Calcium in PDB 3hda: Prtc Methionine Mutants: M226A_DESY

The structure of Prtc Methionine Mutants: M226A_DESY, PDB code: 3hda was solved by A.E.Oberholzer, M.Bumann, T.Hege, S.Russo, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.51 / 2.13
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.858, 101.858, 122.521, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 20.7

The structure of Prtc Methionine Mutants: M226A_DESY also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Prtc Methionine Mutants: M226A_DESY (pdb code 3hda). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Prtc Methionine Mutants: M226A_DESY, PDB code: 3hda:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Prtc Methionine Mutants: M226A_DESY


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Prtc Methionine Mutants: M226A_DESY within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca480 b:23.5 occ:1.00 O P:GLY299 2.4 25.8 1.0 OD2 P:ASP302 2.4 22.2 1.0 O P:ARG265 2.4 22.7 1.0 O P:GLY267 2.5 26.2 1.0 OD2 P:ASP297 2.5 23.0 1.0 OG P:SER269 2.5 21.6 1.0 OD1 P:ASP297 2.6 26.2 1.0 CG P:ASP297 2.9 28.2 1.0 CG P:ASP302 3.2 24.1 1.0 OD1 P:ASP302 3.4 23.2 1.0 CB P:SER269 3.4 19.2 1.0 C P:ARG265 3.5 24.4 1.0 C P:GLY299 3.6 25.9 1.0 C P:GLY267 3.7 27.6 1.0 N P:SER269 3.7 22.7 1.0 C P:THR266 4.0 23.9 1.0 N P:GLY267 4.1 22.0 1.0 CA P:SER269 4.2 21.9 1.0 CA P:THR266 4.2 22.1 1.0 N P:GLY299 4.3 21.8 1.0 CB P:ARG265 4.3 25.9 1.0 N P:THR266 4.3 20.6 1.0 CB P:ASP297 4.4 22.5 1.0 CA P:GLY300 4.4 22.9 1.0 O P:HOH634 4.4 24.2 1.0 N P:GLY300 4.4 22.6 1.0 O P:THR266 4.4 24.0 1.0 CB P:ASP302 4.5 19.6 1.0 CA P:ARG265 4.5 25.9 1.0 CA P:GLY299 4.5 22.6 1.0 CA P:GLY267 4.5 24.0 1.0 CL P:CL1 4.5 37.9 1.0 C P:ASP268 4.5 23.8 1.0 C P:GLY300 4.6 22.7 1.0 N P:ASP268 4.6 25.4 1.0 CA P:ASP268 4.6 24.4 1.0 OH P:TYR271 4.8 25.4 1.0 O P:GLY300 4.8 22.9 1.0

Calcium binding site 2 out of 7 in the Prtc Methionine Mutants: M226A_DESY


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Prtc Methionine Mutants: M226A_DESY within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca481 b:26.9 occ:1.00 O P:THR339 2.4 21.1 1.0 O P:GLY300 2.4 22.9 1.0 OD1 P:ASP302 2.5 23.2 1.0 O P:HOH634 2.5 24.2 1.0 O P:HOH635 2.6 25.4 1.0 OE1 P:GLU341 2.6 27.0 1.0 OE2 P:GLU341 2.6 23.7 1.0 CD P:GLU341 3.0 28.0 1.0 CG P:ASP302 3.5 24.1 1.0 C P:GLY300 3.6 22.7 1.0 C P:THR339 3.6 24.8 1.0 N P:ASP302 4.2 21.1 1.0 N P:GLY300 4.2 22.6 1.0 C P:GLY299 4.2 25.9 1.0 CB P:ASP302 4.3 19.6 1.0 CB P:THR339 4.3 24.8 1.0 OD1 P:ASP297 4.3 26.2 1.0 OD2 P:ASP302 4.3 22.2 1.0 O P:GLY299 4.4 25.8 1.0 O P:HOH15 4.4 29.9 1.0 CA P:THR301 4.5 22.9 1.0 N P:THR301 4.5 20.1 1.0 CA P:THR339 4.5 24.6 1.0 CA P:GLY300 4.5 22.9 1.0 CG P:GLU341 4.5 23.8 1.0 N P:ILE340 4.5 23.8 1.0 CA P:ILE340 4.6 21.0 1.0 CG2 P:THR339 4.6 22.4 1.0 C P:THR301 4.8 23.9 1.0 CA P:GLY299 4.8 22.6 1.0 N P:THR339 4.9 27.9 1.0 N P:GLU341 4.9 21.7 1.0 CA P:ASP302 4.9 21.6 1.0

