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Magnesium in PDB 3nkv: Crystal Structure of RAB1B Covalently Modified with Amp at Y77

Protein crystallography data

The structure of Crystal Structure of RAB1B Covalently Modified with Amp at Y77, PDB code: 3nkv was solved by M.P.Mueller, H.Peters, W.Blankenfeldt, R.S.Goody, A.Itzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.970, 100.589, 45.071, 90.00, 102.43, 90.00
R / Rfree (%) 15 / 18.7

Other elements in 3nkv:

The structure of Crystal Structure of RAB1B Covalently Modified with Amp at Y77 also contains other interesting chemical elements:

Barium (Ba) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of RAB1B Covalently Modified with Amp at Y77 (pdb code 3nkv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of RAB1B Covalently Modified with Amp at Y77, PDB code: 3nkv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3nkv

Go back to Magnesium Binding Sites List in 3nkv
Magnesium binding site 1 out of 2 in the Crystal Structure of RAB1B Covalently Modified with Amp at Y77


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 RAB1B Covalently Modified with Amp at Y77 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:16.7
occ:1.00
O2G A:GNP400 2.0 16.7 1.0
O2B A:GNP400 2.0 15.1 1.0
O A:HOH189 2.1 14.9 1.0
OG A:SER22 2.1 22.1 1.0
O A:HOH218 2.1 18.7 1.0
OG1 A:THR40 2.1 21.0 1.0
CB A:SER22 3.1 24.8 1.0
CB A:THR40 3.1 25.2 1.0
PG A:GNP400 3.2 15.1 1.0
PB A:GNP400 3.2 14.6 1.0
N3B A:GNP400 3.4 15.2 1.0
N A:THR40 3.7 25.1 1.0
O1G A:GNP400 3.8 16.6 1.0
N A:SER22 4.0 19.7 1.0
CA A:THR40 4.0 25.9 1.0
OD2 A:ASP63 4.1 28.5 1.0
CA A:SER22 4.1 18.5 1.0
O2A A:GNP400 4.2 18.0 1.0
OD1 A:ASP63 4.2 28.0 1.0
CG2 A:THR40 4.3 27.6 1.0
O3A A:GNP400 4.3 12.9 1.0
O1B A:GNP400 4.4 14.8 1.0
O3G A:GNP400 4.4 15.4 1.0
PA A:GNP400 4.5 14.4 1.0
CG A:ASP63 4.6 30.8 1.0
O A:ILE38 4.7 25.6 1.0
C A:SER39 4.7 29.9 1.0
O1A A:GNP400 4.7 17.8 1.0
O A:THR64 4.7 25.9 1.0
O A:HOH191 4.7 21.7 1.0
CA A:SER39 4.9 28.9 1.0
CB A:LYS21 5.0 19.2 1.0

Magnesium binding site 2 out of 2 in 3nkv

Go back to Magnesium Binding Sites List in 3nkv
Magnesium binding site 2 out of 2 in the Crystal Structure of RAB1B Covalently Modified with Amp at Y77


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 RAB1B Covalently Modified with Amp at Y77 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg500

b:15.7
occ:1.00
O B:HOH185 2.0 13.5 1.0
O2G B:GNP400 2.0 15.2 1.0
OG B:SER22 2.0 21.5 1.0
O B:HOH199 2.1 15.7 1.0
O2B B:GNP400 2.1 13.1 1.0
OG1 B:THR40 2.1 23.3 1.0
CB B:SER22 3.1 24.2 1.0
PG B:GNP400 3.2 15.4 1.0
CB B:THR40 3.3 23.3 1.0
PB B:GNP400 3.3 15.4 1.0
N3B B:GNP400 3.5 14.8 1.0
O B:HOH215 3.8 20.8 1.0
O1G B:GNP400 3.8 16.3 1.0
N B:SER22 4.0 22.7 1.0
OD2 B:ASP63 4.0 32.7 1.0
CG2 B:THR40 4.1 25.2 1.0
CA B:SER22 4.1 24.0 1.0
O2A B:GNP400 4.2 15.3 1.0
O B:HOH282 4.3 27.2 1.0
O3A B:GNP400 4.3 15.6 1.0
OD1 B:ASP63 4.3 30.5 1.0
O1B B:GNP400 4.4 15.6 1.0
O B:ILE38 4.4 26.5 1.0
O3G B:GNP400 4.4 17.3 1.0
CA B:THR40 4.4 25.2 1.0
N B:THR40 4.5 27.7 1.0
PA B:GNP400 4.5 15.5 1.0
CG B:ASP63 4.6 32.9 1.0
O B:THR64 4.6 27.0 1.0
O1A B:GNP400 4.7 16.3 1.0
CG2 B:ILE38 4.9 27.1 1.0

Reference:

M.P.Muller, H.Peters, J.Blumer, W.Blankenfeldt, R.S.Goody, A.Itzen. The Legionella Effector Protein Drra Ampylates the Membrane Traffic Regulator RAB1B. Science V. 329 946 2010.
ISSN: ISSN 0036-8075
PubMed: 20651120
DOI: 10.1126/SCIENCE.1192276
Page generated: Mon Dec 14 08:28:58 2020

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