Magnesium in PDB 1yrb: PAB0955 Crystal Structure : A Gtpase in Gdp and Mg Bound Form From Pyrococcus Abyssi

The structure of PAB0955 Crystal Structure : A Gtpase in Gdp and Mg Bound Form From Pyrococcus Abyssi, PDB code: 1yrb was solved by S.Gras, P.Carpentier, J.Armengaud, D.Housset, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.470, 85.210, 60.570, 90.00, 94.61, 90.00
R / Rfree (%)	19.5 / 24.7

The binding sites of Magnesium atom in the PAB0955 Crystal Structure : A Gtpase in Gdp and Mg Bound Form From Pyrococcus Abyssi (pdb code 1yrb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the PAB0955 Crystal Structure : A Gtpase in Gdp and Mg Bound Form From Pyrococcus Abyssi, PDB code: 1yrb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the PAB0955 Crystal Structure : A Gtpase in Gdp and Mg Bound Form From Pyrococcus Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PAB0955 Crystal Structure : A Gtpase in Gdp and Mg Bound Form From Pyrococcus Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:23.2 occ:1.00 O A:HOH507 1.9 24.2 1.0 O1B A:GDP401 2.0 22.8 1.0 O A:HOH506 2.0 25.0 1.0 OG1 A:THR14 2.1 21.9 1.0 O A:HOH502 2.2 21.4 1.0 O A:HOH504 2.2 22.1 1.0 CB A:THR14 3.2 21.7 1.0 PB A:GDP401 3.3 24.0 1.0 O2B A:GDP401 3.5 24.2 1.0 N A:THR14 3.9 20.6 1.0 O A:HOH509 4.0 24.4 1.0 CA A:THR14 4.1 21.1 1.0 OD1 A:ASP101 4.2 24.1 1.0 O2A A:GDP401 4.2 25.0 1.0 CG2 A:THR14 4.3 23.0 1.0 O A:HOH582 4.3 43.8 1.0 OD2 A:ASP101 4.3 23.0 1.0 O3B A:GDP401 4.3 25.3 1.0 O3A A:GDP401 4.4 26.2 1.0 O A:HOH510 4.5 26.6 1.0 CE A:LYS13 4.5 20.9 1.0 OD2 A:ASP36 4.6 27.4 1.0 PA A:GDP401 4.6 25.2 1.0 CG A:ASP101 4.7 21.4 1.0 CB A:LYS13 4.7 20.1 1.0 CA A:GLY104 4.7 23.7 1.0 O1A A:GDP401 4.8 24.5 1.0 O A:THR102 4.9 24.5 1.0 C A:LYS13 4.9 19.9 1.0

Magnesium binding site 2 out of 3 in the PAB0955 Crystal Structure : A Gtpase in Gdp and Mg Bound Form From Pyrococcus Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PAB0955 Crystal Structure : A Gtpase in Gdp and Mg Bound Form From Pyrococcus Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:20.3 occ:1.00 O B:HOH505 2.0 20.4 1.0 O1B B:GDP402 2.1 20.2 1.0 OG1 B:THR14 2.1 18.4 1.0 O B:HOH506 2.1 21.1 1.0 O B:HOH507 2.1 22.1 1.0 O B:HOH504 2.2 20.7 1.0 CB B:THR14 3.1 18.2 1.0 PB B:GDP402 3.4 21.7 1.0 O2B B:GDP402 3.6 21.9 1.0 N B:THR14 3.9 18.9 1.0 O B:HOH511 4.0 27.7 1.0 CA B:THR14 4.1 18.9 1.0 O2A B:GDP402 4.1 24.0 1.0 OD1 B:ASP101 4.2 22.0 1.0 CG2 B:THR14 4.2 20.4 1.0 OD2 B:ASP101 4.3 23.1 1.0 O B:HOH521 4.4 33.2 1.0 O A:HOH547 4.4 43.8 1.0 OD2 B:ASP36 4.4 30.6 1.0 O3B B:GDP402 4.4 22.0 1.0 O3A B:GDP402 4.4 22.2 1.0 CE B:LYS13 4.6 22.7 1.0 PA B:GDP402 4.6 22.8 1.0 CG B:ASP101 4.7 23.6 1.0 CB B:LYS13 4.7 19.6 1.0 O1A B:GDP402 4.7 20.9 1.0 CA B:GLY104 4.8 23.6 1.0 O B:THR102 4.8 23.0 1.0 C B:LYS13 5.0 19.8 1.0

Magnesium binding site 3 out of 3 in the PAB0955 Crystal Structure : A Gtpase in Gdp and Mg Bound Form From Pyrococcus Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PAB0955 Crystal Structure : A Gtpase in Gdp and Mg Bound Form From Pyrococcus Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:23.4 occ:1.00 O A:HOH582 3.1 43.8 1.0 O A:HOH510 3.1 26.6 1.0 N B:ASN67 3.3 26.3 1.0 N B:GLY68 3.4 26.3 1.0 C B:GLY65 3.5 25.9 1.0 CA B:GLY65 3.5 26.6 1.0 N B:PRO66 3.6 26.4 1.0 CD B:PRO66 3.7 26.4 1.0 O A:HOH549 3.7 37.5 1.0 CB B:ASN67 3.8 27.6 1.0 CA A:VAL39 3.9 24.6 1.0 CA B:ASN67 3.9 26.4 1.0 O A:GLY38 4.0 24.2 1.0 C A:GLY38 4.0 24.3 1.0 O B:GLY65 4.0 24.0 1.0 N A:VAL39 4.1 23.3 1.0 C B:ASN67 4.1 26.5 1.0 C B:PRO66 4.3 25.7 1.0 CA B:GLY68 4.4 25.2 1.0 CG B:PRO66 4.4 26.7 1.0 ND2 B:ASN67 4.4 28.1 1.0 N B:GLY65 4.4 27.1 1.0 CA B:PRO66 4.5 25.7 1.0 CG B:ASN67 4.5 28.2 1.0 CB A:VAL39 4.6 26.2 1.0 O B:HOH517 4.6 29.3 1.0 CA A:GLY38 4.7 23.7 1.0 O A:HOH542 4.7 38.4 1.0 OD2 A:ASP36 4.8 27.4 1.0 C A:VAL39 4.9 25.1 1.0

S.Gras, V.Chaumont, B.Fernandez, P.Carpentier, F.Charrier-Savournin, S.Schmitt, C.Pineau, D.Flament, A.Hecker, P.Forterre, J.Armengaud, D.Housset. Structural Insights Into A New Homodimeric Self-Activated Gtpase Family. Embo Rep. V. 8 569 2007.
ISSN: ISSN 1469-221X
PubMed: 17468740
DOI: 10.1038/SJ.EMBOR.7400958