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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

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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

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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

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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

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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

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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: Mon Dec 14 06:51:54 2020

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