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Calcium in PDB 1kap: Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif

Protein crystallography data

The structure of Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif, PDB code: 1kap was solved by U.Baumann, S.Wu, K.M.Flaherty, D.B.Mckay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.64
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 106.900, 106.900, 97.000, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / n/a

Other elements in 1kap:

The structure of Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif (pdb code 1kap). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif, PDB code: 1kap:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1kap

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Calcium binding site 1 out of 8 in the Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca614

b:8.1
occ:1.00
 HG1 P:THR257 1.6 0.0 1.0
OD1 P:ASP290 2.3 7.9 1.0
O P:GLY287 2.3 9.0 1.0
O P:ARG253 2.4 7.8 1.0
O P:GLY255 2.4 8.6 1.0
OG1 P:THR257 2.5 7.0 1.0
OD2 P:ASP285 2.5 7.4 1.0
OD1 P:ASP285 2.5 7.2 1.0
CG P:ASP285 2.8 7.8 1.0
CG P:ASP290 3.2 5.7 1.0
OD2 P:ASP290 3.4 7.7 1.0
CB P:THR257 3.4 6.6 1.0
C P:ARG253 3.5 8.5 1.0
C P:GLY287 3.5 9.3 1.0
C P:GLY255 3.6 8.1 1.0
N P:THR257 3.8 7.6 1.0
C P:THR254 4.1 9.1 1.0
N P:GLY255 4.1 8.5 1.0
CB P:ARG253 4.2 8.9 1.0
CA P:GLY288 4.3 8.3 1.0
CA P:THR257 4.3 7.5 1.0
N P:GLY287 4.3 9.0 1.0
CB P:ASP285 4.3 7.2 1.0
CA P:THR254 4.4 10.7 1.0
N P:GLY288 4.4 9.1 1.0
N P:THR254 4.4 8.9 1.0
C P:ASP256 4.4 7.9 1.0
O P:THR254 4.5 11.8 1.0
O P:HOH538 4.5 9.8 1.0
CB P:ASP290 4.5 6.5 1.0
CA P:ARG253 4.5 8.5 1.0
CA P:ASP256 4.5 8.0 1.0
CA P:GLY287 4.5 9.9 1.0
N P:ASP256 4.5 7.9 1.0
CA P:GLY255 4.5 8.6 1.0
C P:GLY288 4.6 7.7 1.0
CG2 P:THR257 4.6 8.1 1.0
O P:GLY288 4.9 9.0 1.0
OH P:TYR259 4.9 8.2 1.0

Calcium binding site 2 out of 8 in 1kap

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Calcium binding site 2 out of 8 in the Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca615

b:9.6
occ:1.00
 OD2 P:ASP290 2.4 7.7 1.0
O P:GLY288 2.4 9.0 1.0
O P:THR327 2.4 8.9 1.0
O P:HOH591 2.4 11.4 1.0
O P:HOH538 2.4 9.8 1.0
OE2 P:GLU329 2.5 10.6 1.0
OE1 P:GLU329 2.5 9.2 1.0
CD P:GLU329 2.9 10.2 1.0
CG P:ASP290 3.5 5.7 1.0
C P:GLY288 3.5 7.7 1.0
C P:THR327 3.6 8.2 1.0
N P:GLY288 4.2 9.1 1.0
C P:GLY287 4.2 9.3 1.0
N P:ASP290 4.2 7.3 1.0
CB P:ASP290 4.2 6.5 1.0
OD1 P:ASP290 4.3 7.9 1.0
O P:GLY287 4.3 9.0 1.0
CA P:GLY288 4.4 8.3 1.0
CG P:GLU329 4.4 9.8 1.0
N P:ASN289 4.5 8.5 1.0
O P:HOH612 4.5 11.3 1.0
N P:VAL328 4.5 8.1 1.0
CB P:THR327 4.5 10.5 1.0
CA P:VAL328 4.5 9.2 1.0
OD1 P:ASP285 4.5 7.2 1.0
CA P:THR327 4.5 8.7 1.0
CA P:ASN289 4.6 9.7 1.0
CA P:GLY287 4.7 9.9 1.0
CG2 P:THR327 4.8 10.4 1.0
N P:GLU329 4.8 8.2 1.0
C P:ASN289 4.8 7.7 1.0
O P:HOH716 4.9 46.7 1.0
CA P:ASP290 4.9 6.7 1.0
N P:THR327 4.9 8.2 1.0