Calcium binding site 3 out of 7 in the Prtc Methionine Mutants: M226A_DESY


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Prtc Methionine Mutants: M226A_DESY within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca482 b:30.2 occ:1.00 OD1 P:ASP368 2.4 29.8 1.0 O P:GLY363 2.4 27.1 1.0 O P:ALA365 2.5 28.7 1.0 O P:GLY346 2.5 28.7 1.0 O P:GLY348 2.5 28.0 1.0 OD2 P:ASP350 2.5 25.9 1.0 OD2 P:ASP368 2.8 29.1 1.0 CG P:ASP368 2.9 30.9 1.0 CG P:ASP350 3.4 31.4 1.0 C P:GLY363 3.5 25.6 1.0 C P:GLY346 3.6 28.0 1.0 C P:GLY348 3.7 34.0 1.0 C P:ALA365 3.7 32.9 1.0 C P:GLY364 3.9 30.4 1.0 O P:GLY364 4.0 27.8 1.0 N P:GLY348 4.0 31.3 1.0 CB P:ASP350 4.1 29.1 1.0 N P:GLY346 4.1 26.6 1.0 C P:SER347 4.2 32.6 1.0 OD1 P:ASP350 4.2 30.4 1.0 N P:ASP350 4.2 28.4 1.0 N P:ALA365 4.2 31.3 1.0 CA P:GLY364 4.3 31.2 1.0 N P:GLY364 4.3 27.4 1.0 CA P:SER347 4.4 30.2 1.0 CB P:ASP368 4.4 26.1 1.0 CA P:GLY363 4.4 21.7 1.0 N P:SER347 4.4 26.9 1.0 O P:HOH489 4.4 30.9 1.0 CA P:GLY348 4.5 30.6 1.0 CA P:GLY366 4.5 29.5 1.0 CA P:GLY346 4.5 25.3 1.0 N P:GLY366 4.5 33.7 1.0 C P:GLY345 4.6 28.1 1.0 C P:GLY366 4.6 32.0 1.0 O P:GLY366 4.6 29.7 1.0 CA P:ALA365 4.6 30.4 1.0 N P:ASN349 4.7 35.3 1.0 CA P:CA484 4.7 30.1 1.0 O P:SER347 4.7 36.7 1.0 CA P:ASN349 4.8 32.9 1.0 CA P:ASP350 4.8 29.1 1.0 CA P:GLY345 4.9 26.4 1.0 C P:ASN349 5.0 30.4 1.0

Calcium binding site 4 out of 7 in the Prtc Methionine Mutants: M226A_DESY


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Prtc Methionine Mutants: M226A_DESY within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca483 b:24.4 occ:1.00 O P:ASN355 2.4 25.9 1.0 OD1 P:ASP377 2.4 21.4 1.0 O P:ALA374 2.4 25.5 1.0 O P:GLY372 2.4 26.0 1.0 O P:ALA357 2.5 24.0 1.0 OD1 P:ASN359 2.5 24.4 1.0 OD2 P:ASP377 2.8 23.3 1.0 CG P:ASP377 3.0 24.0 1.0 CG P:ASN359 3.4 26.3 1.0 C P:ASN355 3.6 28.9 1.0 C P:GLY372 3.6 29.9 1.0 C P:ALA374 3.6 22.7 1.0 C P:ALA357 3.7 26.6 1.0 N P:ASN355 4.0 27.6 1.0 N P:ASN359 4.1 22.6 1.0 C P:GLY373 4.1 26.6 1.0 CB P:ASN359 4.1 24.7 1.0 C P:SER356 4.1 28.1 1.0 N P:ALA357 4.1 22.5 1.0 O P:GLY373 4.2 25.1 1.0 ND2 P:ASN359 4.2 21.5 1.0 N P:ALA374 4.2 23.6 1.0 CA P:GLY372 4.4 24.9 1.0 CA P:SER356 4.4 29.2 1.0 N P:SER356 4.4 24.5 1.0 CB P:ASP377 4.4 23.9 1.0 CA P:ASN355 4.5 28.4 1.0 OD1 P:ASN355 4.5 25.5 1.0 N P:GLY373 4.5 25.2 1.0 CA P:GLY375 4.5 24.1 1.0 N P:GLY375 4.5 25.2 1.0 O P:SER356 4.5 29.7 1.0 CA P:GLY373 4.5 24.7 1.0 CA P:ALA357 4.6 25.0 1.0 CA P:ALA374 4.6 21.4 1.0 N P:ASP358 4.6 21.5 1.0 CA P:ASP358 4.6 25.2 1.0 CA P:CA487 4.6 27.3 1.0 C P:GLY354 4.6 29.5 1.0 O P:GLY375 4.6 23.3 1.0 C P:GLY375 4.7 24.5 1.0 C P:ASP358 4.7 25.1 1.0 CA P:ASN359 4.8 22.7 1.0 CA P:GLY354 4.8 24.4 1.0

