Magnesium in PDB 1w7c: Pplo at 1.23 Angstroms

All present enzymatic activity of Pplo at 1.23 Angstroms:
1.4.3.13;

The structure of Pplo at 1.23 Angstroms, PDB code: 1w7c was solved by A.P.Duff, A.E.Cohen, P.J.Ellis, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.01 / 1.23
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.948, 67.027, 108.688, 90.00, 118.95, 90.00
R / Rfree (%)	11.2 / 14.6

The structure of Pplo at 1.23 Angstroms also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	5 atoms
Copper	(Cu)	1 atom

The binding sites of Magnesium atom in the Pplo at 1.23 Angstroms (pdb code 1w7c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Pplo at 1.23 Angstroms, PDB code: 1w7c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Pplo at 1.23 Angstroms


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pplo at 1.23 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:20.5 occ:1.00 O A:HOH2059 2.0 17.4 1.0 O A:HOH2649 2.0 20.4 1.0 O A:HOH2645 2.1 17.8 1.0 O A:HOH2054 2.1 22.1 1.0 O A:HOH2052 2.1 21.4 1.0 O A:HOH2060 2.1 20.2 1.0 HA A:ALA65 3.7 17.8 1.0 O A:SER63 4.0 16.8 1.0 OD2 A:ASP425 4.0 21.7 1.0 OG A:SER63 4.1 16.3 1.0 O A:HOH2056 4.1 64.3 1.0 HG22 A:THR62 4.2 16.6 1.0 O A:HOH2563 4.3 29.0 1.0 O A:HOH2055 4.3 50.1 1.0 OG1 A:THR62 4.4 15.9 1.0 O A:HOH2562 4.4 20.0 1.0 HB2 A:ALA65 4.4 20.6 1.0 O A:HOH2053 4.4 39.4 1.0 O A:HOH2063 4.5 24.8 1.0 CA A:ALA65 4.5 18.6 1.0 O A:LEU64 4.5 19.4 1.0 N A:ALA65 4.7 17.7 1.0 C A:LEU64 4.8 18.1 1.0 C A:SER63 4.8 16.3 1.0 O A:HOH2311 4.9 35.8 1.0 CB A:ALA65 4.9 21.6 1.0 CG2 A:THR62 5.0 17.6 1.0 CG A:ASP425 5.0 18.0 1.0 H A:ALA65 5.0 16.8 1.0

Magnesium binding site 2 out of 5 in the Pplo at 1.23 Angstroms


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pplo at 1.23 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:21.1 occ:0.50 O A:HOH2097 1.9 44.6 1.0 O A:HOH2190 2.0 28.5 1.0 O A:HOH2191 2.1 42.9 1.0 OD1 A:ASP117 4.3 28.7 1.0 OD2 A:ASP117 4.3 35.0 1.0 CG A:ASP117 4.7 29.1 1.0

Magnesium binding site 3 out of 5 in the Pplo at 1.23 Angstroms


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pplo at 1.23 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg806 b:30.1 occ:0.60 O A:HOH2556 2.0 44.9 1.0 O A:HOH2561 2.1 33.2 1.0 O A:HOH2551 2.1 28.0 1.0 O A:HOH2024 2.1 52.8 1.0 O A:HOH2252 2.3 45.2 0.6 O A:HOH2552 2.3 36.6 1.0 HB2 A:ASP338 3.8 26.1 1.0 HG2 A:GLU339 4.0 18.2 1.0 O A:HOH2558 4.1 48.8 1.0 OD2 A:ASP336 4.2 19.9 1.0 HG3 A:GLU54 4.2 35.5 0.5 OE2 A:GLU54 4.3 45.8 0.5 HG2 A:GLU54 4.4 38.2 0.5 OE2 A:GLU339 4.4 24.3 1.0 OD1 A:ASP336 4.5 20.6 1.0 OD2 A:ASP338 4.5 52.6 1.0 CB A:ASP338 4.6 26.7 1.0 HB3 A:ASP338 4.6 26.1 1.0 HG3 A:GLU339 4.7 18.2 1.0 O A:HOH2027 4.7 39.8 1.0 CG A:GLU339 4.7 19.1 1.0 CG A:ASP336 4.8 22.5 1.0 O A:HOH2557 4.9 45.0 1.0 CG A:ASP338 5.0 51.8 1.0

Magnesium binding site 4 out of 5 in the Pplo at 1.23 Angstroms


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pplo at 1.23 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg807 b:73.1 occ:1.00 O A:HOH2248 2.3 62.4 1.0 O A:HOH2243 2.8 50.0 1.0 O A:HOH2100 2.9 48.8 1.0 O A:HOH2244 3.4 51.2 1.0 HG2 A:PRO144 3.5 32.7 1.0 HB2 A:PRO144 3.6 28.1 1.0 HG3 A:PRO144 3.7 32.7 1.0 OE1 A:GLU150 3.8 65.2 1.0 CG A:PRO144 4.0 34.7 1.0 CB A:PRO144 4.2 30.1 1.0 O A:HOH2202 4.3 26.2 1.0 HB3 A:PRO144 4.6 28.1 1.0 HB2 A:GLU150 4.7 44.2 1.0 CD A:GLU150 4.8 84.4 1.0

Magnesium binding site 5 out of 5 in the Pplo at 1.23 Angstroms


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pplo at 1.23 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg808 b:68.8 occ:1.00 O A:HOH2888 2.3 23.9 1.0 O A:HOH2889 2.4 34.8 1.0 O A:HOH2890 2.9 37.6 1.0 O A:HOH2953 3.3 24.3 1.0 O A:HIS647 4.0 15.5 1.0 O A:HOH2952 4.0 19.8 0.6 HB3 A:ASP683 4.1 14.0 1.0 HB3 A:HIS647 4.2 13.7 1.0 OE2 A:GLU682 4.5 17.4 0.4 O A:HOH2894 4.6 26.4 1.0 ND1 A:HIS647 4.6 17.1 1.0 HB2 A:ASP683 4.6 14.0 1.0 O A:HOH2951 4.7 50.0 1.0 O A:HOH2896 4.8 26.5 0.6 CB A:ASP683 4.8 15.0 1.0 HA A:LYS648 4.9 14.1 1.0 HE3 A:LYS646 4.9 34.6 1.0 HE2 A:LYS646 4.9 34.6 1.0 C A:HIS647 4.9 15.4 1.0 OD2 A:ASP683 5.0 17.0 1.0 O A:HOH2153 5.0 27.8 1.0

A.P.Duff, A.E.Cohen, P.J.Ellis, K.Hilmer, D.B.Langley, D.M.Dooley, H.C.Freeman, J.M.Guss. The 1.23 A Structure of Pichia Pastoris Lysyl Oxidase Reveals A Lysine-Lysine Cross-Link Acta Crystallogr.,Sect.D V. 62 1073 2006.
ISSN: ISSN 0907-4449
PubMed: 16929109
DOI: 10.1107/S0907444906026333