Magnesium in PDB 1t91: Crystal Structure of Human Small Gtpase RAB7(Gtp)
Protein crystallography data
The structure of Crystal Structure of Human Small Gtpase RAB7(Gtp), PDB code: 1t91
was solved by
H.Song,
W.Hong,
M.Wu,
T.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.90
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.695,
56.777,
74.510,
71.51,
71.72,
77.75
|
R / Rfree (%)
|
24.3 /
24.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Human Small Gtpase RAB7(Gtp)
(pdb code 1t91). 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 Human Small Gtpase RAB7(Gtp), PDB code: 1t91:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1t91
Go back to
Magnesium Binding Sites List in 1t91
Magnesium binding site 1 out
of 4 in the Crystal Structure of Human Small Gtpase RAB7(Gtp)
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 Human Small Gtpase RAB7(Gtp) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1301
b:25.5
occ:1.00
|
OG1
|
A:THR40
|
2.0
|
6.7
|
1.0
|
O1G
|
A:GTP1401
|
2.0
|
25.1
|
1.0
|
O2B
|
A:GTP1401
|
2.1
|
24.0
|
1.0
|
OG1
|
A:THR22
|
2.2
|
8.9
|
1.0
|
O
|
A:HOH1406
|
2.3
|
20.8
|
1.0
|
CB
|
A:THR40
|
2.9
|
10.5
|
1.0
|
PG
|
A:GTP1401
|
3.2
|
22.2
|
1.0
|
PB
|
A:GTP1401
|
3.2
|
19.3
|
1.0
|
CB
|
A:THR22
|
3.3
|
10.0
|
1.0
|
O3B
|
A:GTP1401
|
3.5
|
25.6
|
1.0
|
N
|
A:THR40
|
3.6
|
9.7
|
1.0
|
CA
|
A:THR40
|
3.8
|
9.6
|
1.0
|
O2G
|
A:GTP1401
|
3.9
|
21.0
|
1.0
|
CG2
|
A:THR40
|
4.1
|
11.2
|
1.0
|
N
|
A:THR22
|
4.1
|
9.0
|
1.0
|
OD2
|
A:ASP63
|
4.1
|
8.1
|
1.0
|
O2A
|
A:GTP1401
|
4.1
|
24.5
|
1.0
|
OD1
|
A:ASP63
|
4.2
|
7.0
|
1.0
|
O3A
|
A:GTP1401
|
4.3
|
24.0
|
1.0
|
O1B
|
A:GTP1401
|
4.3
|
20.3
|
1.0
|
CA
|
A:THR22
|
4.3
|
9.1
|
1.0
|
O3G
|
A:GTP1401
|
4.4
|
30.2
|
1.0
|
CG2
|
A:THR22
|
4.4
|
9.2
|
1.0
|
O
|
A:HOH1407
|
4.4
|
27.1
|
1.0
|
O
|
A:THR64
|
4.4
|
9.9
|
1.0
|
O
|
A:LYS38
|
4.4
|
7.3
|
1.0
|
CG
|
A:ASP63
|
4.6
|
7.9
|
1.0
|
C
|
A:ALA39
|
4.6
|
8.6
|
1.0
|
PA
|
A:GTP1401
|
4.6
|
24.4
|
1.0
|
O1A
|
A:GTP1401
|
4.8
|
18.7
|
1.0
|
CA
|
A:ALA39
|
5.0
|
9.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1t91
Go back to
Magnesium Binding Sites List in 1t91
Magnesium binding site 2 out