Calcium binding site 3 out of 8 in 1kap

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Calcium binding site 3 out of 8 in the Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca616

b:11.2
occ:1.00
 O P:ALA353 2.3 13.4 1.0
O P:GLY351 2.3 11.6 1.0
O P:GLY334 2.3 11.3 1.0
OD1 P:ASP356 2.4 11.1 1.0
O P:GLY336 2.4 11.0 1.0
OD2 P:ASP338 2.4 9.7 1.0
OD2 P:ASP356 3.1 9.9 1.0
CG P:ASP356 3.1 9.5 1.0
CG P:ASP338 3.4 10.1 1.0
C P:GLY351 3.5 10.7 1.0
C P:GLY334 3.5 11.4 1.0
C P:ALA353 3.6 12.9 1.0
C P:GLY336 3.6 11.0 1.0
C P:GLY352 4.0 11.8 1.0
N P:GLY336 4.0 11.4 1.0
N P:GLY334 4.1 9.7 1.0
O P:GLY352 4.1 12.8 1.0
CB P:ASP338 4.1 9.8 1.0
C P:SER335 4.1 12.7 1.0
OD1 P:ASP338 4.1 13.1 1.0
N P:ASP338 4.1 11.9 1.0
N P:ALA353 4.2 12.4 1.0
CA P:GLY352 4.3 11.5 1.0
CA P:SER335 4.3 12.7 1.0
CA P:GLY354 4.4 11.9 1.0
N P:GLY352 4.4 11.1 1.0
N P:SER335 4.4 11.4 1.0
CA P:GLY351 4.4 9.5 1.0
CA P:GLY334 4.4 10.0 1.0
N P:GLY354 4.4 12.7 1.0
CA P:GLY336 4.5 10.9 1.0
O P:HOH540 4.5 9.9 1.0
CB P:ASP356 4.5 9.5 1.0
CA P:ALA353 4.5 12.1 1.0
C P:GLY333 4.5 8.8 1.0
N P:SER337 4.6 11.6 1.0
CA P:SER337 4.6 12.8 1.0
O P:SER335 4.7 14.7 1.0
C P:GLY354 4.7 11.1 1.0
O P:GLY354 4.7 11.4 1.0
CA P:CA620 4.8 11.8 1.0
CA P:ASP338 4.8 10.5 1.0
C P:SER337 4.8 13.0 1.0
CA P:GLY333 4.9 8.6 1.0

Calcium binding site 4 out of 8 in 1kap

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Calcium binding site 4 out of 8 in the Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca617

b:13.4
occ:1.00
 OD2 P:ASP374 2.3 12.5 1.0
O P:HOH608 2.3 20.3 1.0
O P:GLY370 2.4 12.7 1.0
O P:HOH548 2.4 17.1 1.0
O P:GLY372 2.4 13.3 1.0
OD1 P:ASP400 2.5 12.9 1.0
CG P:ASP400 3.3 11.0 1.0
OD2 P:ASP400 3.3 13.1 1.0
CG P:ASP374 3.4 11.5 1.0
C P:GLY370 3.6 13.1 1.0
C P:GLY372 3.6 11.6 1.0
C P:ALA371 3.9 13.3 1.0
CB P:ASP374 4.0 11.4 1.0
N P:GLY372 4.1 12.6 1.0
N P:ASP374 4.1 12.7 1.0
O P:ALA371 4.1 14.4 1.0
C P:GLY369 4.1 11.5 1.0
N P:GLY370 4.2 11.5 1.0
CA P:ALA371 4.3 13.7 1.0
OD1 P:ASP374 4.4 12.3 1.0
CA P:GLY372 4.4 12.4 1.0
O P:GLY369 4.4 12.8 1.0
N P:ALA371 4.4 13.7 1.0
CA P:GLY369 4.5 11.2 1.0
N P:ALA373 4.6 12.7 1.0
CA P:GLY370 4.6 12.1 1.0
OE1 P:GLN399 4.7 28.3 1.0
CB P:ASP400 4.7 11.8 1.0
CA P:ALA373 4.7 12.3 1.0
CA P:ASP374 4.7 11.6 1.0
CA P:CA620 4.8 11.8 1.0
C P:ALA373 4.8 13.6 1.0
O P:ASP394 4.9 13.0 1.0

