Atomistry » Magnesium » PDB 1tkk-1u3f » 1tu3
Atomistry »
  Magnesium »
    PDB 1tkk-1u3f »
      1tu3 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy