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Cobalt in PDB 1g16: Crystal Structure of SEC4-Gdp

Protein crystallography data

The structure of Crystal Structure of SEC4-Gdp, PDB code: 1g16 was solved by C.Stroupe, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.93 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.007, 56.379, 59.374, 95.25, 101.68, 116.20
R / Rfree (%) 27.6 / 29.6

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of SEC4-Gdp (pdb code 1g16). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Crystal Structure of SEC4-Gdp, PDB code: 1g16:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 1g16

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Cobalt binding site 1 out of 8 in the Crystal Structure of SEC4-Gdp


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 SEC4-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co301

b:10.7
occ:1.00
 O A:HOH402 1.8 17.9 1.0
OG A:SER34 1.9 24.9 1.0
O A:HOH404 1.9 15.2 1.0
O2B A:GDP201 1.9 17.2 1.0
O A:HOH403 2.0 18.7 1.0
O A:HOH401 2.0 20.6 1.0
CB A:SER34 3.1 22.0 1.0
PB A:GDP201 3.2 17.7 1.0
O3B A:GDP201 3.6 18.8 1.0
N A:SER34 3.7 20.4 1.0
CA A:SER34 4.0 19.4 1.0
OD1 A:ASP75 4.0 24.1 1.0
O2A A:GDP201 4.1 18.6 1.0
O A:HOH497 4.2 24.1 1.0
O1B A:GDP201 4.2 16.4 1.0
O3A A:GDP201 4.2 18.7 1.0
OD2 A:ASP75 4.2 24.8 1.0
OG1 A:THR76 4.2 18.2 1.0
O A:HOH479 4.3 31.6 1.0
OE2 A:GLU80 4.4 16.4 1.0
CG A:ASP75 4.5 26.2 1.0
PA A:GDP201 4.6 18.5 1.0
N A:GLY78 4.7 22.4 1.0
O1A A:GDP201 4.8 18.1 1.0
CB A:LYS33 4.8 17.4 1.0
NZ A:LYS33 4.8 17.4 1.0
CE A:LYS33 4.8 14.2 1.0
C A:LYS33 4.8 18.6 1.0
O A:HOH450 5.0 21.5 1.0

Cobalt binding site 2 out of 8 in 1g16

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Cobalt binding site 2 out of 8 in the Crystal Structure of SEC4-Gdp


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 SEC4-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co305

b:31.0
occ:1.00
 OD2 A:ASP166 2.0 39.4 1.0
OD1 A:ASP43 2.1 33.9 1.0
O A:HOH418 2.2 31.4 1.0
O A:HOH419 2.2 24.8 1.0
OD2 A:ASP43 2.4 33.0 1.0
CG A:ASP43 2.5 34.8 1.0
CG A:ASP166 3.2 35.8 1.0
OD1 A:ASP166 3.8 38.8 1.0
NH1 A:ARG39 4.0 31.3 1.0
CB A:ASP43 4.0 34.8 1.0
CB A:ASP166 4.2 33.5 1.0
O A:HOH417 4.3 27.5 1.0
CD A:ARG39 4.5 29.1 1.0
CA A:ASP43 4.7 34.2 1.0
O A:ASP43 4.9 33.9 1.0
CZ A:ARG39 5.0 32.0 1.0

Cobalt binding site 3 out of 8 in 1g16

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Cobalt binding site 3 out of 8 in the Crystal Structure of SEC4-Gdp


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 SEC4-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co304

b:24.2
occ:1.00
 O B:HOH415 1.8 31.1 1.0
OG B:SER34 1.9 25.4 1.0
O B:HOH413 1.9 27.2 1.0
O2B B:GDP202 2.0 31.4 1.0
O B:HOH414 2.2 36.7 1.0
O B:HOH416 2.7 37.8 1.0
CB B:SER34 3.2 23.5 1.0
PB B:GDP202 3.2 33.9 1.0
O3B B:GDP202 3.6 29.9 1.0
N B:SER34 3.9 26.8 1.0
OD2 B:ASP75 4.0 35.3 1.0
O2A B:GDP202 4.0 35.1 1.0
CA B:SER34 4.1 27.0 1.0
O3A B:GDP202 4.2 31.1 1.0
O1B B:GDP202 4.3 29.2 1.0
OD1 B:ASP75 4.3 35.7 1.0
PA B:GDP202 4.5 32.7 1.0
CG B:ASP75 4.5 36.5 1.0
N B:GLY78 4.5 43.2 1.0
OG1 B:THR76 4.6 37.6 1.0
O1A B:GDP202 4.7 31.5 1.0
O B:HOH678 4.7 27.0 1.0
CA B:GLY78 4.9 44.8 1.0
CB B:LYS33 4.9 21.9 1.0
OE1 B:GLU80 5.0 40.0 1.0

Cobalt binding site 4 out of 8 in 1g16

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Cobalt binding site 4 out of 8 in the Crystal Structure of SEC4-Gdp


