Calcium 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:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	5 atoms
Copper	(Cu)	1 atom

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

Calcium binding site 1 out of 2 in the Pplo at 1.23 Angstroms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pplo at 1.23 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:13.6 occ:1.00 OD1 A:ASP539 2.3 15.1 1.0 OD1 A:ASP537 2.3 13.8 1.0 OD1 A:ASP683 2.3 14.4 1.0 O A:LEU538 2.3 12.9 1.0 O A:ILE684 2.4 13.7 1.0 O A:HOH2742 2.4 13.9 1.0 H A:ILE684 3.2 13.3 1.0 C A:LEU538 3.4 13.5 1.0 HZ2 A:LYS105 3.4 13.5 1.0 C A:ILE684 3.5 12.8 1.0 CG A:ASP539 3.5 14.1 1.0 CG A:ASP683 3.5 14.8 1.0 CG A:ASP537 3.5 14.6 1.0 HA A:ASP539 3.5 12.7 1.0 HZ3 A:LYS105 3.6 13.5 1.0 N A:ILE684 3.6 14.2 1.0 HZ1 A:LYS105 3.7 13.5 1.0 NZ A:LYS105 3.8 14.1 1.0 HA A:ASP683 3.9 13.5 1.0 HA A:ASP537 4.0 12.9 1.0 C A:ASP537 4.0 13.9 1.0 N A:ASP539 4.1 13.7 1.0 CA A:ASP539 4.1 13.9 1.0 N A:LEU538 4.1 14.2 1.0 CA A:ILE684 4.2 13.1 1.0 OD2 A:ASP683 4.2 17.0 1.0 C A:ASP683 4.2 13.9 1.0 O A:ASP537 4.2 14.3 1.0 HG21 A:VAL685 4.2 13.9 1.0 OD2 A:ASP537 4.2 15.2 1.0 HA A:VAL685 4.3 12.5 1.0 CA A:ASP537 4.4 13.7 1.0 CB A:ASP539 4.4 13.8 1.0 OD2 A:ASP539 4.4 15.4 1.0 HA A:THR543 4.4 15.3 1.0 CA A:ASP683 4.4 14.5 1.0 H A:LEU538 4.4 13.0 1.0 CA A:LEU538 4.4 13.4 1.0 HB2 A:HIS647 4.4 13.7 1.0 N A:VAL685 4.5 13.4 1.0 HB A:ILE684 4.5 12.5 1.0 CB A:ASP537 4.5 13.9 1.0 O A:THR543 4.6 16.1 1.0 CB A:ASP683 4.6 15.0 1.0 OD1 A:ASN545 4.6 14.9 1.0 HG22 A:VAL685 4.8 13.9 1.0 H A:ASP539 4.9 12.8 1.0 CA A:VAL685 4.9 13.6 1.0 HA A:ILE684 4.9 12.0 1.0 HG23 A:THR543 4.9 19.2 1.0 CG2 A:VAL685 5.0 14.8 1.0 CB A:ILE684 5.0 13.6 1.0 HB3 A:ASP539 5.0 12.9 1.0

Calcium binding site 2 out of 2 in the Pplo at 1.23 Angstroms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pplo at 1.23 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:15.1 occ:1.00 OE1 A:GLU677 2.3 16.6 1.0 O A:PHE673 2.3 15.5 1.0 OD2 A:ASP675 2.4 15.9 1.0 O A:HOH2903 2.4 16.1 1.0 O A:HOH2904 2.4 16.7 1.0 OE2 A:GLU580 2.5 14.7 1.0 OE1 A:GLU580 2.5 15.3 1.0 CD A:GLU580 2.8 14.9 1.0 CD A:GLU677 3.3 17.7 1.0 H A:ASP675 3.3 14.7 1.0 CG A:ASP675 3.4 18.3 1.0 C A:PHE673 3.5 16.6 1.0 HB2 A:GLU677 3.5 14.3 1.0 HG3 A:GLU677 3.6 15.8 1.0 OD1 A:ASP675 3.8 21.2 1.0 CG A:GLU677 3.8 16.6 1.0 HB3 A:LYS646 3.9 15.2 1.0 HE3 A:LYS648 3.9 14.9 1.0 H A:LYS646 3.9 13.2 1.0 HA A:PHE673 4.0 14.6 1.0 N A:ASP675 4.1 15.7 1.0 HB A:THR645 4.1 13.9 1.0 HA A:LEU674 4.1 14.4 1.0 NZ A:LYS648 4.2 17.8 1.0 CB A:GLU677 4.2 15.5 1.0 H A:GLU677 4.2 14.8 1.0 OE2 A:GLU677 4.3 21.7 1.0 OE1 A:GLU651 4.3 15.8 1.0 CG A:GLU580 4.3 15.1 1.0 CA A:PHE673 4.3 15.7 1.0 HB3 A:PHE673 4.4 14.6 1.0 N A:LEU674 4.4 15.3 1.0 OE2 A:GLU651 4.5 17.1 1.0 CE A:LYS648 4.5 15.8 1.0 HD2 A:LYS648 4.6 15.4 1.0 CB A:ASP675 4.6 17.6 1.0 CA A:LEU674 4.7 15.4 1.0 HG2 A:GLU580 4.7 14.3 1.0 HG3 A:GLU580 4.7 14.3 1.0 N A:LYS646 4.7 14.2 1.0 CA A:ASP675 4.7 16.4 1.0 HG2 A:GLU677 4.8 15.8 1.0 HB3 A:GLU677 4.8 14.3 1.0 CB A:LYS646 4.8 16.2 1.0 CD A:GLU651 4.9 15.6 1.0 C A:LEU674 4.9 16.4 1.0 CB A:PHE673 4.9 15.6 1.0 HD3 A:LYS646 4.9 24.6 1.0 N A:GLU677 4.9 15.7 1.0 HB2 A:GLU580 5.0 13.6 1.0 CB A:THR645 5.0 14.7 1.0 O A:LYS646 5.0 14.8 1.0 HA A:THR645 5.0 13.2 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