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Calcium in PDB 1k7i: Prtc From Erwinia Chrysanthemi: Y228F Mutant

Protein crystallography data

The structure of Prtc From Erwinia Chrysanthemi: Y228F Mutant, PDB code: 1k7i was solved by U.Baumann, T.Hege, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.98 / 1.59
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.967, 101.967, 122.298, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 20.4

Other elements in 1k7i:

The structure of Prtc From Erwinia Chrysanthemi: Y228F Mutant also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Prtc From Erwinia Chrysanthemi: Y228F Mutant (pdb code 1k7i). 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 From Erwinia Chrysanthemi: Y228F Mutant, PDB code: 1k7i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1k7i

Go back to Calcium Binding Sites List in 1k7i
Calcium binding site 1 out of 7 in the Prtc From Erwinia Chrysanthemi: Y228F Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Prtc From Erwinia Chrysanthemi: Y228F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca480

b:13.3
occ:1.00
O A:GLY299 2.4 14.7 1.0
OD2 A:ASP302 2.4 14.8 1.0
O A:ARG265 2.4 15.3 1.0
O A:GLY267 2.5 15.0 1.0
OD2 A:ASP297 2.6 14.6 1.0
OD1 A:ASP297 2.6 14.5 1.0
OG A:SER269 2.6 14.9 1.0
CG A:ASP297 2.9 15.4 1.0
CG A:ASP302 3.2 13.7 1.0
OD1 A:ASP302 3.3 13.8 1.0
CB A:SER269 3.5 13.8 1.0
C A:ARG265 3.6 14.2 1.0
C A:GLY299 3.6 15.0 1.0
C A:GLY267 3.7 13.6 1.0
N A:SER269 3.7 14.3 1.0
N A:GLY267 4.0 14.8 1.0
C A:THR266 4.0 14.1 1.0
CB A:ARG265 4.3 14.8 1.0
N A:GLY299 4.3 14.7 1.0
CA A:SER269 4.3 12.8 1.0
CA A:THR266 4.3 14.8 1.0
O A:HOH653 4.3 13.6 1.0
CA A:GLY300 4.3 14.5 1.0
N A:THR266 4.4 13.8 1.0
CB A:ASP297 4.4 14.3 1.0
N A:GLY300 4.4 14.9 1.0
O A:THR266 4.5 15.0 1.0
CA A:GLY267 4.5 14.4 1.0
O A:HOH489 4.5 9.5 1.0
CB A:ASP302 4.5 14.5 1.0
CA A:ARG265 4.5 13.9 1.0
CA A:GLY299 4.5 14.3 1.0
C A:ASP268 4.5 15.3 1.0
N A:ASP268 4.6 14.0 1.0
CA A:ASP268 4.6 13.1 1.0
C A:GLY300 4.6 12.3 1.0
OH A:TYR271 4.8 14.0 1.0
O A:GLY300 4.9 16.0 1.0

Calcium binding site 2 out of 7 in 1k7i

Go back to Calcium Binding Sites List in 1k7i
Calcium binding site 2 out of 7 in the Prtc From Erwinia Chrysanthemi: Y228F Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Prtc From Erwinia Chrysanthemi: Y228F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca481

b:13.1
occ:1.00
O A:GLY300 2.4 16.0 1.0
O A:THR339 2.4 14.9 1.0
OD1 A:ASP302 2.5 13.8 1.0
O A:HOH653 2.5 13.6 1.0
O A:HOH797 2.6 16.6 1.0
OE2 A:GLU341 2.6 14.7 1.0
OE1 A:GLU341 2.6 15.8 1.0
CD A:GLU341 3.0 16.2 1.0
CG A:ASP302 3.5 13.7 1.0
C A:GLY300 3.6 12.3 1.0
C A:THR339 3.6 14.2 1.0
N A:ASP302 4.1 12.7 1.0
C A:GLY299 4.3 15.0 1.0
N A:GLY300 4.3 14.9 1.0
CB A:ASP302 4.3 14.5 1.0
CB A:THR339 4.3 14.5 1.0
OD2 A:ASP302 4.4 14.8 1.0
O A:GLY299 4.4 14.7 1.0
CA A:THR301 4.4 13.7 1.0
N A:THR301 4.4 12.6 1.0
O A:HOH511 4.4 16.2 1.0
OD1 A:ASP297 4.5 14.5 1.0
CA A:GLY300 4.5 14.5 1.0
CG A:GLU341 4.5 16.5 1.0
CA A:THR339 4.5 13.9 1.0
N A:ILE340 4.5 14.9 1.0
CA A:ILE340 4.6 14.4 1.0
CG2 A:THR339 4.6 16.0 1.0
C A:THR301 4.7 14.1 1.0
N A:GLU341 4.8 14.4 1.0
N A:THR339 4.9 14.9 1.0
CA A:GLY299 4.9 14.3 1.0
O A:HOH554 4.9 17.4 1.0
CA A:ASP302 4.9 13.2 1.0

