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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

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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

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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

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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

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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: Sun Dec 13 10:36:13 2020

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