Magnesium in PDB 6p2a: Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment

All present enzymatic activity of Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment:
3.2.1.17;

The structure of Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment, PDB code: 6p2a was solved by S.A.Buth, M.M.Shneider, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.50 / 1.90
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	140.013, 140.013, 63.161, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 15.8

The structure of Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment (pdb code 6p2a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment, PDB code: 6p2a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:22.2 occ:1.00 O C:HOH822 2.1 21.4 1.0 O B:HOH830 2.1 20.2 1.0 O C:HOH836 2.1 21.5 1.0 O A:HOH833 2.1 22.8 1.0 O B:HOH810 2.2 22.8 1.0 O A:HOH810 2.2 20.5 1.0 HE1 A:MET557 3.4 29.7 0.2 HE1 C:MET557 3.7 33.1 0.2 HE3 A:MET557 4.0 32.2 0.8 HE3 C:MET557 4.0 30.3 0.8 OE1 C:GLU552 4.1 23.2 1.0 HE1 C:MET557 4.1 30.3 0.8 OE1 B:GLU552 4.1 21.8 1.0 HE2 A:MET557 4.2 29.7 0.2 OE1 A:GLU552 4.2 22.8 1.0 HE3 B:MET557 4.2 32.8 1.0 CE A:MET557 4.2 24.8 0.2 O C:HOH1015 4.2 32.2 1.0 OE2 A:GLU552 4.2 20.0 1.0 OE2 C:GLU552 4.2 22.5 1.0 OE2 B:GLU552 4.3 21.1 1.0 HE1 A:MET557 4.3 32.2 0.8 HE1 B:MET557 4.4 32.8 1.0 O B:HOH998 4.4 27.1 1.0 O A:HOH981 4.4 29.1 1.0 HZ2 B:TRP550 4.5 22.4 1.0 CE C:MET557 4.5 27.6 0.2 HZ2 C:TRP550 4.5 27.3 1.0 CE C:MET557 4.6 25.3 0.8 HE2 C:MET557 4.6 33.1 0.2 CE A:MET557 4.6 26.8 0.8 HZ2 A:TRP550 4.6 22.6 1.0 CD C:GLU552 4.6 23.0 1.0 CD B:GLU552 4.6 24.0 1.0 CD A:GLU552 4.7 21.6 1.0 CE B:MET557 4.8 27.4 1.0 SD C:MET557 4.8 29.3 0.2 CZ2 B:TRP550 4.9 18.7 1.0 CZ2 C:TRP550 4.9 22.8 1.0 SD A:MET557 4.9 24.4 0.2 HE3 A:MET557 5.0 29.7 0.2

Magnesium binding site 2 out of 2 in the Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:21.8 occ:1.00 O E:HOH740 2.1 21.9 1.0 O F:HOH820 2.1 23.9 1.0 O F:HOH815 2.1 19.7 1.0 O D:HOH805 2.1 20.9 1.0 O D:HOH816 2.1 22.6 1.0 O E:HOH704 2.1 20.1 1.0 HE1 D:MET557 3.6 35.9 0.4 HE1 E:MET557 3.8 33.0 0.3 HE3 D:MET557 3.9 32.3 0.6 OE1 F:GLU552 4.1 20.4 1.0 OE1 D:GLU552 4.1 21.2 1.0 HE3 F:MET557 4.1 36.1 1.0 OE1 E:GLU552 4.2 21.1 1.0 HE3 E:MET557 4.2 27.5 0.7 HE1 D:MET557 4.2 32.3 0.6 HE1 F:MET557 4.2 36.1 1.0 OE2 F:GLU552 4.2 20.4 1.0 HE1 E:MET557 4.2 27.5 0.7 OE2 D:GLU552 4.2 23.9 1.0 OE2 E:GLU552 4.3 19.3 1.0 O D:HOH971 4.3 34.7 1.0 O F:HOH986 4.4 34.3 1.0 CE D:MET557 4.4 29.9 0.4 O E:HOH887 4.4 35.2 1.0 HZ2 E:TRP550 4.5 21.4 1.0 HE2 D:MET557 4.5 35.9 0.4 CE D:MET557 4.5 26.9 0.6 HZ2 D:TRP550 4.5 24.8 1.0 HZ2 F:TRP550 4.6 22.4 1.0 CD F:GLU552 4.6 23.4 1.0 CD D:GLU552 4.6 23.0 1.0 CE E:MET557 4.6 27.5 0.3 CE F:MET557 4.6 30.1 1.0 CE E:MET557 4.7 22.9 0.7 CD E:GLU552 4.7 21.9 1.0 HE2 E:MET557 4.7 33.0 0.3 CZ2 E:TRP550 4.9 17.8 1.0 SD D:MET557 4.9 43.4 0.4 CZ2 F:TRP550 4.9 18.7 1.0 CZ2 D:TRP550 5.0 20.6 1.0

S.A.Buth, M.M.Shneider, P.G.Leiman. Chimera of Bacteriophage Obp GP146 Central Spike Protein and A T4 GP5 Beta-Helix Fragment To Be Published.