Calcium binding site 3 out of 7 in 1k7i

Go back to Calcium Binding Sites List in 1k7i
Calcium binding site 3 out of 7 in the Prtc From Erwinia Chrysanthemi: Y228F Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Prtc From Erwinia Chrysanthemi: Y228F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca482

b:17.4
occ:1.00
O A:GLY363 2.4 16.9 1.0
O A:ALA365 2.5 19.4 1.0
O A:GLY348 2.5 20.5 1.0
O A:GLY346 2.5 20.2 1.0
OD1 A:ASP368 2.5 18.7 1.0
OD2 A:ASP350 2.6 18.9 1.0
OD2 A:ASP368 2.8 18.7 1.0
CG A:ASP368 3.0 18.2 1.0
CG A:ASP350 3.4 18.7 1.0
C A:GLY363 3.5 17.6 1.0
C A:GLY346 3.6 19.1 1.0
C A:ALA365 3.7 20.4 1.0
C A:GLY348 3.7 21.4 1.0
C A:GLY364 3.9 19.0 1.0
N A:GLY348 4.0 20.8 1.0
O A:GLY364 4.0 18.2 1.0
N A:GLY346 4.1 16.6 1.0
C A:SER347 4.1 20.4 1.0
N A:ASP350 4.1 19.6 1.0
OD1 A:ASP350 4.1 18.7 1.0
CB A:ASP350 4.2 18.2 1.0
N A:ALA365 4.2 17.9 1.0
CA A:GLY364 4.3 17.4 1.0
N A:GLY364 4.3 17.4 1.0
CA A:SER347 4.3 20.1 1.0
N A:SER347 4.4 19.1 1.0
CA A:GLY366 4.4 21.2 1.0
CA A:GLY346 4.4 19.2 1.0
CA A:GLY348 4.4 20.8 1.0
O A:HOH514 4.4 19.7 1.0
CA A:GLY363 4.5 17.4 1.0
CB A:ASP368 4.5 17.5 1.0
N A:GLY366 4.5 20.5 1.0
O A:SER347 4.5 20.4 1.0
C A:GLY345 4.6 17.0 1.0
CA A:ALA365 4.6 19.7 1.0
C A:GLY366 4.6 21.3 1.0
N A:ASN349 4.6 20.3 1.0
O A:GLY366 4.7 21.0 1.0
CA A:CA484 4.7 18.4 1.0
CA A:ASN349 4.8 19.8 1.0
CA A:ASP350 4.8 17.8 1.0
CA A:GLY345 4.9 15.4 1.0
C A:ASN349 4.9 21.0 1.0

Calcium binding site 4 out of 7 in 1k7i

Go back to Calcium Binding Sites List in 1k7i
Calcium binding site 4 out of 7 in the Prtc From Erwinia Chrysanthemi: Y228F Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Prtc From Erwinia Chrysanthemi: Y228F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca483

