Atomistry » Cobalt » PDB 1e31-1hgw » 1g16
Atomistry »
  Cobalt »
    PDB 1e31-1hgw »
      1g16 »

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

Go back to Cobalt Binding Sites List in 1g16
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

Go back to Cobalt Binding Sites List in 1g16
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

Go back to Cobalt Binding Sites List in 1g16
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

Go back to Cobalt Binding Sites List in 1g16
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

Go back to Cobalt Binding Sites List in 1g16
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

Go back to Cobalt Binding Sites List in 1g16
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

Go back to Cobalt Binding Sites List in 1g16
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

Go back to Cobalt Binding Sites List in 1g16
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: Tue Jul 30 14:16:29 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