Atomistry » Cobalt » PDB 1rrk-1vlx » 1tu4
Atomistry »
  Cobalt »
    PDB 1rrk-1vlx »
      1tu4 »

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
Page generated: Tue Jul 30 14:38:38 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy