Atomistry » Magnesium » PDB 1yzu-1z6k » 1z08
Atomistry »
  Magnesium »
    PDB 1yzu-1z6k »
      1z08 »

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

Go back to Magnesium Binding Sites List in 1z08
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

Go back to Magnesium Binding Sites List in 1z08
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

Go back to Magnesium Binding Sites List in 1z08
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

Go back to Magnesium Binding Sites List in 1z08
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

Go back to Magnesium Binding Sites List in 1z08
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

Go back to Magnesium Binding Sites List in 1z08
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

Go back to Magnesium Binding Sites List in 1z08
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

Go back to Magnesium Binding Sites List in 1z08
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: Mon Dec 14 07:10:59 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy