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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

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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

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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

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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

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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

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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

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