Calcium binding site 5 out of 7 in the Prtc Methionine Mutants: M226A_DESY


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Prtc Methionine Mutants: M226A_DESY within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca484 b:30.1 occ:1.00 O P:GLY381 2.4 29.1 1.0 OD1 P:ASP386 2.4 31.8 1.0 O P:GLY364 2.4 27.8 1.0 O P:GLY366 2.5 29.7 1.0 O P:ALA383 2.5 34.6 1.0 OD2 P:ASP368 2.5 29.1 1.0 OD2 P:ASP386 2.7 30.4 1.0 CG P:ASP386 2.9 33.9 1.0 C P:GLY381 3.5 27.9 1.0 CG P:ASP368 3.6 30.9 1.0 C P:GLY366 3.6 32.0 1.0 C P:ALA383 3.6 35.0 1.0 C P:GLY364 3.6 30.4 1.0 O P:ALA365 3.8 28.7 1.0 C P:ALA365 3.8 32.9 1.0 C P:GLY382 3.8 33.0 1.0 O P:GLY382 4.0 28.6 1.0 CA P:GLY382 4.1 26.0 1.0 N P:ASP368 4.1 29.8 1.0 N P:GLY366 4.1 33.7 1.0 N P:ALA383 4.2 35.6 1.0 CB P:ASP368 4.2 26.1 1.0 N P:GLY382 4.2 26.1 1.0 CA P:ALA365 4.3 30.4 1.0 C P:GLY363 4.3 25.6 1.0 CB P:ASP386 4.4 32.5 1.0 N P:GLY364 4.4 27.4 1.0 N P:ALA365 4.4 31.3 1.0 CA P:GLY384 4.4 34.9 1.0 CA P:GLY366 4.5 29.5 1.0 N P:GLY384 4.5 37.1 1.0 N P:ASN367 4.5 31.7 1.0 OD1 P:ASP368 4.6 29.8 1.0 CA P:GLY381 4.6 24.5 1.0 CA P:ALA383 4.6 34.8 1.0 CA P:GLY363 4.6 21.7 1.0 CA P:ASN367 4.6 31.4 1.0 O P:GLY363 4.6 27.1 1.0 CA P:GLY364 4.7 31.2 1.0 CA P:CA482 4.7 30.2 1.0 C P:GLY384 4.7 38.4 1.0 CA P:CA485 4.7 23.7 0.5 CA P:ASP368 4.8 27.5 1.0 C P:ASN367 4.8 30.6 1.0 O P:GLY384 4.9 36.5 1.0

