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Magnesium in PDB 1z08: Gppnhp-Bound RAB21 Q53G Mutant Gtpase

Protein crystallography data

The structure of Gppnhp-Bound RAB21 Q53G Mutant Gtpase, PDB code: 1z08 was solved by S.Eathiraj, X.Pan, C.Ritacco, D.G.Lambright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.200, 77.425, 107.965, 90.00, 89.86, 90.00
R / Rfree (%) 18.8 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Gppnhp-Bound RAB21 Q53G Mutant Gtpase (pdb code 1z08). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Gppnhp-Bound RAB21 Q53G Mutant Gtpase, PDB code: 1z08:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1z08

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Magnesium binding site 1 out of 8 in the Gppnhp-Bound RAB21 Q53G Mutant Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gppnhp-Bound RAB21 Q53G Mutant Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1300

b:11.8
occ:1.00
 O2G A:GNP1200 1.9 13.7 1.0
O2B A:GNP1200 2.0 11.6 1.0
OG1 A:THR33 2.0 11.4 1.0
O A:HOH1307 2.0 13.3 1.0
O A:HOH1315 2.1 12.1 1.0
OG1 A:THR51 2.1 14.5 1.0
CB A:THR33 3.1 11.3 1.0
PG A:GNP1200 3.2 13.5 1.0
PB A:GNP1200 3.2 12.5 1.0
CB A:THR51 3.2 14.8 1.0
N3B A:GNP1200 3.4 12.6 1.0
N A:THR33 3.9 11.4 1.0
O3G A:GNP1200 3.9 14.1 1.0
N A:THR51 3.9 15.1 1.0
CA A:THR33 4.1 11.2 1.0
OD2 A:ASP74 4.1 12.5 1.0
O2A A:GNP1200 4.1 11.2 1.0
CA A:THR51 4.1 15.0 1.0
CG2 A:THR33 4.2 11.6 1.0
O3A A:GNP1200 4.2 10.5 1.0
O1B A:GNP1200 4.2 11.4 1.0
CG2 A:THR51 4.3 14.8 1.0
OD1 A:ASP74 4.3 13.6 1.0
O A:HOH1305 4.3 16.1 1.0
O A:ILE49 4.4 15.0 1.0
O1G A:GNP1200 4.4 12.6 1.0
PA A:GNP1200 4.4 10.6 1.0
O A:THR75 4.5 16.8 1.0
CG A:ASP74 4.6 13.9 1.0
O1A A:GNP1200 4.6 10.3 1.0
C A:THR50 4.9 15.3 1.0
CB A:LYS32 4.9 11.7 1.0
CE A:LYS32 5.0 11.5 1.0

Magnesium binding site 2 out of 8 in 1z08

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Magnesium binding site 2 out of 8 in the Gppnhp-Bound RAB21 Q53G Mutant Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gppnhp-Bound RAB21 Q53G Mutant Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2300

b:13.7
occ:1.00
 O2G B:GNP2200 1.9 14.4 1.0
OG1 B:THR33 1.9 12.6 1.0
O B:HOH2309 1.9 14.3 1.0
O2B B:GNP2200 2.0 14.1 1.0
O B:HOH2308 2.1 12.1 1.0
OG1 B:THR51 2.2 15.6 1.0
CB B:THR33 3.1 12.5 1.0
PG B:GNP2200 3.1 14.9 1.0
PB B:GNP2200 3.2 14.6 1.0
CB B:THR51 3.2 16.6 1.0
N3B B:GNP2200 3.4 14.5 1.0
N B:THR33 3.9 12.5 1.0
N B:THR51 3.9 16.9 1.0
O3G B:GNP2200 3.9 15.3 1.0
CA B:THR33 4.0 12.3 1.0
OD2 B:ASP74 4.0 12.9 1.0
O2A B:GNP2200 4.1 13.2 1.0
CG2 B:THR33 4.1 13.2 1.0
CA B:THR51 4.1 16.6 1.0
O3A B:GNP2200 4.2 12.9 1.0
O B:HOH2344 4.2 22.1 1.0
O1B B:GNP2200 4.2 14.2 1.0
CG2 B:THR51 4.3 16.6 1.0
O1G B:GNP2200 4.4 14.9 1.0
OD1 B:ASP74 4.4 13.8 1.0
O B:ILE49 4.4 16.5 1.0
PA B:GNP2200 4.4 13.1 1.0
O B:THR75 4.5 18.9 1.0
O1A B:GNP2200 4.6 12.5 1.0
CG B:ASP74 4.6 14.4 1.0
C B:THR50 4.8 16.9 1.0
CE B:LYS32 5.0 13.3 1.0
CB B:LYS32 5.0 12.4 1.0