of 4 in the Crystal Structure of Human Small Gtpase RAB7(Gtp)
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 Human Small Gtpase RAB7(Gtp) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1302
b:27.0
occ:1.00
|
OG1
|
B:THR40
|
1.9
|
21.8
|
1.0
|
O1G
|
B:GTP1402
|
2.0
|
22.3
|
1.0
|
O2B
|
B:GTP1402
|
2.1
|
18.6
|
1.0
|
OG1
|
B:THR22
|
2.1
|
22.9
|
1.0
|
O
|
B:HOH1430
|
2.3
|
19.3
|
1.0
|
CB
|
B:THR40
|
2.9
|
24.4
|
1.0
|
PG
|
B:GTP1402
|
3.2
|
24.4
|
1.0
|
PB
|
B:GTP1402
|
3.2
|
22.7
|
1.0
|
CB
|
B:THR22
|
3.3
|
23.1
|
1.0
|
O3B
|
B:GTP1402
|
3.5
|
23.9
|
1.0
|
N
|
B:THR40
|
3.6
|
27.2
|
1.0
|
CA
|
B:THR40
|
3.8
|
26.2
|
1.0
|
O2G
|
B:GTP1402
|
3.9
|
26.6
|
1.0
|
OD2
|
B:ASP63
|
4.1
|
21.1
|
1.0
|
CG2
|
B:THR40
|
4.1
|
26.3
|
1.0
|
N
|
B:THR22
|
4.1
|
21.2
|
1.0
|
O2A
|
B:GTP1402
|
4.1
|
30.2
|
1.0
|
OD1
|
B:ASP63
|
4.2
|
20.4
|
1.0
|
CA
|
B:THR22
|
4.3
|
22.2
|
1.0
|
CG2
|
B:THR22
|
4.3
|
24.3
|
1.0
|
O3A
|
B:GTP1402
|
4.3
|
23.8
|
1.0
|
O1B
|
B:GTP1402
|
4.3
|
22.4
|
1.0
|
O3G
|
B:GTP1402
|
4.4
|
28.8
|
1.0
|
O
|
B:THR64
|
4.5
|
20.3
|
1.0
|
O
|
B:LYS38
|
4.5
|
26.7
|
1.0
|
CG
|
B:ASP63
|
4.5
|
19.1
|
1.0
|
PA
|
B:GTP1402
|
4.6
|
25.4
|
1.0
|
C
|
B:ALA39
|
4.6
|
28.0
|
1.0
|
O1A
|
B:GTP1402
|
4.8
|
18.6
|
1.0
|
CA
|
B:ALA39
|
5.0
|
28.2
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1t91
Go back to
Magnesium Binding Sites List in 1t91
Magnesium binding site 3 out
of 4 in the Crystal Structure of Human Small Gtpase RAB7(Gtp)
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 Human Small Gtpase RAB7(Gtp) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1303
b:27.9
occ:1.00
|
OG1
|
C:THR40
|
2.0
|
21.7
|
1.0
|
O1G
|
C:GTP1403
|
2.0
|
21.6
|
1.0
|
O2B
|
C:GTP1403
|
2.1
|
20.1
|
1.0
|
OG1
|
C:THR22
|
2.2
|
20.3
|
1.0
|
O
|
C:HOH1434
|
2.2
|
18.4
|
1.0
|
CB
|
C:THR40
|
2.9
|
24.9
|
1.0
|
PG
|
C:GTP1403
|
3.2
|
24.9
|
1.0
|
PB
|
C:GTP1403
|
3.2
|
22.1
|
1.0
|
CB
|
C:THR22
|
3.3
|
22.0
|
1.0
|
O3B
|
C:GTP1403
|
3.5
|
23.4
|
1.0
|
N
|
C:THR40
|
3.6
|
26.3
|
1.0
|
CA
|
C:THR40
|
3.8
|
26.2
|
1.0
|
O2G
|
C:GTP1403
|
3.9
|
23.6
|
1.0
|
O
|
C:HOH1456
|
4.1
|
27.1
|
1.0
|
OD2
|
C:ASP63
|
4.1
|
21.5
|
1.0
|
N
|
C:THR22
|
4.1
|
20.0
|
1.0
|
CG2
|
C:THR40
|
4.1
|
24.8
