0
|
CE
|
D:LYS33
|
4.8
|
61.3
|
1.0
|
PA
|
D:GDP4200
|
4.9
|
52.6
|
1.0
|
CB
|
D:LYS33
|
4.9
|
51.8
|
1.0
|
|
Cobalt binding site 6 out
of 6 in 1tu4
Go back to
Cobalt Binding Sites List in 1tu4
Cobalt binding site 6 out
of 6 in the Crystal Structure of RAB5-Gdp Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Crystal Structure of RAB5-Gdp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co252
b:51.5
occ:1.00
|
OE1
|
D:GLU80
|
2.0
|
50.5
|
1.0
|
OE2
|
D:GLU80
|
2.1
|
46.1
|
1.0
|
ND1
|
C:HIS83
|
2.1
|
45.7
|
1.0
|
O
|
C:HOH398
|
2.1
|
65.9
|
1.0
|
ND1
|
D:HIS83
|
2.3
|
53.1
|
1.0
|
CD
|
D:GLU80
|
2.3
|
47.3
|
1.0
|
O
|
C:HOH397
|
2.4
|
42.0
|
1.0
|
CE1
|
C:HIS83
|
2.9
|
49.1
|
1.0
|
CG
|
C:HIS83
|
3.2
|
47.3
|
1.0
|
CG
|
D:HIS83
|
3.3
|
51.9
|
1.0
|
CE1
|
D:HIS83
|
3.3
|
53.5
|
1.0
|
CB
|
D:HIS83
|
3.5
|
48.4
|
1.0
|
CB
|
C:HIS83
|
3.7
|
44.6
|
1.0
|
CG
|
D:GLU80
|
3.8
|
49.1
|
1.0
|
O
|
C:TYR82
|
4.0
|
43.2
|
1.0
|
CA
|
C:HIS83
|
4.1
|
41.5
|
1.0
|
NE2
|
C:HIS83
|
4.1
|
47.3
|
1.0
|
CD2
|
C:HIS83
|
4.3
|
48.2
|
1.0
|
NE2
|
D:HIS83
|
4.4
|
54.0
|
1.0
|
CD2
|
D:HIS83
|
4.4
|
52.0
|
1.0
|
CZ2
|
D:TRP114
|
4.4
|
39.2
|
1.0
|
O
|
D:HOH409
|
4.4
|
43.4
|
1.0
|
OE2
|
D:GLU28
|
4.5
|
56.1
|
1.0
|
O
|
D:GLU80
|
4.5
|
51.2
|
1.0
|
CB
|
D:GLU80
|
4.6
|
48.6
|
1.0
|
C
|
C:TYR82
|
4.7
|
42.3
|
1.0
|
CA
|
D:GLU80
|
4.8
|
51.2
|
1.0
|
N
|
C:HIS83
|
4.8
|
40.3
|
1.0
|
OE1
|
D:GLU28
|
4.9
|
55.2
|
1.0
|
CH2
|
D:TRP114
|
5.0
|
37.0
|
1.0
|
CE2
|
D:TRP114
|
5.0
|
36.6
|
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
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