b:14.2
occ:1.00
O A:ASN355 2.4 15.3 1.0
O A:ALA374 2.4 17.7 1.0
O A:ALA357 2.5 16.1 1.0
OD1 A:ASN359 2.5 14.9 1.0
O A:GLY372 2.5 17.0 1.0
OD1 A:ASP377 2.5 15.9 1.0
OD2 A:ASP377 2.9 16.7 1.0
CG A:ASP377 3.0 14.4 1.0
CG A:ASN359 3.4 15.8 1.0
C A:GLY372 3.5 15.9 1.0
C A:ASN355 3.6 16.2 1.0
C A:ALA374 3.6 17.4 1.0
C A:ALA357 3.7 16.2 1.0
C A:GLY373 4.0 17.1 1.0
N A:ASN355 4.0 15.5 1.0
N A:ASN359 4.1 14.1 1.0
C A:SER356 4.1 17.1 1.0
N A:ALA357 4.2 16.0 1.0
N A:ALA374 4.2 17.5 1.0
O A:GLY373 4.2 17.1 1.0
CB A:ASN359 4.2 14.3 1.0
ND2 A:ASN359 4.3 15.0 1.0
CA A:GLY372 4.4 16.2 1.0
CA A:GLY373 4.4 16.4 1.0
N A:GLY373 4.4 15.6 1.0
CA A:SER356 4.4 17.5 1.0
CA A:GLY375 4.4 15.3 1.0
O A:SER356 4.5 18.1 1.0
N A:SER356 4.5 15.9 1.0
CA A:ASN355 4.5 15.6 1.0
N A:GLY375 4.5 17.6 1.0
CB A:ASP377 4.5 13.7 1.0
OD1 A:ASN355 4.5 16.1 1.0
CA A:ALA374 4.6 16.8 1.0
CA A:CA487 4.6 15.6 1.0
CA A:ALA357 4.6 16.1 1.0
CA A:ASP358 4.6 16.9 1.0
N A:ASP358 4.6 16.6 1.0
C A:GLY354 4.7 15.9 1.0
C A:GLY375 4.7 15.4 1.0
O A:GLY375 4.7 15.7 1.0
C A:ASP358 4.8 16.3 1.0
CA A:ASN359 4.8 13.7 1.0
CA A:GLY354 4.8 15.9 1.0

Calcium binding site 5 out of 7 in 1k7i

Go back to Calcium Binding Sites List in 1k7i
Calcium binding site 5 out of 7 in the Prtc From Erwinia Chrysanthemi: Y228F Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Prtc From Erwinia Chrysanthemi: Y228F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca484

b:18.4
occ:1.00
O A:GLY381 2.5 17.7 1.0
O A:GLY366 2.5 21.0 1.0
O A:GLY364 2.5 18.2 1.0
O A:ALA383 2.5 23.8 1.0
OD2 A:ASP368 2.6 18.7 1.0
OD1 A:ASP386 2.6 20.8 1.0
OD2 A:ASP386 2.8 21.8 1.0
CG A:ASP386 3.0 18.1 1.0
C A:GLY381 3.5 19.6 1.0
C A:ALA383 3.6 22.9 1.0
C A:GLY366 3.6 21.3 1.0
CG A:ASP368 3.6 18.2 1.0
C A:GLY364 3.7 19.0 1.0
C A:GLY382 3.8 18.6 1.0
C A:ALA365 3.8 20.4 1.0
O A:GLY382 3.9 19.0 1.0
O A:ALA365 3.9 19.4 1.0
N A:GLY366 4.1 20.5 1.0
CA A:GLY382 4.1 18.1 1.0
N A:ALA383 4.1 20.6 1.0
N A:ASP368 4.2 20.2 1.0
N A:GLY382 4.2 18.6 1.0
CB A:ASP368 4.2 17.5 1.0
CA A:ALA365 4.2 19.7 1.0
C A:GLY363 4.3 17.6 1.0
CA A:GLY384 4.3 21.6 1.0
N A:GLY364 4.4 17.4 1.0
N A:GLY384 4.4 23.5 1.0
CA A:GLY366 4.4 21.2 1.0
N A:ALA365 4.4 17.9 1.0
CB A:ASP386 4.5 19.4 1.0
CA A:GLY381 4.5 19.5 1.0
CA A:ALA383 4.6 21.0 1.0
N A:ASN367 4.6 20.4 1.0
O A:GLY363 4.6 16.9 1.0
OD1 A:ASP368 4.6 18.7 1.0
CA A:ASN367 4.7 19.7 1.0
CA A:GLY364 4.7 17.4 1.0
C A:GLY384 4.7 23.9 1.0
CA A:GLY363 4.7 17.4 1.0
CA A:CA485 4.7 21.5 1.0
CA A:CA482 4.7 17.4 1.0
CA A:ASP368 4.9 19.1 1.0
C A:ASN367 4.9 20.7 1.0
O A:GLY384 4.9 24.4 1.0