|
1.0
|
O2A
|
C:GTP1403
|
4.1
|
25.8
|
1.0
|
OD1
|
C:ASP63
|
4.2
|
19.6
|
1.0
|
CA
|
C:THR22
|
4.3
|
21.5
|
1.0
|
O3A
|
C:GTP1403
|
4.3
|
24.6
|
1.0
|
O1B
|
C:GTP1403
|
4.3
|
22.7
|
1.0
|
CG2
|
C:THR22
|
4.3
|
21.3
|
1.0
|
O3G
|
C:GTP1403
|
4.4
|
27.5
|
1.0
|
O
|
C:THR64
|
4.4
|
19.4
|
1.0
|
O
|
C:LYS38
|
4.5
|
25.6
|
1.0
|
CG
|
C:ASP63
|
4.5
|
20.8
|
1.0
|
PA
|
C:GTP1403
|
4.6
|
24.5
|
1.0
|
C
|
C:ALA39
|
4.6
|
27.2
|
1.0
|
O1A
|
C:GTP1403
|
4.8
|
18.4
|
1.0
|
CA
|
C:ALA39
|
5.0
|
27.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1t91
Go back to
Magnesium Binding Sites List in 1t91
Magnesium binding site 4 out
of 4 in the Crystal Structure of Human Small Gtpase RAB7(Gtp)
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 Human Small Gtpase RAB7(Gtp) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1304
b:25.4
occ:1.00
|
OG1
|
D:THR40
|
1.9
|
21.5
|
1.0
|
O1G
|
D:GTP1404
|
2.0
|
21.4
|
1.0
|
O2B
|
D:GTP1404
|
2.1
|
20.8
|
1.0
|
OG1
|
D:THR22
|
2.2
|
22.7
|
1.0
|
O
|
D:HOH1482
|
2.4
|
18.8
|
1.0
|
CB
|
D:THR40
|
2.9
|
22.9
|
1.0
|
PG
|
D:GTP1404
|
3.2
|
23.1
|
1.0
|
PB
|
D:GTP1404
|
3.2
|
19.9
|
1.0
|
CB
|
D:THR22
|
3.3
|
20.6
|
1.0
|
O3B
|
D:GTP1404
|
3.5
|
24.7
|
1.0
|
N
|
D:THR40
|
3.6
|
24.2
|
1.0
|
CA
|
D:THR40
|
3.8
|
23.7
|
1.0
|
O2G
|
D:GTP1404
|
3.9
|
22.9
|
1.0
|
CG2
|
D:THR40
|
4.1
|
26.5
|
1.0
|
OD2
|
D:ASP63
|
4.1
|
16.2
|
1.0
|
N
|
D:THR22
|
4.1
|
19.8
|
1.0
|
O2A
|
D:GTP1404
|
4.1
|
26.0
|
1.0
|
OD1
|
D:ASP63
|
4.2
|
15.4
|
1.0
|
O
|
D:HOH1407
|
4.3
|
22.0
|
1.0
|
O3A
|
D:GTP1404
|
4.3
|
22.3
|
1.0
|
O1B
|
D:GTP1404
|
4.3
|
19.4
|
1.0
|
CA
|
D:THR22
|
4.3
|
20.5
|
1.0
|
O3G
|
D:GTP1404
|
4.4
|
27.7
|
1.0
|
CG2
|
D:THR22
|
4.4
|
22.8
|
1.0
|
O
|
D:LYS38
|
4.4
|
22.5
|
1.0
|
O
|
D:THR64
|
4.4
|
21.8
|
1.0
|
CG
|
D:ASP63
|
4.6
|
20.3
|
1.0
|
C
|
D:ALA39
|
4.6
|
24.3
|
1.0
|
PA
|
D:GTP1404
|
4.6
|
23.8
|
1.0
|
O1A
|
D:GTP1404
|
4.8
|
22.9
|
1.0
|
CA
|
D:ALA39
|
5.0
|
24.4
|
1.0
|
|
Reference:
M.Wu,
T.Wang,
E.Loh,
W.Hong,
H.Song.
Structural Basis For Recruitment of Rilp By Small Gtpase RAB7. Embo J. V. 24 1491 2005.
ISSN: ISSN 0261-4189
PubMed: 15933719
DOI: 10.1038/SJ.EMBOJ.7600643
Page generated: Tue Aug 13 14:28:12 2024
|