Calcium in PDB 5twt: Characterization of Class III Peroxidase From Switchgrass (Panicum Virgatum)

All present enzymatic activity of Characterization of Class III Peroxidase From Switchgrass (Panicum Virgatum):
1.11.1.7;

The structure of Characterization of Class III Peroxidase From Switchgrass (Panicum Virgatum), PDB code: 5twt was solved by T.W.Moural, C.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.55 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.854, 59.432, 96.874, 90.00, 90.00, 90.00
R / Rfree (%)	13.5 / 14.5

The structure of Characterization of Class III Peroxidase From Switchgrass (Panicum Virgatum) also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Calcium atom in the Characterization of Class III Peroxidase From Switchgrass (Panicum Virgatum) (pdb code 5twt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Characterization of Class III Peroxidase From Switchgrass (Panicum Virgatum), PDB code: 5twt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Characterization of Class III Peroxidase From Switchgrass (Panicum Virgatum)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Characterization of Class III Peroxidase From Switchgrass (Panicum Virgatum) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:8.4 occ:1.00 OD2 A:ASP211 2.3 11.6 1.0 O A:THR214 2.4 11.2 1.0 O A:THR168 2.4 8.0 1.0 O A:THR217 2.4 8.8 1.0 OG1 A:THR214 2.4 11.1 1.0 OG1 A:THR168 2.4 8.5 1.0 OD1 A:ASP219 2.5 9.5 1.0 C A:THR168 3.3 7.3 1.0 C A:THR214 3.4 11.7 1.0 CG A:ASP219 3.4 10.8 1.0 CG A:ASP211 3.4 9.4 1.0 HB3 A:ALA221 3.5 11.7 1.0 CB A:THR214 3.5 11.8 1.0 HA A:THR168 3.5 8.7 1.0 CB A:THR168 3.6 8.2 1.0 H A:THR217 3.6 11.5 1.0 C A:THR217 3.6 8.4 1.0 H A:ASP219 3.6 11.9 1.0 HB A:THR214 3.7 14.2 1.0 CA A:THR168 3.7 7.3 1.0 HB3 A:ASP211 3.7 10.4 1.0 H A:THR214 3.7 14.8 1.0 HB A:THR217 3.8 13.5 1.0 OD2 A:ASP219 3.8 12.7 1.0 CA A:THR214 3.9 11.6 1.0 HG23 A:THR168 3.9 11.0 1.0 CB A:ASP211 4.0 8.6 1.0 HB2 A:ASP211 4.2 10.4 1.0 HA A:PHE218 4.2 10.2 1.0 N A:ASP219 4.2 10.0 1.0 N A:THR214 4.2 12.3 1.0 CG2 A:THR168 4.3 9.2 1.0 N A:THR217 4.3 9.6 1.0 HB A:THR168 4.3 9.9 1.0 HG23 A:ILE169 4.3 11.6 1.0 CA A:THR217 4.3 9.2 1.0 H A:ALA221 4.4 10.6 1.0 OD1 A:ASP211 4.4 9.6 1.0 CB A:ALA221 4.4 9.7 1.0 HA A:PRO215 4.5 18.2 1.0 N A:PRO215 4.5 13.5 1.0 O A:ASP219 4.5 9.4 1.0 CB A:THR217 4.5 11.3 1.0 H A:TYR222 4.5 10.1 1.0 N A:ILE169 4.5 7.6 1.0 HG22 A:ILE169 4.6 11.6 1.0 HG21 A:THR168 4.6 11.0 1.0 HA A:ILE169 4.6 9.9 1.0 N A:PHE218 4.6 8.5 1.0 CB A:ASP219 4.7 10.2 1.0 HB2 A:ALA221 4.7 11.7 1.0 CA A:PHE218 4.7 8.5 1.0 HA A:THR214 4.8 13.9 1.0 CG2 A:THR214 4.8 13.0 1.0 CA A:ASP219 4.8 9.9 1.0 CA A:PRO215 4.8 15.1 1.0 C A:ASP219 4.9 9.6 1.0 C A:PHE218 4.9 9.5 1.0 CG2 A:ILE169 4.9 9.7 1.0 HG22 A:THR217 4.9 14.2 1.0 HB1 A:ALA221 5.0 11.7 1.0 HG21 A:THR214 5.0 15.6 1.0 C A:PRO215 5.0 12.6 1.0 N A:ALA221 5.0 8.9 1.0 HG23 A:THR214 5.0 15.6 1.0