Calcium binding site 6 out of 7 in the Prtc Methionine Mutants: M226A_DESY


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Prtc Methionine Mutants: M226A_DESY within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca485 b:23.7 occ:0.50 OE1 P:GLN408 2.4 44.0 1.0 O P:GLY382 2.5 28.6 1.0 OD2 P:ASP386 2.5 30.4 1.0 O P:GLY384 2.5 36.5 1.0 OD1 P:ASP412 2.5 31.9 1.0 O P:HOH10 2.6 26.4 1.0 OD2 P:ASP412 3.2 37.3 1.0 CG P:ASP412 3.2 36.1 1.0 CG P:ASP386 3.5 33.9 1.0 C P:GLY384 3.6 38.4 1.0 CD P:GLN408 3.7 46.9 1.0 C P:GLY382 3.7 33.0 1.0 C P:ALA383 3.9 35.0 1.0 N P:GLY384 3.9 37.1 1.0 CB P:ASP386 3.9 32.5 1.0 N P:ASP386 4.1 35.6 1.0 O P:ALA383 4.2 34.6 1.0 C P:GLY381 4.3 27.9 1.0 O P:HOH629 4.3 45.6 1.0 CA P:GLY384 4.3 34.9 1.0 N P:GLY382 4.3 26.1 1.0 CA P:ALA383 4.4 34.8 1.0 N P:ALA383 4.5 35.6 1.0 N P:ARG385 4.5 35.2 1.0 CA P:GLY381 4.5 24.5 1.0 O P:GLY381 4.5 29.1 1.0 CG P:GLN408 4.6 45.5 1.0 NE2 P:GLN408 4.6 45.9 1.0 OD1 P:ASP386 4.6 31.8 1.0 CG2 P:ILE411 4.6 32.7 1.0 CA P:GLY382 4.7 26.0 1.0 CA P:ASP386 4.7 32.7 1.0 CA P:ARG385 4.7 39.4 1.0 CB P:ASP412 4.7 32.1 1.0 CA P:CA484 4.7 30.1 1.0 CB P:GLN408 4.8 41.7 1.0 C P:ARG385 4.8 38.9 1.0

Calcium binding site 7 out of 7 in the Prtc Methionine Mutants: M226A_DESY


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Prtc Methionine Mutants: M226A_DESY within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca487 b:27.3 occ:1.00 O P:ASP395 2.4 26.8 1.0 OD2 P:ASP377 2.4 23.3 1.0 O P:GLY373 2.4 25.1 1.0 O P:GLY375 2.5 23.3 1.0 O P:HOH636 2.5 23.4 1.0 OD1 P:ASP402 2.5 27.3 1.0 CG P:ASP402 3.4 26.3 1.0 CG P:ASP377 3.4 24.0 1.0 C P:ASP395 3.5 29.1 1.0 OD2 P:ASP402 3.5 29.8 1.0 C P:GLY373 3.6 26.6 1.0 C P:GLY375 3.6 24.5 1.0 C P:ALA374 3.8 22.7 1.0 O P:ALA374 3.9 25.5 1.0 CB P:ASP377 4.0 23.9 1.0 N P:GLY375 4.1 25.2 1.0 N P:ASP377 4.1 24.7 1.0 C P:GLY372 4.1 29.9 1.0 CA P:ASP395 4.2 26.6 1.0 N P:GLY373 4.3 25.2 1.0 CA P:ALA374 4.3 21.4 1.0 O P:GLY372 4.3 26.0 1.0 OD1 P:ASP377 4.4 21.4 1.0 N P:ALA374 4.4 23.6 1.0 CA P:GLY372 4.4 24.9 1.0 CA P:GLY375 4.4 24.1 1.0 CB P:ASP395 4.5 31.6 1.0 CA P:GLY373 4.6 24.7 1.0 N P:ALA376 4.6 22.5 1.0 N P:SER396 4.6 26.5 1.0 CA P:CA483 4.6 24.4 1.0 CA P:ALA376 4.7 23.5 1.0 CB P:ASP402 4.7 23.3 1.0 CA P:SER396 4.7 22.3 1.0 CA P:ASP377 4.8 26.1 1.0 O P:HOH488 4.8 23.1 1.0 C P:ALA376 4.9 26.1 1.0 O P:HOH530 4.9 34.8 1.0 CB P:SER396 4.9 23.8 1.0

A.E.Oberholzer, M.Bumann, T.Hege, S.Russo, U.Baumann. Metzincin'S Canonical Methionine Is Responsible For the Structural Integrity of the Zinc-Binding Site Biol.Chem. V. 390 875 2009.
ISSN: ISSN 1431-6730
PubMed: 19558324
DOI: 10.1515/BC.2009.100