Calcium in PDB 5uw5: PCY1 H695A Variant in Complex with Follower Peptide

The structure of PCY1 H695A Variant in Complex with Follower Peptide, PDB code: 5uw5 was solved by J.R.Chekan, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.90 / 2.94
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	65.020, 85.614, 137.870, 87.49, 78.51, 89.44
R / Rfree (%)	18.6 / 22.7

The structure of PCY1 H695A Variant in Complex with Follower Peptide also contains other interesting chemical elements:

Arsenic

(As)

4 atoms

The binding sites of Calcium atom in the PCY1 H695A Variant in Complex with Follower Peptide (pdb code 5uw5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the PCY1 H695A Variant in Complex with Follower Peptide, PDB code: 5uw5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the PCY1 H695A Variant in Complex with Follower Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of PCY1 H695A Variant in Complex with Follower Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:0.7 occ:1.00 OE2 A:GLU64 3.0 71.5 1.0 CG A:GLU61 3.4 85.7 1.0 O A:GLU61 3.4 65.5 1.0 OE2 A:GLU61 3.8 89.8 1.0 CD A:GLU64 4.0 63.7 1.0 CD A:GLU61 4.1 90.2 1.0 C A:GLU61 4.3 70.3 1.0 OE1 A:GLU64 4.3 62.5 1.0 CB A:GLU61 4.4 79.9 1.0 CA A:GLU61 4.6 73.2 1.0

Calcium binding site 2 out of 6 in the PCY1 H695A Variant in Complex with Follower Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of PCY1 H695A Variant in Complex with Follower Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:41.4 occ:1.00 OE2 A:GLU719 2.7 34.0 1.0 O A:ALA717 2.8 30.4 1.0 OE1 A:GLU719 3.2 30.8 1.0 CD A:GLU719 3.4 31.9 1.0 OD1 A:ASN683 3.8 34.6 1.0 C A:ALA717 4.0 30.2 1.0 O A:GLY580 4.6 26.9 1.0 CG A:ASN683 4.6 37.6 1.0 ND2 A:ASN683 4.7 36.1 1.0 CA A:ALA717 4.8 29.8 1.0 O A:ARG554 4.8 37.8 1.0 CG A:GLU719 4.9 30.4 1.0 N A:LEU718 5.0 29.8 1.0

Calcium binding site 3 out of 6 in the PCY1 H695A Variant in Complex with Follower Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of PCY1 H695A Variant in Complex with Follower Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:31.7 occ:1.00 OE2 B:GLU719 2.5 39.0 1.0 O B:ALA717 2.6 28.0 1.0 OE1 B:GLU719 2.9 37.2 1.0 CD B:GLU719 3.1 35.3 1.0 C B:ALA717 3.8 27.7 1.0 OD1 B:ASN683 4.2 18.8 1.0 CG B:GLU719 4.6 32.3 1.0 O B:ARG554 4.7 28.6 1.0 CA B:ALA717 4.7 28.2 1.0 N B:LEU718 4.7 28.4 1.0 O B:GLY580 4.7 24.4 1.0 CA B:LEU718 4.7 30.4 1.0 CG B:ASN683 5.0 20.0 1.0

Calcium binding site 4 out of 6 in the PCY1 H695A Variant in Complex with Follower Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of PCY1 H695A Variant in Complex with Follower Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:70.5 occ:1.00 O B:GLU639 2.1 34.0 1.0 C B:GLU639 3.2 33.7 1.0 CG B:GLN641 3.9 20.7 1.0 NE2 B:GLN641 4.1 20.1 1.0 CA B:GLU639 4.1 37.3 1.0 N B:THR640 4.2 30.6 1.0 N B:GLN641 4.2 24.5 1.0 C B:THR640 4.2 26.7 1.0 CA B:THR640 4.3 28.6 1.0 CD B:GLN641 4.3 20.4 1.0 CB B:GLN641 4.5 21.8 1.0 CB B:GLU639 4.6 39.8 1.0 O B:THR640 4.7 25.3 1.0

Calcium binding site 5 out of 6 in the PCY1 H695A Variant in Complex with Follower Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of PCY1 H695A Variant in Complex with Follower Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca802 b:73.3 occ:1.00 OE2 C:GLU64 3.2 70.4 1.0 O C:GLU61 3.3 49.1 1.0 OE1 C:GLU64 3.7 67.5 1.0 CD C:GLU64 3.8 64.5 1.0 CB C:GLU61 4.1 55.0 1.0 C C:GLU61 4.1 48.4 1.0 CA C:GLU61 4.2 48.6 1.0 CG C:GLU61 4.6 61.8 1.0

Calcium binding site 6 out of 6 in the PCY1 H695A Variant in Complex with Follower Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of PCY1 H695A Variant in Complex with Follower Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca803 b:44.4 occ:1.00 OE1 C:GLU639 1.8 49.0 1.0 CD C:GLU639 2.8 43.5 1.0 OE2 C:GLU639 3.5 40.6 1.0 CG C:GLU639 4.0 40.3 1.0

J.R.Chekan, P.Estrada, P.S.Covello, S.K.Nair. Characterization of the Macrocyclase Involved in the Biosynthesis of Ripp Cyclic Peptides in Plants. Proc. Natl. Acad. Sci. V. 114 6551 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28584123
DOI: 10.1073/PNAS.1620499114