Calcium binding site 2 out of 2 in the Characterization of Class III Peroxidase From Switchgrass (Panicum Virgatum)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Characterization of Class III Peroxidase From Switchgrass (Panicum Virgatum) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:8.1 occ:1.00 O A:VAL46 2.3 8.8 1.0 OD1 A:ASP50 2.4 8.8 1.0 OD1 A:ASP43 2.4 8.4 1.0 O A:GLY48 2.4 8.5 1.0 O A:HOH422 2.4 9.4 1.0 O A:ASP43 2.4 7.8 1.0 OG A:SER52 2.5 9.7 1.0 H A:SER52 3.1 9.5 1.0 HA A:ASP43 3.2 9.3 1.0 H A:ASP50 3.2 10.3 1.0 C A:ASP43 3.3 7.1 1.0 CG A:ASP50 3.4 9.2 1.0 C A:VAL46 3.5 8.4 1.0 CG A:ASP43 3.5 8.3 1.0 HG3 A:GLN47 3.6 13.8 1.0 HB A:VAL46 3.6 11.3 1.0 C A:GLY48 3.6 8.5 1.0 CB A:SER52 3.6 9.2 1.0 CA A:ASP43 3.7 7.8 1.0 HB3 A:SER52 3.7 11.0 1.0 H A:VAL46 3.7 10.3 1.0 N A:SER52 3.9 7.9 1.0 H A:VAL53 3.9 9.9 1.0 HG2 A:GLN47 4.0 13.8 1.0 N A:ASP50 4.0 8.6 1.0 OD2 A:ASP50 4.0 10.2 1.0 HA A:CYS49 4.0 11.5 1.0 C A:GLN47 4.1 9.8 1.0 N A:GLY48 4.2 9.5 1.0 CG A:GLN47 4.2 11.5 1.0 CB A:ASP43 4.2 8.7 1.0 CA A:VAL46 4.3 8.4 1.0 O A:GLN47 4.3 11.6 1.0 CA A:SER52 4.3 8.3 1.0 CB A:VAL46 4.3 9.4 1.0 H A:ALA51 4.4 10.5 1.0 N A:VAL46 4.4 8.6 1.0 HB2 A:SER52 4.4 11.0 1.0 H A:GLY48 4.4 11.4 1.0 N A:CYS44 4.4 7.8 1.0 OD2 A:ASP43 4.4 9.5 1.0 HA A:CYS44 4.4 9.5 1.0 HG12 A:VAL46 4.5 13.1 1.0 N A:GLN47 4.5 9.6 1.0 CA A:GLY48 4.5 9.1 1.0 N A:VAL53 4.5 8.2 1.0 N A:ALA51 4.6 8.7 1.0 CB A:ASP50 4.6 9.1 1.0 N A:CYS49 4.6 9.4 1.0 CA A:CYS49 4.6 9.6 1.0 OE1 A:GLU62 4.7 10.8 1.0 CA A:ASP50 4.7 8.7 1.0 OE2 A:GLU62 4.7 10.5 1.0 O A:HIS42 4.7 9.7 1.0 HB A:VAL53 4.7 12.2 1.0 CA A:GLN47 4.7 9.7 1.0 HE21 A:GLN47 4.7 14.8 1.0 C A:ASP50 4.8 8.7 1.0 HB2 A:ASP43 4.8 10.5 1.0 HB3 A:ASP50 4.8 10.9 1.0 CA A:CYS44 4.8 7.9 1.0 C A:CYS49 4.9 8.9 1.0 C A:SER52 4.9 8.7 1.0 HB3 A:ASP43 4.9 10.5 1.0 C A:ALA51 4.9 8.6 1.0 CG1 A:VAL46 5.0 10.9 1.0 N A:ASP43 5.0 7.9 1.0 HG12 A:VAL53 5.0 12.2 1.0

T.W.Moural, K.M.Lewis, C.Barnaba, F.Zhu, N.A.Palmer, G.Sarath, E.D.Scully, J.P.Jones, S.E.Sattler, C.Kang. Characterization of Class III Peroxidases From Switchgrass. Plant Physiol. V. 173 417 2017.
ISSN: ESSN 1532-2548
PubMed: 27879392
DOI: 10.1104/PP.16.01426