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Calcium in PDB 3hbu: Prtc Methionine Mutants: M226H Desy

Protein crystallography data

The structure of Prtc Methionine Mutants: M226H Desy, PDB code: 3hbu 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) 37.16 / 1.77
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.112, 102.112, 122.863, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 18.7

Other elements in 3hbu:

The structure of Prtc Methionine Mutants: M226H Desy also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Prtc Methionine Mutants: M226H Desy (pdb code 3hbu). 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: M226H Desy, PDB code: 3hbu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3hbu

Go back to Calcium Binding Sites List in 3hbu
Calcium binding site 1 out of 7 in the Prtc Methionine Mutants: M226H 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: M226H Desy within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca480

b:13.2
occ:1.00
O P:GLY299 2.3 13.0 1.0
OD2 P:ASP302 2.3 12.1 1.0
O P:ARG265 2.4 13.1 1.0
O P:GLY267 2.4 13.4 1.0
OG P:SER269 2.5 13.9 1.0
OD1 P:ASP297 2.5 14.8 1.0
OD2 P:ASP297 2.5 13.0 1.0
CG P:ASP297 2.8 12.5 1.0
CG P:ASP302 3.1 13.4 1.0
OD1 P:ASP302 3.4 13.0 1.0
CB P:SER269 3.5 13.8 1.0
C P:ARG265 3.5 14.8 1.0
C P:GLY299 3.5 14.3 1.0
C P:GLY267 3.6 13.1 1.0
N P:SER269 3.8 13.5 1.0
N P:GLY267 4.1 13.7 1.0
C P:THR266 4.1 15.4 1.0
N P:GLY299 4.2 11.9 1.0
CA P:THR266 4.3 13.6 1.0
CB P:ARG265 4.3 12.7 1.0
CA P:SER269 4.3 11.5 1.0
N P:THR266 4.3 13.5 1.0
CB P:ASP297 4.3 12.8 1.0
O P:HOH902 4.3 13.8 1.0
CA P:GLY300 4.3 12.0 1.0
N P:GLY300 4.4 12.3 1.0
CB P:ASP302 4.4 11.4 1.0
CA P:GLY267 4.5 13.2 1.0
CA P:ARG265 4.5 13.4 1.0
CA P:GLY299 4.5 12.3 1.0
O P:THR266 4.5 14.4 1.0
N P:ASP268 4.5 13.1 1.0
C P:ASP268 4.6 16.9 1.0
C P:GLY300 4.6 13.7 1.0
O P:HOH2 4.6 12.3 1.0
CA P:ASP268 4.6 12.2 1.0
OH P:TYR271 4.8 13.7 1.0
O P:GLY300 4.8 14.9 1.0
N P:ALA298 4.9 11.4 1.0

Calcium binding site 2 out of 7 in 3hbu

Go back to Calcium Binding Sites List in 3hbu
Calcium binding site 2 out of 7 in the Prtc Methionine Mutants: M226H 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: M226H Desy within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca481

b:13.5
occ:1.00
O P:HOH902 2.4 13.8 1.0
OD1 P:ASP302 2.4 13.0 1.0
O P:THR339 2.4 13.3 1.0
O P:GLY300 2.4 14.9 1.0
O P:HOH903 2.5 14.8 1.0
OE1 P:GLU341 2.5 14.8 1.0
OE2 P:GLU341 2.5 13.9 1.0
CD P:GLU341 2.8 16.4 1.0
CG P:ASP302 3.5 13.4 1.0
C P:GLY300 3.6 13.7 1.0
C P:THR339 3.6 14.1 1.0
N P:ASP302 4.2 12.2 1.0
N P:GLY300 4.2 12.3 1.0
CB P:ASP302 4.3 11.4 1.0
C P:GLY299 4.3 14.3 1.0
CB P:THR339 4.3 14.6 1.0
OD2 P:ASP302 4.3 12.1 1.0
CG P:GLU341 4.4 15.0 1.0
O P:GLY299 4.4 13.0 1.0
O P:HOH498 4.4 17.0 1.0
N P:THR301 4.4 12.7 1.0
CA P:THR301 4.4 12.7 1.0
CA P:THR339 4.5 11.9 1.0
OD1 P:ASP297 4.5 14.8 1.0
N P:ILE340 4.5 12.1 1.0
CA P:GLY300 4.5 12.0 1.0
CA P:ILE340 4.5 13.0 1.0
CG2 P:THR339 4.7 13.5 1.0
C P:THR301 4.8 12.6 1.0
N P:THR339 4.8 12.3 1.0
N P:GLU341 4.9 12.1 1.0
CA P:GLY299 4.9 12.3 1.0
CA P:ASP302 5.0 11.6 1.0
O P:HOH527 5.0 18.9 1.0

