Atomistry » Magnesium » PDB 4la6-4lj0 » 4lhw
Atomistry »
  Magnesium »
    PDB 4la6-4lj0 »
      4lhw »

Magnesium in PDB 4lhw: Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form

Protein crystallography data

The structure of Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form, PDB code: 4lhw was solved by Z.Guo, X.M.Hou, R.S.Goody, A.Itzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.381, 96.676, 105.090, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 18.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form (pdb code 4lhw). 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 RAB8 in Its Active Gppnhp-Bound Form, PDB code: 4lhw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4lhw

Go back to Magnesium Binding Sites List in 4lhw
Magnesium binding site 1 out of 5 in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form


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 RAB8 in Its Active Gppnhp-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:8.9
occ:1.00
 O2G A:GNP302 2.0 9.4 1.0
O2B A:GNP302 2.0 8.7 1.0
OG1 A:THR22 2.0 8.9 1.0
OG1 A:THR40 2.1 8.7 1.0
O A:HOH402 2.1 9.6 1.0
O A:HOH425 2.1 10.4 1.0
CB A:THR22 3.1 8.7 1.0
CB A:THR40 3.2 9.0 1.0
PG A:GNP302 3.2 8.7 1.0
PB A:GNP302 3.3 8.5 1.0
N3B A:GNP302 3.4 8.7 1.0
N A:THR40 3.8 9.3 1.0
O1G A:GNP302 3.9 9.8 1.0
N A:THR22 3.9 8.2 1.0
CA A:THR40 4.0 9.6 1.0
OD1 A:ASP63 4.1 12.6 1.0
CA A:THR22 4.1 7.9 1.0
O2A A:GNP302 4.2 10.4 1.0
CG2 A:THR22 4.2 10.1 1.0
OD2 A:ASP63 4.2 14.2 1.0
O3A A:GNP302 4.2 9.3 1.0
CG2 A:THR40 4.2 9.8 1.0
O A:HOH412 4.3 12.9 1.0
O1B A:GNP302 4.4 9.2 1.0
O3G A:GNP302 4.4 10.6 1.0
CG A:ASP63 4.5 12.3 1.0
PA A:GNP302 4.5 9.0 1.0
O A:ILE38 4.6 10.8 1.0
O1A A:GNP302 4.7 9.3 1.0
C A:SER39 4.8 9.9 1.0
O A:THR64 4.8 13.2 1.0
CB A:LYS21 4.9 9.0 1.0
CA A:SER39 5.0 10.6 1.0

Magnesium binding site 2 out of 5 in 4lhw

Go back to Magnesium Binding Sites List in 4lhw
Magnesium binding site 2 out of 5 in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form


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 RAB8 in Its Active Gppnhp-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:11.3
occ:1.00
 O2G B:GNP202 2.0 12.1 1.0
OG1 B:THR22 2.1 11.1 1.0
O2B B:GNP202 2.1 10.9 1.0
OG1 B:THR40 2.1 11.9 1.0
O B:HOH322 2.1 12.9 1.0
O B:HOH327 2.1 12.9 1.0
CB B:THR40 3.1 9.4 1.0
CB B:THR22 3.2 11.6 1.0
PG B:GNP202 3.2 11.0 1.0
PB B:GNP202 3.3 10.7 1.0
N3B B:GNP202 3.4 10.5 1.0
N B:THR40 3.7 10.3 1.0
O1G B:GNP202 3.9 11.8 1.0
N B:THR22 3.9 11.0 1.0
CA B:THR40 4.0 9.9 1.0
OD1 B:ASP63 4.0 16.3 1.0
CA B:THR22 4.1 11.6 1.0
OD2 B:ASP63 4.2 14.6 1.0
CG2 B:THR22 4.2 13.9 1.0
O2A B:GNP202 4.2 12.7 1.0
O3A B:GNP202 4.2 10.7 1.0
CG2 B:THR40 4.3 10.8 1.0
O B:HOH314 4.3 16.9 1.0
O1B B:GNP202 4.3 12.7 1.0
O3G B:GNP202 4.4 12.5 1.0
CG B:ASP63 4.5 13.8 1.0
PA B:GNP202 4.6 11.6 1.0
O B:ILE38 4.6 11.3 1.0
O1A B:GNP202 4.6 12.3 1.0
C B:SER39 4.7 11.2 1.0
O B:THR64 4.7 13.1 1.0
CB B:LYS21 4.9 11.4 1.0
CA B:SER39 4.9 10.4 1.0

Magnesium binding site 3 out of 5 in 4lhw

Go back to Magnesium Binding Sites List in 4lhw
Magnesium binding site 3 out of 5 in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form