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 SEC4-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co302

b:12.8
occ:1.00
 O C:HOH407 1.7 24.5 1.0
O C:HOH406 1.7 17.1 1.0
O2B C:GDP203 1.9 18.3 1.0
OG C:SER34 2.0 21.4 1.0
O C:HOH405 2.0 19.3 1.0
O C:HOH408 2.1 19.8 1.0
CB C:SER34 3.1 17.5 1.0
PB C:GDP203 3.2 22.0 1.0
O3B C:GDP203 3.6 17.9 1.0
N C:SER34 3.8 18.0 1.0
OD2 C:ASP75 4.0 28.5 1.0
O C:THR76 4.0 43.1 1.0
O2A C:GDP203 4.0 27.9 1.0
CA C:SER34 4.0 18.6 1.0
O3A C:GDP203 4.1 22.7 1.0
OD1 C:ASP75 4.3 26.9 1.0
O1B C:GDP203 4.3 21.1 1.0
O C:HOH530 4.4 33.3 1.0
PA C:GDP203 4.5 24.6 1.0
O C:HOH529 4.5 37.8 1.0
CG C:ASP75 4.5 31.4 1.0
OG1 C:THR51 4.6 51.5 1.0
O1A C:GDP203 4.7 26.2 1.0
CA C:ALA77 4.8 43.6 1.0
C C:THR76 4.9 42.5 1.0
CB C:LYS33 4.9 18.3 1.0
C C:LYS33 5.0 20.1 1.0

Cobalt binding site 5 out of 8 in 1g16

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Cobalt binding site 5 out of 8 in the Crystal Structure of SEC4-Gdp


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 SEC4-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co306

b:32.2
occ:1.00
 O C:HOH421 1.9 29.1 1.0
O C:HOH420 2.0 31.7 1.0
O C:HOH422 2.0 39.0 1.0
OD2 C:ASP166 2.4 35.8 1.0
O C:HOH429 2.5 35.2 1.0
OD1 C:ASP166 3.0 32.1 1.0
CG C:ASP166 3.1 33.6 1.0
ND2 C:ASN170 3.5 36.8 1.0
OD1 C:ASP43 3.8 38.2 1.0
O C:HOH431 3.9 37.4 1.0
O C:HOH585 4.0 40.6 1.0
OD1 C:ASN170 4.1 36.0 1.0
CG C:ASN170 4.2 34.1 1.0
O C:HOH464 4.3 29.4 1.0
O C:HOH430 4.3 36.6 1.0
CG C:ASP43 4.6 39.1 1.0
CB C:ASP166 4.6 32.3 1.0
CD C:ARG39 4.6 27.7 1.0
O C:ARG39 4.9 24.2 1.0

Cobalt binding site 6 out of 8 in 1g16

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Cobalt binding site 6 out of 8 in the Crystal Structure of SEC4-Gdp


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 SEC4-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co303

b:19.5
occ:1.00
 O D:HOH412 1.5 25.0 1.0
O D:HOH409 1.7 28.0 1.0
OG D:SER34 2.0 22.2 1.0
O D:HOH411 2.0 24.2 1.0
O D:HOH410 2.1 33.9 1.0
O2B D:GDP204 2.2 25.6 1.0
CB D:SER34 3.1 22.4 1.0
PB D:GDP204 3.4 26.9 1.0
O3B D:GDP204 3.7 28.1 1.0
O2A D:GDP204 3.9 29.1 1.0
N D:SER34 3.9 22.2 1.0
OD1 D:ASP75 3.9 33.4 1.0
CA D:SER34 4.1 23.3 1.0
O D:THR76 4.2 41.3 1.0
O3A D:GDP204 4.2 25.9 1.0
OD2 D:ASP75 4.3 34.4 1.0
PA D:GDP204 4.5 28.7 1.0
O1B D:GDP204 4.5 27.9 1.0
CG D:ASP75 4.5 35.1 1.0
O1A D:GDP204 4.6 29.1 1.0
CA D:ALA77 4.7 44.5 1.0
O D:HOH664 4.9 35.8 1.0
C D:THR76 4.9 40.8 1.0

Cobalt binding site 7 out of 8 in 1g16

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Cobalt binding site 7 out of 8 in the Crystal Structure of SEC4-Gdp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of SEC4-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co307

b:32.8
occ:1.00
 O D:HOH424 2.1 29.9 1.0
OD2 D:ASP166 2.2 32.4 1.0
OD2 D:ASP43 2.2 46.1 1.0
O D:HOH423 2.2 34.6 1.0
O D:HOH425 2.3 34.7 1.0
CG D:ASP166 2.9 32.9 1.0
OD1 D:ASP166 3.0 31.1 1.0
CG D:ASP43 3.2 45.3 1.0
OD1 D:ASP43 3.7 46.9 1.0
ND2 D:ASN170 3.7 37.8 1.0
O D:HOH428 4.2 48.9 1.0
O D:HOH679 4.3 28.9 1.0
OD1 D:ASN170 4.3 36.8 1.0
CB D:ASP43 4.4 45.5 1.0
CB D:ASP166 4.4 32.5 1.0
CG D:ASN170 4.5 34.3 1.0
CD D:ARG39 4.5 29.6 1.0
O D:ARG39 4.8 25.9 1.0

Cobalt binding site 8 out of 8 in 1g16

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Cobalt binding site 8 out of 8 in the Crystal Structure of SEC4-Gdp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of SEC4-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co308

b:40.6
occ:1.00
 NE2 D:HIS121 2.1 32.4 1.0
O D:HOH426 2.3 40.2 1.0
O D:HOH427 2.4 34.6 1.0
CE1 D:HIS121 2.8 34.5 1.0
CD2 D:HIS121 3.3 35.5 1.0
ND1 D:HIS121 4.0 34.9 1.0
O D:ILE85 4.0 49.2 1.0
CG D:HIS121 4.3 36.5 1.0
CG2 D:THR87 5.0 47.6 1.0

Reference:

C.Stroupe, A.T.Brunger. Crystal Structures of A Rab Protein in Its Inactive and Active Conformations. J.Mol.Biol. V. 304 585 2000.
ISSN: ISSN 0022-2836
PubMed: 11099382
DOI: 10.1006/JMBI.2000.4236
Page generated: Sun Jul 13 17:30:35 2025

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