Calcium binding site 5 out of 8 in 1kap

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Calcium binding site 5 out of 8 in the Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca618

b:9.6
occ:1.00
 O P:GLY360 2.3 8.8 1.0
O P:LEU362 2.4 11.1 1.0
OD1 P:ASP365 2.4 9.9 1.0
O P:ASN343 2.4 9.1 1.0
O P:VAL345 2.4 10.5 1.0
OD1 P:ASN347 2.4 7.4 1.0
CG P:ASP365 3.1 9.4 1.0
OD2 P:ASP365 3.1 8.0 1.0
CG P:ASN347 3.4 7.0 1.0
C P:GLY360 3.5 8.4 1.0
C P:ASN343 3.6 9.8 1.0
C P:LEU362 3.6 11.5 1.0
C P:VAL345 3.6 10.5 1.0
N P:ASN343 3.9 8.3 1.0
C P:GLY361 3.9 9.9 1.0
N P:VAL345 4.1 10.5 1.0
N P:LEU362 4.1 10.3 1.0
O P:GLY361 4.1 10.1 1.0
N P:ASN347 4.1 9.2 1.0
C P:ASP344 4.2 12.1 1.0
CB P:ASN347 4.2 7.7 1.0
ND2 P:ASN347 4.2 7.6 1.0
CA P:GLY361 4.3 9.3 1.0
N P:GLY361 4.3 8.3 1.0
CA P:GLY360 4.4 8.6 1.0
CA P:ASN343 4.4 8.8 1.0
CA P:LEU362 4.5 11.3 1.0
N P:ASP344 4.5 11.0 1.0
CA P:VAL345 4.5 10.3 1.0
N P:ALA346 4.5 10.7 1.0
OD1 P:ASN343 4.5 9.0 1.0
N P:GLY363 4.5 11.5 1.0
CA P:ALA346 4.5 10.2 1.0
C P:GLY342 4.5 8.1 1.0
CA P:ASP344 4.5 12.8 1.0
CB P:ASP365 4.5 8.7 1.0
CA P:GLY363 4.6 11.0 1.0
O P:ASP344 4.6 13.9 1.0
C P:ALA346 4.7 10.5 1.0
CA P:GLY342 4.7 8.4 1.0
CA P:CA619 4.7 10.9 1.0
O P:GLY363 4.7 12.3 1.0
C P:GLY363 4.8 10.9 1.0
CA P:ASN347 4.9 9.1 1.0

Calcium binding site 6 out of 8 in 1kap

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Calcium binding site 6 out of 8 in the Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca619

b:10.9
occ:1.00
 OD2 P:ASP365 2.2 8.0 1.0
O P:GLU383 2.3 12.2 1.0
O P:GLY361 2.4 10.1 1.0
O P:HOH544 2.4 9.8 1.0
O P:GLY363 2.4 12.3 1.0
OD1 P:ASP390 2.4 11.8 1.0
CG P:ASP390 3.3 11.7 1.0
CG P:ASP365 3.4 9.4 1.0
OD2 P:ASP390 3.4 12.8 1.0
C P:GLU383 3.5 12.6 1.0
C P:GLY361 3.6 9.9 1.0
C P:GLY363 3.6 10.9 1.0
C P:LEU362 3.9 11.5 1.0
O P:LEU362 3.9 11.1 1.0
N P:ASP365 4.0 9.7 1.0
C P:GLY360 4.1 8.4 1.0
N P:GLY363 4.1 11.5 1.0
CB P:ASP365 4.1 8.7 1.0
CA P:GLU383 4.2 12.1 1.0
N P:GLY361 4.2 8.3 1.0
OD1 P:ASP365 4.3 9.9 1.0
CA P:LEU362 4.3 11.3 1.0
CB P:GLU383 4.3 11.4 1.0
O P:GLY360 4.4 8.8 1.0
N P:LEU362 4.4 10.3 1.0
CA P:GLY363 4.4 11.0 1.0
CA P:GLY360 4.4 8.6 1.0
CA P:GLY361 4.5 9.3 1.0
N P:SER384 4.5 11.7 1.0
N P:ALA364 4.5 10.7 1.0
CA P:ALA364 4.6 10.7 1.0
CA P:CA618 4.7 9.6 1.0
CA P:SER384 4.7 11.9 1.0
CB P:ASP390 4.7 10.1 1.0
CA P:ASP365 4.7 10.5 1.0
O P:HOH545 4.8 10.1 1.0
C P:ALA364 4.8 11.0 1.0
CB P:SER384 4.9 10.9 1.0