Magnesium binding site 3 out of 8 in 1z08

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Magnesium binding site 3 out of 8 in the Gppnhp-Bound RAB21 Q53G Mutant Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gppnhp-Bound RAB21 Q53G Mutant Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3300

b:9.9
occ:1.00
 O2G C:GNP3200 1.9 12.8 1.0
O2B C:GNP3200 2.0 10.5 1.0
OG1 C:THR33 2.0 9.1 1.0
O C:HOH5014 2.1 11.9 1.0
O C:HOH5009 2.2 10.9 1.0
O C:HOH5007 2.2 9.8 1.0
PG C:GNP3200 3.1 13.0 1.0
CB C:THR33 3.2 9.4 1.0
PB C:GNP3200 3.2 11.6 1.0
N3B C:GNP3200 3.4 11.9 1.0
O C:HOH5051 3.8 17.0 1.0
N C:THR33 3.9 9.2 1.0
O3G C:GNP3200 4.1 13.7 1.0
CA C:THR33 4.1 9.3 1.0
OD2 C:ASP74 4.1 11.3 1.0
O2A C:GNP3200 4.2 10.7 1.0
O3A C:GNP3200 4.2 10.7 1.0
CG2 C:THR33 4.2 9.5 1.0
O1G C:GNP3200 4.3 13.7 1.0
O1B C:GNP3200 4.3 10.6 1.0
OD1 C:ASP74 4.3 11.6 1.0
O C:HOH5090 4.4 28.2 1.0
O C:ILE49 4.5 18.9 1.0
PA C:GNP3200 4.5 10.6 1.0
OG1 C:THR51 4.6 20.8 1.0
CG C:ASP74 4.7 10.9 1.0
O1A C:GNP3200 4.7 10.4 1.0
O C:THR75 4.7 11.1 1.0
CA C:ALA76 4.8 10.9 1.0
CB C:LYS32 4.9 9.0 1.0
CE C:LYS32 4.9 8.9 1.0
C C:THR75 5.0 10.8 1.0
N C:ALA76 5.0 10.9 1.0

Magnesium binding site 4 out of 8 in 1z08

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Magnesium binding site 4 out of 8 in the Gppnhp-Bound RAB21 Q53G Mutant Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Gppnhp-Bound RAB21 Q53G Mutant Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg5004

b:35.5
occ:1.00
 O C:HOH5052 1.9 16.2 1.0
O C:HOH5041 2.0 15.5 1.0
O C:HOH5185 2.2 33.0 1.0
O C:HOH5109 2.2 31.6 1.0
O C:HOH5070 2.2 14.6 1.0
OE2 C:GLU79 2.5 18.1 1.0
CD C:GLU79 3.3 16.1 1.0
OE1 C:GLU79 3.4 15.4 1.0
O1G C:GNP3200 3.9 13.7 1.0
O C:HOH5145 4.1 36.4 1.0
CA C:GLY28 4.2 12.1 1.0
O C:HOH5092 4.2 22.9 1.0
O C:HOH5290 4.3 37.7 1.0
O C:HOH5244 4.5 30.9 1.0
O C:GLY28 4.5 12.6 1.0
O C:GLY77 4.6 11.4 1.0
NE2 C:HIS48 4.7 18.5 1.0
CG C:ARG80 4.7 15.8 1.0
CG C:GLU79 4.8 13.9 1.0
C C:GLY28 4.8 12.3 1.0
O C:HOH5260 4.9 43.5 1.0
CB C:GLN78 4.9 12.1 1.0

Magnesium binding site 5 out of 8 in 1z08

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Magnesium binding site 5 out of 8 in the Gppnhp-Bound RAB21 Q53G Mutant Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Gppnhp-Bound RAB21 Q53G Mutant Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4300

b:10.2
occ:1.00
 O2G D:GNP4200 1.9 12.7 1.0
O2B D:GNP4200 2.0 11.4 1.0
O D:HOH5032 2.0 13.3 1.0
OG1 D:THR33 2.1 11.8 1.0
O D:HOH5011 2.1 11.5 1.0
O D:HOH5022 2.2 13.4 1.0
PG D:GNP4200 3.2 13.1 1.0
CB D:THR33 3.2 11.3 1.0
PB D:GNP4200 3.2 11.6 1.0
N3B D:GNP4200 3.4 12.3 1.0
O D:HOH5095 3.8 23.8 1.0
N D:THR33 4.0 11.3 1.0
OD2 D:ASP74 4.1 11.6 1.0
O3G D:GNP4200 4.1 13.8 1.0
CA D:THR33 4.2 11.3 1.0
O3A D:GNP4200 4.2 11.4 1.0
CG2 D:THR33 4.2 11.1 1.0
O2A D:GNP4200 4.2 12.1 1.0
O D:HOH5070 4.3 37.0 1.0
OD1 D:ASP74 4.3 12.5 1.0
O1B D:GNP4200 4.3 11.3 1.0
O1G D:GNP4200 4.3 13.2 1.0
OG1 D:THR51 4.6 22.9 1.0
PA D:GNP4200 4.6 11.8 1.0
CG D:ASP74 4.6 11.9 1.0
O D:ILE49 4.6 20.9 1.0
O D:HOH5196 4.6 85.7 1.0
O D:THR75 4.7 10.4 1.0
CA D:ALA76 4.7 10.9 1.0
O1A D:GNP4200 4.7 11.3 1.0
CE D:LYS32 4.8 11.4 1.0
CB D:LYS32 4.9 11.4 1.0
N D:ALA76 4.9 10.8 1.0
C D:THR75 4.9 10.8 1.0