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 RAB8 in Its Active Gppnhp-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:11.1
occ:1.00
 O2G C:GNP202 2.0 11.0 1.0
O2B C:GNP202 2.0 9.9 1.0
O C:HOH307 2.1 12.6 1.0
OG1 C:THR22 2.1 10.1 1.0
O C:HOH318 2.1 12.2 1.0
OG1 C:THR40 2.1 10.6 1.0
CB C:THR22 3.1 9.2 1.0
PG C:GNP202 3.2 11.7 1.0
CB C:THR40 3.2 11.2 1.0
PB C:GNP202 3.2 10.7 1.0
N3B C:GNP202 3.4 11.1 1.0
N C:THR40 3.7 11.8 1.0
O1G C:GNP202 3.9 13.0 1.0
N C:THR22 3.9 8.8 1.0
CA C:THR40 4.0 12.1 1.0
CA C:THR22 4.1 9.1 1.0
OD1 C:ASP63 4.1 14.1 1.0
O2A C:GNP202 4.2 11.1 1.0
CG2 C:THR22 4.2 10.7 1.0
O3A C:GNP202 4.3 10.3 1.0
OD2 C:ASP63 4.3 12.7 1.0
O1B C:GNP202 4.3 10.2 1.0
CG2 C:THR40 4.3 12.8 1.0
O C:HOH331 4.4 16.5 1.0
O3G C:GNP202 4.4 14.0 1.0
PA C:GNP202 4.5 10.9 1.0
CG C:ASP63 4.6 11.5 1.0
O C:ILE38 4.6 15.6 1.0
O C:THR64 4.6 12.4 1.0
O1A C:GNP202 4.6 10.6 1.0
C C:SER39 4.7 13.3 1.0
CA C:SER39 4.9 14.9 1.0
O C:HOH344 4.9 19.3 1.0
CB C:LYS21 5.0 9.7 1.0

Magnesium binding site 4 out of 5 in 4lhw

Go back to Magnesium Binding Sites List in 4lhw
Magnesium binding site 4 out of 5 in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form


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 RAB8 in Its Active Gppnhp-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:12.4
occ:1.00
 O2G D:GNP202 2.0 13.8 1.0
O2B D:GNP202 2.0 11.1 1.0
O D:HOH311 2.1 14.8 1.0
OG1 D:THR22 2.1 11.2 1.0
OG1 D:THR40 2.2 13.8 1.0
O D:HOH314 2.2 14.1 1.0
PG D:GNP202 3.1 13.5 1.0
CB D:THR22 3.2 10.5 1.0
CB D:THR40 3.2 15.1 1.0
PB D:GNP202 3.2 12.3 1.0
N3B D:GNP202 3.4 13.5 1.0
N D:THR40 3.7 15.6 1.0
O1G D:GNP202 3.8 14.6 1.0
N D:THR22 3.9 10.2 1.0
CA D:THR40 4.1 15.2 1.0
OD1 D:ASP63 4.1 17.1 1.0
CA D:THR22 4.1 10.8 1.0
O2A D:GNP202 4.1 15.1 1.0
O3A D:GNP202 4.2 12.3 1.0
CG2 D:THR22 4.2 12.9 1.0
OD2 D:ASP63 4.2 15.3 1.0
O1B D:GNP202 4.3 11.8 1.0
CG2 D:THR40 4.3 15.7 1.0
O D:HOH317 4.3 25.0 1.0
O3G D:GNP202 4.4 15.4 1.0
PA D:GNP202 4.5 12.7 1.0
CG D:ASP63 4.6 14.1 1.0
O D:THR64 4.6 17.2 1.0
O1A D:GNP202 4.6 12.3 1.0
O D:ILE38 4.6 20.4 1.0
C D:SER39 4.7 17.5 1.0
CA D:SER39 4.8 18.8 0.7
CA D:SER39 4.9 17.3 0.3

Magnesium binding site 5 out of 5 in 4lhw

Go back to Magnesium Binding Sites List in 4lhw
Magnesium binding site 5 out of 5 in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form


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 RAB8 in Its Active Gppnhp-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:12.2
occ:1.00
 O2G E:GNP202 2.0 11.1 1.0
O2B E:GNP202 2.1 10.0 1.0
O E:HOH309 2.1 13.9 1.0
OG1 E:THR22 2.1 9.8 1.0
OG1 E:THR40 2.1 10.3 1.0
O E:HOH304 2.2 12.4 1.0
PG E:GNP202 3.1 11.9 1.0
CB E:THR22 3.1 9.2 1.0
CB E:THR40 3.2 10.9 1.0
PB E:GNP202 3.2 11.0 1.0
N3B E:GNP202 3.4 11.4 1.0
N E:THR40 3.6 12.0 1.0
O1G E:GNP202 3.8 12.5 1.0
N E:THR22 3.9 8.8 1.0
CA E:THR40 4.0 11.5 1.0
OD1 E:ASP63 4.1 15.7 1.0
CA E:THR22 4.1 9.3 1.0
OD2 E:ASP63 4.1 14.3 1.0
CG2 E:THR22 4.2 10.8 1.0
O2A E:GNP202 4.2 13.0 1.0
O E:HOH325 4.2 22.3 1.0
O3A E:GNP202 4.3 10.1 1.0
O1B E:GNP202 4.3 11.6 1.0
CG2 E:THR40 4.4 12.7 1.0
O3G E:GNP202 4.4 13.5 1.0
O E:THR64 4.5 14.1 1.0
CG E:ASP63 4.5 14.0 1.0
PA E:GNP202 4.6 11.1 1.0
C E:SER39 4.6 12.9 1.0
O E:ILE38 4.6 15.9 1.0
O1A E:GNP202 4.7 12.1 1.0
CA E:SER39 4.8 13.9 1.0
CB E:LYS21 4.9 10.2 1.0
O E:HOH308 5.0 20.0 1.0

Reference:

Z.Guo, X.Hou, R.S.Goody, A.Itzen. Intermediates in the Guanine Nucleotide Exchange Reaction of RAB8 Protein Catalyzed By Guanine Nucleotide Exchange Factors RABIN8 and Grab. J.Biol.Chem. V. 288 32466 2013.
ISSN: ISSN 0021-9258
PubMed: 24072714
DOI: 10.1074/JBC.M113.498329
Page generated: Mon Aug 19 17:43:27 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy