Manganese in PDB 2vbm: Tailspike Protein of Bacteriophage SF6 Complexed with Tetrasaccharide

The structure of Tailspike Protein of Bacteriophage SF6 Complexed with Tetrasaccharide, PDB code: 2vbm was solved by J.J.Mueller, S.Barbirz, A.Freiberg, R.Seckler, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 2.00
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	95.358, 95.358, 182.765, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 23.2

The structure of Tailspike Protein of Bacteriophage SF6 Complexed with Tetrasaccharide also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Tailspike Protein of Bacteriophage SF6 Complexed with Tetrasaccharide (pdb code 2vbm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Tailspike Protein of Bacteriophage SF6 Complexed with Tetrasaccharide, PDB code: 2vbm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Tailspike Protein of Bacteriophage SF6 Complexed with Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Tailspike Protein of Bacteriophage SF6 Complexed with Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn876 b:12.7 occ:0.22 OE1 A:GLU394 2.1 15.2 1.0 O A:HOH2245 2.4 32.0 1.0 CD A:GLU394 3.2 13.9 1.0 OE2 A:GLU394 3.6 10.9 1.0 MG A:MG875 4.1 13.1 0.3 O A:HOH2116 4.2 16.0 1.0 CG A:GLU394 4.5 10.5 1.0 CB A:GLU394 4.8 10.3 1.0 NE2 A:GLN395 4.9 12.9 1.0

Manganese binding site 2 out of 2 in the Tailspike Protein of Bacteriophage SF6 Complexed with Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Tailspike Protein of Bacteriophage SF6 Complexed with Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn877 b:31.3 occ:1.00 OD1 A:ASP135 2.1 28.9 1.0 ND1 A:HIS153 2.1 33.1 1.0 O A:HOH2246 2.3 25.5 1.0 CE1 A:HIS153 2.9 36.2 1.0 CG A:ASP135 3.1 32.1 1.0 CG A:HIS153 3.2 36.7 1.0 OD2 A:ASP135 3.5 32.0 1.0 CB A:HIS153 3.6 37.4 1.0 OE1 A:GLN123 3.9 48.1 1.0 NE2 A:HIS153 4.1 35.2 1.0 CA A:HIS153 4.2 36.7 1.0 CD2 A:HIS153 4.3 35.8 1.0 N A:ALA136 4.4 36.6 1.0 O A:LYS133 4.4 37.7 1.0 O A:ASN131 4.4 38.5 1.0 CB A:ASP135 4.5 34.0 1.0 N A:ASP135 4.5 36.9 1.0 CA A:ASP135 4.7 35.3 1.0 C A:ASP135 4.8 35.4 1.0 CB A:ALA136 4.9 38.3 1.0 CD A:GLN123 5.0 44.4 1.0

J.J.Muller, S.Barbirz, K.Heinle, A.Freiberg, R.Seckler, U.Heinemann. An Intersubunit Active Site Between Supercoiled Parallel Beta Helices in the Trimeric Tailspike Endorhamnosidase of Shigella Flexneri Phage SF6. Structure V. 16 766 2008.
ISSN: ISSN 0969-2126
PubMed: 18462681
DOI: 10.1016/J.STR.2008.01.019