Magnesium in PDB 7vjo: Pectobacterium Phage ZF40 Apo-ACA2

The structure of Pectobacterium Phage ZF40 Apo-ACA2, PDB code: 7vjo was solved by Y.H.Liu, L.S.Zhang, B.X.Wu, H.D.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.60 / 1.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.201, 34.566, 81.299, 90, 124.58, 90
R / Rfree (%)	15.6 / 18.5

The structure of Pectobacterium Phage ZF40 Apo-ACA2 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Pectobacterium Phage ZF40 Apo-ACA2 (pdb code 7vjo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pectobacterium Phage ZF40 Apo-ACA2, PDB code: 7vjo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pectobacterium Phage ZF40 Apo-ACA2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pectobacterium Phage ZF40 Apo-ACA2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:13.3 occ:1.00 O B:HOH498 2.0 15.8 1.0 O B:HOH443 2.1 14.4 1.0 O B:HOH336 2.1 13.7 1.0 O B:HOH318 2.1 13.1 1.0 O B:HOH326 2.1 14.6 1.0 NE2 B:HIS92 2.2 13.3 1.0 CD2 B:HIS92 3.2 12.2 1.0 CE1 B:HIS92 3.2 11.8 1.0 HD2 B:HIS92 3.3 14.6 1.0 HE1 B:HIS92 3.4 14.1 1.0 OD1 B:ASP91 4.0 13.9 1.0 OD2 B:ASP91 4.1 14.5 1.0 O B:HOH537 4.2 29.1 0.5 ND1 B:HIS92 4.3 11.3 1.0 O B:HOH502 4.3 36.1 1.0 O B:HOH350 4.3 30.0 1.0 CG B:HIS92 4.3 11.8 1.0 OD1 B:ASN89 4.4 16.4 1.0 O B:HOH511 4.5 27.5 1.0 O B:HOH397 4.5 17.9 1.0 CG B:ASP91 4.5 13.8 1.0 O B:HOH543 4.5 26.3 1.0 HB3 B:ASN89 4.5 16.3 1.0 HA B:ASN89 4.9 15.9 1.0

Magnesium binding site 2 out of 4 in the Pectobacterium Phage ZF40 Apo-ACA2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pectobacterium Phage ZF40 Apo-ACA2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:28.7 occ:1.00 O B:HOH444 2.0 29.0 1.0 O A:HOH466 2.0 28.9 1.0 O B:HOH441 2.0 28.9 1.0 O B:HOH342 2.0 28.7 1.0 O A:HOH333 2.1 28.6 1.0 O A:HOH407 2.1 28.8 1.0 HG B:SER0 3.6 40.8 1.0 OD1 A:ASP114 3.8 16.9 1.0 O A:HOH326 4.1 30.9 1.0 OG B:SER0 4.1 34.0 1.0 OE1 B:GLU5 4.2 15.7 1.0 OE2 B:GLU5 4.2 15.2 1.0 HB2 B:SER0 4.3 31.9 1.0 O A:HOH456 4.3 42.3 1.0 O A:HOH452 4.3 43.0 1.0 HB3 A:ASP114 4.3 18.1 1.0 O A:HOH450 4.4 26.4 1.0 O B:SER0 4.4 22.8 1.0 CG A:ASP114 4.4 14.7 1.0 O A:HOH327 4.6 22.2 1.0 HE1 A:TYR108 4.6 16.1 1.0 CD B:GLU5 4.6 16.1 1.0 O B:HOH529 4.7 31.6 1.0 O B:HOH349 4.7 32.5 1.0 CB B:SER0 4.8 26.6 1.0 CB A:ASP114 4.9 15.1 1.0 HH21 A:ARG73 4.9 26.3 1.0 HA B:MET1 5.0 20.1 1.0 O A:HOH379 5.0 34.0 1.0

Magnesium binding site 3 out of 4 in the Pectobacterium Phage ZF40 Apo-ACA2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pectobacterium Phage ZF40 Apo-ACA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:36.3 occ:1.00 O A:HOH516 2.0 36.4 1.0 O A:HOH383 2.0 36.2 1.0 O A:HOH425 2.0 36.3 1.0 O A:HOH488 2.1 36.4 1.0 HA A:ASN89 3.9 18.6 1.0 O A:HOH380 4.0 34.9 1.0 O A:HOH438 4.1 43.5 1.0 HD2 A:PRO90 4.1 25.6 1.0 OD1 A:ASP91 4.3 26.9 1.0 OD1 A:ASN89 4.3 22.8 1.0 O A:HOH346 4.4 40.0 1.0 O A:ASP88 4.4 21.5 1.0 CA A:ASN89 4.8 15.6 1.0 CD A:PRO90 4.9 21.4 1.0 HD3 A:PRO90 5.0 25.6 1.0

Magnesium binding site 4 out of 4 in the Pectobacterium Phage ZF40 Apo-ACA2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pectobacterium Phage ZF40 Apo-ACA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:30.0 occ:0.68 O A:HOH313 2.0 30.0 1.0 O A:HOH457 2.1 36.2 1.0 O A:HOH306 2.1 31.3 1.0 O A:HOH318 2.1 35.6 1.0 O B:HOH422 2.2 47.2 1.0 HG A:SER0 3.2 55.8 1.0 OG A:SER0 3.7 46.5 1.0 OE2 A:GLU5 4.0 22.1 1.0 HB3 B:ASP114 4.1 27.8 1.0 OE1 A:GLU5 4.1 22.8 1.0 OD1 B:ASP114 4.1 24.0 1.0 O A:SER0 4.2 28.2 1.0 O B:HOH522 4.4 36.1 1.0 CD A:GLU5 4.5 23.1 1.0 CG B:ASP114 4.5 25.4 1.0 O B:HOH379 4.6 32.1 1.0 HG23 A:THR2 4.6 25.3 1.0 CB B:ASP114 4.8 23.2 1.0 HA B:ASP114 5.0 21.5 1.0 HE1 B:TYR108 5.0 20.2 1.0

Y.H.Liu, L.S.Zhang, B.X.Wu, H.D.Huang. Pectobacterium Phage ZF40 Apo-ACA2 To Be Published.