Magnesium in PDB 1yzt: Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution
Protein crystallography data
The structure of Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution, PDB code: 1yzt
was solved by
S.Eathiraj,
X.Pan,
C.Ritacco,
D.G.Lambright,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
12.00 /
2.05
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
130.357,
36.567,
86.666,
90.00,
113.40,
90.00
|
R / Rfree (%)
|
21 /
28.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution
(pdb code 1yzt). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution, PDB code: 1yzt:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 1yzt
Go back to
Magnesium Binding Sites List in 1yzt
Magnesium binding site 1 out
of 2 in the Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg700
b:26.1
occ:1.00
|
O2B
|
A:GNP701
|
2.0
|
20.4
|
1.0
|
OG1
|
A:THR51
|
2.0
|
22.6
|
1.0
|
O
|
A:HOH704
|
2.0
|
16.2
|
1.0
|
O
|
A:HOH716
|
2.0
|
20.8
|
1.0
|
OG1
|
A:THR33
|
2.0
|
18.8
|
1.0
|
O2G
|
A:GNP701
|
2.1
|
19.1
|
1.0
|
CB
|
A:THR51
|
3.1
|
25.4
|
1.0
|
CB
|
A:THR33
|
3.2
|
19.0
|
1.0
|
PB
|
A:GNP701
|
3.3
|
21.6
|
1.0
|
PG
|
A:GNP701
|
3.3
|
21.9
|
1.0
|
N3B
|
A:GNP701
|
3.6
|
19.5
|
1.0
|
N
|
A:THR51
|
3.8
|
26.4
|
1.0
|
N
|
A:THR33
|
3.9
|
18.9
|
1.0
|
OD2
|
A:ASP74
|
4.0
|
21.2
|
1.0
|
O
|
A:HOH767
|
4.0
|
29.1
|
1.0
|
CA
|
A:THR51
|
4.1
|
26.3
|
1.0
|
CA
|
A:THR33
|
4.1
|
18.8
|
1.0
|
OD1
|
A:ASP74
|
4.1
|
19.9
|
1.0
|
CG2
|
A:THR51
|
4.2
|
25.2
|
1.0
|
CG2
|
A:THR33
|
4.2
|
19.5
|
1.0
|
O3G
|
A:GNP701
|
4.2
|
19.9
|
1.0
|
O2A
|
A:GNP701
|
4.3
|
19.0
|
1.0
|
O3A
|
A:GNP701
|
4.3
|
19.5
|
1.0
|
O1B
|
A:GNP701
|
4.3
|
16.9
|
1.0
|
O1G
|
A:GNP701
|
4.4
|
22.9
|
1.0
|
O
|
A:THR75
|
4.4
|
25.8
|
1.0
|
O
|
A:ILE49
|
4.4
|
28.9
|
1.0
|
CG
|
A:ASP74
|
4.5
|
22.1
|
1.0
|
PA
|
A:GNP701
|
4.6
|
20.6
|
1.0
|
O1A
|
A:GNP701
|
4.8
|
20.4
|
1.0
|
CE
|
A:LYS32
|
4.8
|
17.0
|
1.0
|
C
|
A:THR50
|
4.8
|
28.3
|
1.0
|
CB
|
A:LYS32
|
4.9
|
19.6
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 1yzt
Go back to
Magnesium Binding Sites List in 1yzt
Magnesium binding site 2 out
of 2 in the Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg800
b:24.1
occ:1.00
|
O2G
|
B:GNP801
|
1.9
|
19.5
|
1.0
|
O
|
B:HOH803
|
2.0
|
15.6
|
1.0
|
O
|
B:HOH870
|
2.1
|
21.4
|
1.0
|
OG1
|
B:THR33
|
2.1
|
19.3
|
1.0
|
O2B
|
B:GNP801
|
2.1
|
22.7
|
1.0
|
OG1
|
B:THR51
|
2.1
|
24.8
|
1.0
|
CB
|
B:THR51
|
3.1
|
27.0
|
1.0
|
CB
|
B:THR33
|
3.2
|
19.9
|
1.0
|
PG
|
B:GNP801
|
3.2
|
22.3
|
1.0
|
PB
|
B:GNP801
|
3.3
|
22.3
|
1.0
|
N3B
|
B:GNP801
|
3.5
|
19.9
|
1.0
|
N
|
B:THR51
|
3.8
|
28.3
|
1.0
|
OD2
|
B:ASP74
|
3.9
|
22.2
|
1.0
|
N
|
B:THR33
|
3.9
|
20.0
|
1.0
|
CA
|
B:THR51
|
4.0
|
27.7
|
1.0
|
O
|
B:HOH902
|
4.1
|
35.9
|
1.0
|
O3G
|
B:GNP801
|
4.1
|
20.6
|
1.0
|
CA
|
B:THR33
|
4.1
|
20.1
|
1.0
|
OD1
|
B:ASP74
|
4.1
|
22.3
|
1.0
|
CG2
|
B:THR33
|
4.2
|
20.5
|
1.0
|
CG2
|
B:THR51
|
4.2
|
27.6
|
1.0
|
O
|
B:THR75
|
4.3
|
23.8
|
1.0
|
O1B
|
B:GNP801
|
4.3
|
18.9
|
1.0
|
O1G
|
B:GNP801
|
4.4
|
21.3
|
1.0
|
O2A
|
B:GNP801
|
4.4
|
23.5
|
1.0
|
O3A
|
B:GNP801
|
4.4
|
20.2
|
1.0
|
CG
|
B:ASP74
|
4.4
|
22.8
|
1.0
|
O
|
B:ILE49
|
4.5
|
30.1
|
1.0
|
PA
|
B:GNP801
|
4.7
|
23.1
|
1.0
|
CE
|
B:LYS32
|
4.8
|
19.7
|
1.0
|
C
|
B:THR50
|
4.8
|
29.2
|
1.0
|
CB
|
B:LYS32
|
4.9
|
20.1
|
1.0
|
O1A
|
B:GNP801
|
4.9
|
21.4
|
1.0
|
|
Reference:
S.Eathiraj,
X.Pan,
C.Ritacco,
D.G.Lambright.
Structural Basis of Family-Wide Rab Gtpase Recognition By Rabenosyn-5. Nature V. 436 415 2005.
ISSN: ISSN 0028-0836
PubMed: 16034420
DOI: 10.1038/NATURE03798
Page generated: Mon Dec 14 07:10:56 2020
|