Calcium binding site 3 out of 7 in 3hbu

Go back to Calcium Binding Sites List in 3hbu
Calcium binding site 3 out of 7 in the Prtc Methionine Mutants: M226H 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: M226H Desy within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca482

b:17.7
occ:1.00
O P:GLY363 2.3 16.4 1.0
O P:ALA365 2.4 20.5 1.0
OD2 P:ASP350 2.4 18.2 1.0
OD1 P:ASP368 2.4 18.8 1.0
O P:GLY346 2.4 18.0 1.0
O P:GLY348 2.4 16.4 1.0
OD2 P:ASP368 2.9 17.9 1.0
CG P:ASP368 3.0 18.7 1.0
CG P:ASP350 3.3 18.7 1.0
C P:GLY363 3.5 17.3 1.0
C P:GLY346 3.5 18.2 1.0
C P:ALA365 3.6 21.4 1.0
C P:GLY348 3.6 20.2 1.0
C P:GLY364 3.9 18.4 1.0
O P:GLY364 4.0 17.2 1.0
N P:GLY348 4.0 19.4 1.0
CB P:ASP350 4.0 16.5 1.0
N P:GLY346 4.1 16.2 1.0
C P:SER347 4.1 23.2 1.0
OD1 P:ASP350 4.1 19.9 1.0
N P:ALA365 4.2 16.3 1.0
N P:ASP350 4.2 17.5 1.0
CA P:GLY364 4.2 17.6 1.0
N P:GLY364 4.3 16.6 1.0
CA P:GLY366 4.3 18.7 1.0
CA P:SER347 4.4 18.3 1.0
N P:SER347 4.4 17.2 1.0
O P:HOH501 4.4 17.9 1.0
CA P:GLY348 4.4 20.8 1.0
CA P:GLY363 4.4 11.7 1.0
CA P:GLY346 4.4 17.4 1.0
CB P:ASP368 4.4 14.1 1.0
N P:GLY366 4.5 19.1 1.0
C P:GLY345 4.5 16.5 1.0
C P:GLY366 4.5 21.1 1.0
CA P:ALA365 4.6 17.2 1.0
O P:SER347 4.6 20.5 1.0
N P:ASN349 4.6 18.1 1.0
O P:GLY366 4.6 17.9 1.0
CA P:CA484 4.7 17.9 1.0
CA P:ASN349 4.8 18.9 1.0
CA P:GLY345 4.8 14.6 1.0
CA P:ASP350 4.8 15.9 1.0
C P:ASN349 4.9 20.8 1.0

Calcium binding site 4 out of 7 in 3hbu

Go back to Calcium Binding Sites List in 3hbu
Calcium binding site 4 out of 7 in the Prtc Methionine Mutants: M226H 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: M226H Desy within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca483

