Magnesium in PDB 4ag5: Structure of VIRB4 of Thermoanaerobacter Pseudethanolicus

The structure of Structure of VIRB4 of Thermoanaerobacter Pseudethanolicus, PDB code: 4ag5 was solved by K.Wallden, R.Williams, J.Yan, P.W.Lian, L.Wang, K.Thalassinos, E.V.Orlova, G.Waksman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.040 / 2.45
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	108.080, 110.800, 156.430, 90.00, 90.00, 90.00
R / Rfree (%)	23.34 / 28.77

The binding sites of Magnesium atom in the Structure of VIRB4 of Thermoanaerobacter Pseudethanolicus (pdb code 4ag5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of VIRB4 of Thermoanaerobacter Pseudethanolicus, PDB code: 4ag5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of VIRB4 of Thermoanaerobacter Pseudethanolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of VIRB4 of Thermoanaerobacter Pseudethanolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1589 b:50.9 occ:1.00 OG A:SER251 2.2 64.1 1.0 OE1 A:GLU274 2.3 40.1 1.0 O2B A:ADP1591 2.4 39.0 1.0 O A:HOH2018 3.1 53.4 1.0 CD A:GLU274 3.1 56.3 1.0 OE2 A:GLU274 3.3 66.3 1.0 O A:HOH2017 3.5 51.4 1.0 PB A:ADP1591 3.5 42.9 1.0 CB A:SER251 3.5 55.5 1.0 O1B A:ADP1591 3.6 44.7 1.0 N A:SER251 3.9 37.4 1.0 OE2 A:GLU472 4.0 42.5 1.0 O A:HOH2016 4.0 50.5 1.0 OD1 A:ASP471 4.0 53.4 1.0 OD2 A:ASP471 4.2 66.3 1.0 CA A:SER251 4.2 45.1 1.0 CE A:LYS250 4.3 39.6 1.0 NZ A:LYS250 4.4 40.9 1.0 CB A:LYS250 4.4 38.6 1.0 O3B A:ADP1591 4.5 38.4 1.0 CG A:ASP471 4.5 48.7 1.0 CG A:GLU274 4.6 48.9 1.0 CD A:GLU472 4.7 51.9 1.0 O3A A:ADP1591 4.7 52.1 1.0 C A:LYS250 4.9 37.6 1.0 O2A A:ADP1591 5.0 52.0 1.0 O A:HOH2023 5.0 53.7 1.0 CG A:GLU472 5.0 41.6 1.0

Magnesium binding site 2 out of 3 in the Structure of VIRB4 of Thermoanaerobacter Pseudethanolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of VIRB4 of Thermoanaerobacter Pseudethanolicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1588 b:70.7 occ:1.00 OE1 B:GLU274 2.1 63.4 1.0 OG B:SER251 2.3 78.0 1.0 O2B B:ADP1589 2.3 50.7 1.0 OE2 B:GLU274 2.4 61.1 1.0 CD B:GLU274 2.6 60.3 1.0 O B:HOH2023 3.0 50.2 1.0 O B:HOH2017 3.0 60.7 1.0 CB B:SER251 3.5 70.0 1.0 PB B:ADP1589 3.6 48.0 1.0 OD2 B:ASP471 3.8 55.9 1.0 O1B B:ADP1589 3.9 47.6 1.0 OD1 B:ASP471 3.9 54.4 1.0 CG B:GLU274 4.1 50.8 1.0 O B:HOH2016 4.1 34.1 1.0 N B:SER251 4.2 57.5 1.0 CG B:ASP471 4.3 45.5 1.0 OE1 B:GLU472 4.3 48.1 1.0 CA B:SER251 4.4 61.0 1.0 CE B:LYS250 4.5 32.4 1.0 O3B B:ADP1589 4.5 45.5 1.0 CG B:GLU276 4.6 50.6 1.0 O2A B:ADP1589 4.7 46.1 1.0 NZ B:LYS250 4.7 32.5 1.0 O3A B:ADP1589 4.8 45.6 1.0 CD B:GLU472 4.8 52.2 1.0 CB B:LYS250 4.8 39.1 1.0 CB B:GLU274 4.8 43.2 1.0 CG B:GLU472 4.9 45.8 1.0

Magnesium binding site 3 out of 3 in the Structure of VIRB4 of Thermoanaerobacter Pseudethanolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of VIRB4 of Thermoanaerobacter Pseudethanolicus within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1533 b:77.3 occ:1.00 OE2 C:GLU354 2.4 58.6 1.0 OE2 B:GLU354 2.4 71.5 1.0 O B:HOH2045 2.4 56.7 1.0 OD1 C:ASP350 3.1 56.5 1.0 CD C:GLU354 3.2 56.7 1.0 CG C:GLU354 3.3 61.4 1.0 CD B:GLU354 3.4 69.0 1.0 CG C:ASP350 3.7 49.6 1.0 CG B:GLU354 3.8 57.2 1.0 OD2 B:ASP350 3.8 37.4 1.0 OD1 B:ASP350 3.8 49.6 1.0 OD2 C:ASP350 3.9 53.0 1.0 O C:ASP350 4.1 51.1 1.0 CG B:ASP350 4.2 43.5 1.0 OE1 C:GLU354 4.4 61.2 1.0 OE1 B:GLU354 4.5 71.9 1.0 CG1 C:VAL353 4.6 36.6 1.0 CB C:GLU354 4.7 57.9 1.0 C C:ASP350 4.8 44.0 1.0 CB C:VAL353 4.8 38.2 1.0 NZ B:LYS357 4.8 84.8 1.0 O B:ASP350 4.8 45.1 1.0 CA C:ASP350 4.9 42.3 1.0 CB C:ASP350 4.9 40.6 1.0 N C:GLU354 4.9 43.2 1.0

K.Wallden, R.Williams, J.Yan, P.W.Lian, L.Wang, K.Thalassinos, E.V.Orlova, G.Waksman. Structure of the VIRB4 Atpase, Alone and Bound to the Core Complex of A Type IV Secretion System. Proc.Natl.Acad.Sci.Usa V. 109 11348 2012.
ISSN: ISSN 0027-8424
PubMed: 22745169
DOI: 10.1073/PNAS.1201428109