Calcium binding site 6 out of 7 in 1k7i

Go back to Calcium Binding Sites List in 1k7i
Calcium binding site 6 out of 7 in the Prtc From Erwinia Chrysanthemi: Y228F Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Prtc From Erwinia Chrysanthemi: Y228F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca485

b:21.5
occ:1.00
OD2 A:ASP386 2.5 21.8 1.0
O A:GLY382 2.5 19.0 1.0
O A:GLY384 2.6 24.4 1.0
OE1 A:GLN408 2.6 27.2 1.0
OD1 A:ASP412 2.6 21.9 1.0
O A:HOH505 2.6 18.9 1.0
OD2 A:ASP412 3.3 22.1 1.0
CG A:ASP412 3.3 23.1 1.0
CG A:ASP386 3.6 18.1 1.0
C A:GLY384 3.6 23.9 1.0
C A:GLY382 3.7 18.6 1.0
CD A:GLN408 3.7 27.1 1.0
N A:GLY384 3.9 23.5 1.0
CB A:ASP386 4.0 19.4 1.0
C A:ALA383 4.0 22.9 1.0
N A:ASP386 4.1 21.5 1.0
C A:GLY381 4.2 19.6 1.0
N A:GLY382 4.2 18.6 1.0
CA A:GLY384 4.3 21.6 1.0
O A:ALA383 4.4 23.8 1.0
CG A:GLN408 4.4 25.1 1.0
CA A:ALA383 4.4 21.0 1.0
CA A:GLY381 4.5 19.5 1.0
N A:ALA383 4.6 20.6 1.0
N A:ARG385 4.6 23.5 1.0
O A:GLY381 4.6 17.7 1.0
OD1 A:ASP386 4.6 20.8 1.0
CG2 A:ILE411 4.6 23.9 1.0
CA A:GLY382 4.7 18.1 1.0
CB A:GLN408 4.7 22.9 1.0
CA A:CA484 4.7 18.4 1.0
CA A:ASP386 4.7 21.4 1.0
CB A:ASP412 4.8 21.4 1.0
CA A:ARG385 4.8 23.9 1.0
NE2 A:GLN408 4.8 28.9 1.0
C A:ARG385 4.9 24.1 1.0

Calcium binding site 7 out of 7 in 1k7i

Go back to Calcium Binding Sites List in 1k7i
Calcium binding site 7 out of 7 in the Prtc From Erwinia Chrysanthemi: Y228F Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Prtc From Erwinia Chrysanthemi: Y228F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca487

b:15.6
occ:1.00
O A:ASP395 2.4 18.5 1.0
O A:GLY373 2.5 17.1 1.0
OD2 A:ASP377 2.5 16.7 1.0
O A:GLY375 2.5 15.7 1.0
OD1 A:ASP402 2.5 18.1 1.0
O A:HOH534 2.6 18.3 1.0
CG A:ASP402 3.4 17.6 1.0
CG A:ASP377 3.5 14.4 1.0
C A:ASP395 3.5 19.2 1.0
OD2 A:ASP402 3.6 18.4 1.0
C A:GLY373 3.6 17.1 1.0
C A:GLY375 3.6 15.4 1.0
O A:ALA374 3.8 17.7 1.0
C A:ALA374 3.8 17.4 1.0
N A:ASP377 4.1 13.4 1.0
N A:GLY375 4.1 17.6 1.0
C A:GLY372 4.1 15.9 1.0
CB A:ASP377 4.1 13.7 1.0
N A:GLY373 4.2 15.6 1.0
CA A:ASP395 4.2 17.5 1.0
CA A:ALA374 4.3 16.8 1.0
N A:ALA374 4.4 17.5 1.0
CA A:GLY375 4.4 15.3 1.0
CA A:GLY372 4.4 16.2 1.0
O A:GLY372 4.4 17.0 1.0
OD1 A:ASP377 4.4 15.9 1.0
CA A:GLY373 4.5 16.4 1.0
N A:SER396 4.6 16.8 1.0
N A:ALA376 4.6 14.3 1.0
CA A:CA483 4.6 14.2 1.0
CB A:ASP395 4.6 18.3 1.0
CB A:ASP402 4.7 15.3 1.0
CA A:ALA376 4.7 13.8 1.0
CA A:SER396 4.7 16.9 1.0
O A:HOH496 4.7 17.7 1.0
CA A:ASP377 4.8 13.6 1.0
C A:ALA376 4.8 15.1 1.0
CB A:SER396 4.9 17.2 1.0
O A:HOH564 5.0 23.8 1.0

Reference:

T.Hege, U.Baumann. Protease C of Erwinia Chrysanthemi: the Crystal Structure and Role of Amino Acids Y228 and E189 J.Mol.Biol. V. 314 187 2001.
ISSN: ISSN 0022-2836
PubMed: 11718553
DOI: 10.1006/JMBI.2001.5124
Page generated: Sat Dec 12 03:03:18 2020

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