b:15.3
occ:1.00
O P:ASN355 2.3 16.4 1.0
O P:ALA374 2.4 16.6 1.0
O P:GLY372 2.4 14.1 1.0
OD1 P:ASN359 2.4 14.5 1.0
OD1 P:ASP377 2.4 15.3 1.0
O P:ALA357 2.4 13.6 1.0
OD2 P:ASP377 3.0 14.9 1.0
CG P:ASP377 3.0 15.2 1.0
CG P:ASN359 3.4 16.2 1.0
C P:GLY372 3.5 15.4 1.0
C P:ASN355 3.5 13.9 1.0
C P:ALA374 3.6 16.3 1.0
C P:ALA357 3.7 16.8 1.0
N P:ASN355 4.0 14.6 1.0
C P:GLY373 4.0 17.3 1.0
C P:SER356 4.1 15.9 1.0
O P:GLY373 4.1 17.1 1.0
N P:ALA357 4.1 14.6 1.0
N P:ASN359 4.2 12.8 1.0
N P:ALA374 4.2 16.1 1.0
CB P:ASN359 4.2 13.0 1.0
ND2 P:ASN359 4.3 13.5 1.0
CA P:GLY372 4.3 17.9 1.0
CA P:SER356 4.4 15.2 1.0
CA P:GLY375 4.4 14.5 1.0
N P:GLY373 4.4 16.5 1.0
CA P:ASN355 4.4 14.1 1.0
N P:SER356 4.4 16.2 1.0
CA P:GLY373 4.4 16.7 1.0
N P:GLY375 4.4 15.1 1.0
O P:SER356 4.5 17.2 1.0
CB P:ASP377 4.5 12.5 1.0
OD1 P:ASN355 4.5 15.5 1.0
CA P:ALA374 4.5 15.8 1.0
CA P:ALA357 4.6 16.6 1.0
CA P:CA489 4.6 16.8 1.0
N P:ASP358 4.6 14.2 1.0
CA P:ASP358 4.6 13.3 1.0
C P:GLY375 4.6 14.9 1.0
C P:GLY354 4.6 14.4 1.0
O P:GLY375 4.7 15.8 1.0
CA P:GLY354 4.8 13.8 1.0
C P:ASP358 4.8 16.4 1.0
CA P:ASN359 4.9 12.5 1.0

Calcium binding site 5 out of 7 in 3hbu

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Calcium binding site 5 out of 7 in the Prtc Methionine Mutants: M226H 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: M226H Desy within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca484

b:17.9
occ:1.00
OD2 P:ASP368 2.4 17.9 1.0
O P:GLY381 2.4 15.7 1.0
O P:GLY366 2.4 17.9 1.0
OD1 P:ASP386 2.4 19.1 1.0
O P:ALA383 2.4 21.7 1.0
O P:GLY364 2.4 17.2 1.0
OD2 P:ASP386 2.8 21.8 1.0
CG P:ASP386 2.9 17.4 1.0
CG P:ASP368 3.5 18.7 1.0
C P:GLY381 3.5 17.1 1.0
C P:GLY366 3.6 21.1 1.0
C P:ALA383 3.6 24.7 1.0
C P:GLY364 3.6 18.4 1.0
C P:ALA365 3.8 21.4 1.0
O P:ALA365 3.8 20.5 1.0
C P:GLY382 3.8 19.4 1.0
O P:GLY382 4.0 21.1 1.0
CA P:GLY382 4.1 13.4 1.0
CB P:ASP368 4.1 14.1 1.0
N P:GLY366 4.1 19.1 1.0
N P:ASP368 4.1 18.3 1.0
CA P:ALA365 4.2 17.2 1.0
N P:ALA383 4.2 19.3 1.0
N P:GLY382 4.2 14.9 1.0
CA P:GLY384 4.3 21.8 1.0
C P:GLY363 4.3 17.3 1.0
CA P:GLY366 4.4 18.7 1.0
N P:ALA365 4.4 16.3 1.0
N P:GLY384 4.4 24.7 1.0
N P:GLY364 4.4 16.6 1.0
CB P:ASP386 4.4 16.9 1.0
OD1 P:ASP368 4.4 18.8 1.0
N P:ASN367 4.5 19.4 1.0
CA P:GLY381 4.5 14.1 1.0
CA P:ALA383 4.6 20.6 1.0
O P:GLY363 4.6 16.4 1.0
C P:GLY384 4.6 21.4 1.0
CA P:GLY363 4.6 11.7 1.0
CA P:ASN367 4.7 18.9 1.0
CA P:GLY364 4.7 17.6 1.0
CA P:CA482 4.7 17.7 1.0
CA P:CA485 4.7 12.9 0.5
O P:GLY384 4.8 20.6 1.0
CA P:ASP368 4.8 17.1 1.0
C P:ASN367 4.9 18.6 1.0