Magnesium binding site 6 out of 8 in 1z08

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Magnesium binding site 6 out of 8 in the Gppnhp-Bound RAB21 Q53G Mutant Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Gppnhp-Bound RAB21 Q53G Mutant Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5001

b:21.7
occ:1.00
 O D:HOH5093 2.0 20.6 1.0
O D:THR183 2.1 22.1 1.0
O D:MET180 2.1 15.6 1.0
O D:HOH5104 2.1 23.7 1.0
O D:HOH5110 2.1 24.0 1.0
O D:HOH5061 2.1 18.3 1.0
C D:MET180 3.2 15.6 1.0
C D:THR183 3.3 21.9 1.0
CA D:MET180 3.8 14.9 1.0
O D:HOH5025 3.9 13.1 1.0
N D:ILE181 4.3 16.6 1.0
N D:THR183 4.4 21.6 1.0
CA D:THR183 4.4 21.7 1.0
O D:HOH5090 4.5 20.4 1.0
O D:HOH5150 4.5 39.1 1.0
O D:ARG179 4.5 14.9 1.0
CB D:MET180 4.6 14.8 1.0
CA D:ILE181 4.7 17.6 1.0
C D:ILE181 4.8 18.5 1.0
CE2 D:PHE20 4.8 15.0 1.0
O D:ILE181 4.9 18.6 1.0
N D:MET180 5.0 14.8 1.0

Magnesium binding site 7 out of 8 in 1z08

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Magnesium binding site 7 out of 8 in the Gppnhp-Bound RAB21 Q53G Mutant Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Gppnhp-Bound RAB21 Q53G Mutant Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5002

b:30.4
occ:1.00
 O D:HOH5128 2.0 29.6 1.0
O D:HOH5064 2.0 15.4 1.0
O D:HOH5214 2.2 34.6 1.0
O D:HOH5103 2.3 22.1 1.0
O D:HOH5063 2.3 16.7 1.0
OE2 D:GLU79 2.3 18.7 1.0
CD D:GLU79 3.2 16.4 1.0
OE1 D:GLU79 3.4 16.4 1.0
O1G D:GNP4200 3.9 13.2 1.0
O D:HOH5101 4.1 27.0 1.0
O D:HOH5155 4.2 34.9 1.0
O D:HOH5049 4.2 25.6 1.0
CA D:GLY28 4.4 14.6 1.0
NE2 D:HIS48 4.6 20.4 1.0
CG D:GLU79 4.6 15.2 1.0
O D:GLY77 4.7 12.5 1.0

Magnesium binding site 8 out of 8 in 1z08

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Magnesium binding site 8 out of 8 in the Gppnhp-Bound RAB21 Q53G Mutant Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Gppnhp-Bound RAB21 Q53G Mutant Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5003

b:14.7
occ:1.00
 O D:HOH5068 2.1 18.5 1.0
O D:HOH5045 2.1 13.8 1.0
O D:HOH5042 2.1 12.6 1.0
O D:HOH5005 4.0 9.6 1.0
O D:HOH5176 4.1 34.6 1.0
O D:ASP91 4.2 10.8 1.0
OD1 D:ASN93 4.4 12.9 1.0
OD2 D:ASP91 4.4 11.9 1.0
CA D:ASP91 4.4 10.9 1.0
O D:HOH5019 4.6 14.4 1.0
C D:ASP91 4.6 10.8 1.0
CB D:ASP91 4.7 11.3 1.0
O D:HOH5010 5.0 14.0 1.0

Reference:

S.Eathiraj, X.Pan, C.Ritacco, D.G.Lambright. Structural Basis of Family-Wide Rab Gtpase Recognition By Rabenosyn-5. Nature V. 436 415 2005.
ISSN: ISSN 0028-0836
PubMed: 16034420
DOI: 10.1038/NATURE03798
Page generated: Tue Aug 13 19:59:16 2024

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