Calcium binding site 7 out of 8 in 1kap

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Calcium binding site 7 out of 8 in the Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca620

b:11.8
occ:1.00
 O P:GLY369 2.3 12.8 1.0
O P:GLY352 2.3 12.8 1.0
OD2 P:ASP356 2.3 9.9 1.0
O P:ALA371 2.4 14.4 1.0
OD1 P:ASP374 2.4 12.3 1.0
O P:GLY354 2.4 11.4 1.0
OD2 P:ASP374 3.1 12.5 1.0
CG P:ASP374 3.1 11.5 1.0
C P:GLY369 3.5 11.5 1.0
CG P:ASP356 3.5 9.5 1.0
C P:GLY352 3.5 11.8 1.0
C P:ALA371 3.5 13.3 1.0
C P:GLY354 3.6 11.1 1.0
C P:ALA353 3.8 12.9 1.0
C P:GLY370 3.8 13.1 1.0
O P:ALA353 3.9 13.4 1.0
N P:GLY354 4.0 12.7 1.0
O P:GLY370 4.0 12.7 1.0
N P:ALA371 4.0 13.7 1.0
N P:ASP356 4.1 10.3 1.0
CA P:ALA353 4.1 12.1 1.0
CB P:ASP356 4.2 9.5 1.0
CA P:GLY370 4.2 12.1 1.0
N P:GLY370 4.2 11.5 1.0
C P:GLY351 4.3 10.7 1.0
N P:ALA353 4.3 12.4 1.0
N P:GLY352 4.3 11.1 1.0
CA P:GLY354 4.3 11.9 1.0
OD1 P:ASP356 4.4 11.1 1.0
CA P:ALA371 4.4 13.7 1.0
N P:GLY372 4.5 12.6 1.0
CA P:GLY369 4.5 11.2 1.0
CA P:GLY372 4.5 12.4 1.0
O P:GLY351 4.5 11.6 1.0
CB P:ASP374 4.5 11.4 1.0
N P:ASN355 4.6 11.4 1.0
CA P:GLY352 4.6 11.5 1.0
CA P:GLY351 4.6 9.5 1.0
C P:GLY372 4.7 11.6 1.0
O P:GLY372 4.7 13.3 1.0
CA P:ASN355 4.7 12.6 1.0
CA P:CA616 4.8 11.2 1.0
CA P:CA617 4.8 13.4 1.0
CA P:ASP356 4.8 10.3 1.0
C P:ASN355 4.9 12.1 1.0

Calcium binding site 8 out of 8 in 1kap

Go back to Calcium Binding Sites List in 1kap
Calcium binding site 8 out of 8 in the Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca621

b:24.0
occ:1.00
 HG P:SER448 1.9 0.0 1.0
OG P:SER448 2.2 23.9 1.0
O P:HIS452 2.2 20.5 1.0
OD1 P:ASP450 2.3 20.4 1.0
OD1 P:ASP446 2.3 18.0 1.0
OD2 P:ASP454 2.6 19.9 1.0
OD1 P:ASP454 2.6 24.1 1.0
O P:HOH692 2.8 45.6 1.0
CG P:ASP454 2.9 20.8 1.0
CG P:ASP450 3.3 22.0 1.0
C P:HIS452 3.4 20.2 1.0
CG P:ASP446 3.5 18.5 1.0
CB P:SER448 3.5 21.7 1.0
N P:SER448 3.8 22.0 1.0
OD2 P:ASP450 3.8 22.3 1.0
N P:HIS452 4.0 21.3 1.0
CA P:HIS452 4.1 22.2 1.0
CA P:SER448 4.1 23.1 1.0
CB P:HIS452 4.1 25.1 1.0
N P:ASP450 4.2 21.8 1.0
N P:GLY449 4.2 23.6 1.0
CB P:ASP454 4.2 19.4 1.0
OD2 P:ASP446 4.3 19.6 1.0
N P:ASP454 4.3 18.6 1.0
CA P:ASP446 4.3 17.7 1.0
CB P:ASP446 4.4 17.2 1.0
C P:ALA453 4.4 19.0 1.0
N P:PHE447 4.4 19.0 1.0
N P:ALA453 4.4 20.3 1.0
C P:SER448 4.5 23.6 1.0
CB P:ASP450 4.5 21.2 1.0
C P:ASP446 4.6 18.0 1.0
CA P:ASP454 4.7 18.3 1.0
CA P:ALA453 4.7 19.4 1.0
O P:ALA453 4.8 20.3 1.0
CA P:ASP450 4.8 20.7 1.0
N P:ALA451 4.9 19.5 1.0
C P:PHE447 5.0 21.7 1.0
C P:ASP450 5.0 19.8 1.0

Reference:

U.Baumann, S.Wu, K.M.Flaherty, D.B.Mckay. Three-Dimensional Structure of the Alkaline Protease of Pseudomonas Aeruginosa: A Two-Domain Protein with A Calcium Binding Parallel Beta Roll Motif. Embo J. V. 12 3357 1993.
ISSN: ISSN 0261-4189
PubMed: 8253063
Page generated: Thu Jul 11 11:19:31 2024

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