Calcium binding site 6 out of 7 in 3hbu

Go back to Calcium Binding Sites List in 3hbu
Calcium binding site 6 out of 7 in the Prtc Methionine Mutants: M226H 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: M226H Desy within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca485

b:12.9
occ:0.50
OD2 P:ASP386 2.3 21.8 1.0
O P:GLY384 2.4 20.6 1.0
O P:HOH15 2.4 18.1 1.0
OE1 P:GLN408 2.4 29.2 1.0
OD1 P:ASP412 2.5 19.8 1.0
O P:GLY382 2.5 21.1 1.0
CG P:ASP412 3.3 20.6 1.0
OD2 P:ASP412 3.4 21.4 1.0
CG P:ASP386 3.4 17.4 1.0
C P:GLY384 3.5 21.4 1.0
CD P:GLN408 3.6 30.7 1.0
C P:GLY382 3.7 19.4 1.0
CB P:ASP386 3.8 16.9 1.0
N P:GLY384 3.9 24.7 1.0
C P:ALA383 4.0 24.7 1.0
N P:ASP386 4.0 20.5 1.0
O P:ALA383 4.2 21.7 1.0
CG P:GLN408 4.2 27.1 1.0
C P:GLY381 4.2 17.1 1.0
CA P:GLY384 4.3 21.8 1.0
N P:GLY382 4.3 14.9 1.0
OD1 P:ASP386 4.5 19.1 1.0
CA P:GLY381 4.5 14.1 1.0
CA P:ALA383 4.5 20.6 1.0
N P:ARG385 4.5 22.4 1.0
O P:GLY381 4.5 15.7 1.0
N P:ALA383 4.6 19.3 1.0
CA P:ASP386 4.6 18.1 1.0
CA P:GLY382 4.7 13.4 1.0
NE2 P:GLN408 4.7 25.4 1.0
CA P:ARG385 4.7 18.3 1.0
CA P:CA484 4.7 17.9 1.0
CG2 P:ILE411 4.7 22.1 1.0
CB P:ASP412 4.8 18.4 1.0
C P:ARG385 4.8 22.4 1.0
CB P:GLN408 4.8 22.3 1.0
O P:HOH603 4.9 23.6 1.0

Calcium binding site 7 out of 7 in 3hbu

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Calcium binding site 7 out of 7 in the Prtc Methionine Mutants: M226H 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: M226H Desy within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca489

b:16.8
occ:1.00
OD2 P:ASP377 2.3 14.9 1.0
O P:ASP395 2.3 17.7 1.0
O P:GLY373 2.4 17.1 1.0
O P:GLY375 2.4 15.8 1.0
O P:HOH904 2.5 15.7 1.0
OD1 P:ASP402 2.5 14.6 1.0
CG P:ASP402 3.4 16.9 1.0
CG P:ASP377 3.4 15.2 1.0
C P:ASP395 3.5 19.5 1.0
C P:GLY375 3.5 14.9 1.0
C P:GLY373 3.6 17.3 1.0
OD2 P:ASP402 3.6 16.4 1.0
O P:ALA374 3.8 16.6 1.0
C P:ALA374 3.8 16.3 1.0
N P:GLY375 4.1 15.1 1.0
N P:ASP377 4.1 14.4 1.0
CB P:ASP377 4.1 12.5 1.0
C P:GLY372 4.1 15.4 1.0
CA P:ASP395 4.2 16.6 1.0
N P:GLY373 4.2 16.5 1.0
CA P:ALA374 4.3 15.8 1.0
OD1 P:ASP377 4.3 15.3 1.0
CA P:GLY375 4.3 14.5 1.0
N P:ALA374 4.4 16.1 1.0
O P:GLY372 4.4 14.1 1.0
CB P:ASP395 4.4 16.7 1.0
N P:ALA376 4.5 13.6 1.0
CA P:GLY372 4.5 17.9 1.0
N P:SER396 4.5 14.9 1.0
CA P:GLY373 4.5 16.7 1.0
CA P:CA483 4.6 15.3 1.0
CA P:ALA376 4.6 13.4 1.0
CA P:SER396 4.7 14.3 1.0
CB P:ASP402 4.7 13.0 1.0
CA P:ASP377 4.8 12.8 1.0
C P:ALA376 4.8 15.3 1.0
O P:HOH8 4.8 18.3 1.0
CB P:SER396 4.8 16.8 1.0

Reference:

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
Page generated: Sat Dec 12 04:13:51 2020

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