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Calcium in PDB 1jiw: Crystal Structure of the Apr-Aprin Complex

Protein crystallography data

The structure of Crystal Structure of the Apr-Aprin Complex, PDB code: 1jiw was solved by T.Hege, R.E.Feltzer, R.D.Gray, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.93 / 1.74
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 75.627, 118.432, 91.995, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.4

Other elements in 1jiw:

The structure of Crystal Structure of the Apr-Aprin Complex also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Apr-Aprin Complex (pdb code 1jiw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Apr-Aprin Complex, PDB code: 1jiw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1jiw

Go back to Calcium Binding Sites List in 1jiw
Calcium binding site 1 out of 8 in the Crystal Structure of the Apr-Aprin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Apr-Aprin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca482

b:13.4
occ:1.00
OD1 P:ASP290 2.2 12.8 1.0
O P:GLY287 2.3 14.8 1.0
O P:ARG253 2.4 12.9 1.0
O P:GLY255 2.4 14.1 1.0
OD2 P:ASP285 2.5 11.7 1.0
OD1 P:ASP285 2.5 13.2 1.0
OG1 P:THR257 2.5 12.2 1.0
CG P:ASP285 2.8 13.7 1.0
CG P:ASP290 3.0 11.7 1.0
OD2 P:ASP290 3.2 14.5 1.0
CB P:THR257 3.5 11.2 1.0
C P:GLY287 3.5 15.7 1.0
C P:ARG253 3.5 13.4 1.0
C P:GLY255 3.6 16.7 1.0
N P:THR257 3.7 13.7 1.0
N P:GLY255 4.0 15.2 1.0
C P:THR254 4.0 14.8 1.0
CA P:GLY288 4.2 14.8 1.0
CA P:THR254 4.3 13.0 1.0
CA P:THR257 4.3 12.9 1.0
CB P:ASP285 4.3 13.4 1.0
CB P:ARG253 4.3 12.8 1.0
N P:GLY288 4.3 15.7 1.0
N P:GLY287 4.3 14.1 1.0
N P:THR254 4.3 14.0 1.0
CB P:ASP290 4.4 12.8 1.0
O P:HOH491 4.4 26.0 1.0
CA P:GLY255 4.4 15.6 1.0
O P:THR254 4.4 14.8 1.0
CA P:GLY287 4.5 17.1 1.0
CA P:ARG253 4.5 13.3 1.0
N P:ASP256 4.5 15.4 1.0
C P:GLY288 4.6 15.6 1.0
CA P:ASP256 4.6 14.9 1.0
C P:ASP256 4.6 14.9 1.0
CG2 P:THR257 4.7 9.4 1.0
O P:GLY288 4.8 15.5 1.0
OH P:TYR259 5.0 13.3 1.0

Calcium binding site 2 out of 8 in 1jiw

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Calcium binding site 2 out of 8 in the Crystal Structure of the Apr-Aprin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Apr-Aprin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca483

b:16.6
occ:1.00
OD2 P:ASP290 2.4 14.5 1.0
O P:GLY288 2.4 15.5 1.0
O P:THR327 2.4 12.3 1.0
O P:HOH491 2.4 26.0 1.0
O P:HOH520 2.5 19.6 1.0
OE1 P:GLU329 2.5 13.2 1.0
OE2 P:GLU329 2.5 16.4 1.0
CD P:GLU329 2.9 16.2 1.0
CG P:ASP290 3.5 11.7 1.0
C P:GLY288 3.5 15.6 1.0
C P:THR327 3.6 14.2 1.0
N P:ASP290 4.1 12.7 1.0
N P:GLY288 4.1 15.7 1.0
C P:GLY287 4.2 15.7 1.0
CB P:ASP290 4.2 12.8 1.0
O P:GLY287 4.3 14.8 1.0
OD1 P:ASP290 4.3 12.8 1.0
CG P:GLU329 4.4 15.2 1.0
CA P:GLY288 4.4 14.8 1.0
N P:ASN289 4.4 14.9 1.0
CB P:THR327 4.4 15.4 1.0
O P:HOH574 4.5 13.2 1.0
CA P:VAL328 4.5 13.5 1.0
N P:VAL328 4.5 14.8 1.0
OD1 P:ASP285 4.5 13.2 1.0
CA P:ASN289 4.5 15.5 1.0
CA P:THR327 4.6 14.5 1.0
N P:GLU329 4.6 12.6 1.0
CG2 P:THR327 4.6 16.3 1.0
CA P:GLY287 4.7 17.1 1.0
O P:HOH871 4.7 39.0 1.0
C P:ASN289 4.8 14.5 1.0
CA P:ASP290 4.8 11.8 1.0
O P:HOH698 4.9 29.5 1.0
N P:THR327 5.0 13.0 1.0
C P:VAL328 5.0 14.2 1.0

Calcium binding site 3 out of 8 in 1jiw

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Calcium binding site 3 out of 8 in the Crystal Structure of the Apr-Aprin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Apr-Aprin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca484

b:16.2
occ:1.00
O P:GLY351 2.3 15.7 1.0
OD1 P:ASP356 2.3 13.4 1.0
O P:GLY336 2.3 17.0 1.0
O P:ALA353 2.4 17.6 1.0
O P:GLY334 2.4 13.8 1.0
OD2 P:ASP338 2.5 14.3 1.0
CG P:ASP356 3.1 15.8 1.0
OD2 P:ASP356 3.1 13.6 1.0
C P:GLY351 3.4 16.2 1.0
CG P:ASP338 3.4 14.3 1.0
C P:GLY334 3.5 12.9 1.0
C P:GLY336 3.6 14.5 1.0
C P:ALA353 3.6 19.2 1.0
C P:GLY352 3.9 16.5 1.0
N P:GLY334 3.9 13.6 1.0
N P:GLY336 4.0 13.5 1.0
O P:GLY352 4.0 16.1 1.0
N P:ASP338 4.1 13.2 1.0
N P:ALA353 4.1 16.7 1.0
C P:SER335 4.2 17.1 1.0
CB P:ASP338 4.2 12.5 1.0
OD1 P:ASP338 4.2 14.2 1.0
CA P:GLY352 4.2 17.0 1.0
N P:GLY352 4.2 15.9 1.0
CA P:GLY351 4.3 16.2 1.0
CA P:GLY334 4.3 15.5 1.0
N P:SER335 4.4 13.9 1.0
O P:HOH506 4.4 13.1 1.0
CA P:GLY336 4.4 14.0 1.0
CA P:GLY354 4.4 16.1 1.0
CA P:SER335 4.4 15.1 1.0
C P:GLY333 4.4 13.4 1.0
N P:GLY354 4.5 16.8 1.0
CB P:ASP356 4.5 14.4 1.0
N P:SER337 4.5 15.2 1.0
CA P:ALA353 4.5 17.5 1.0
CA P:SER337 4.5 14.5 1.0
O P:SER335 4.7 17.4 1.0
CA P:GLY333 4.7 12.6 1.0
C P:SER337 4.7 13.6 1.0
O P:GLY354 4.8 15.3 1.0
C P:GLY354 4.8 15.2 1.0
CA P:ASP338 4.8 11.4 1.0
CA P:CA485 4.9 16.0 1.0

Calcium binding site 4 out of 8 in 1jiw

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Calcium binding site 4 out of 8 in the Crystal Structure of the Apr-Aprin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Apr-Aprin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca485

b:16.0
occ:1.00
O P:GLY369 2.3 16.1 1.0
OD2 P:ASP356 2.4 13.6 1.0
O P:ALA371 2.4 15.6 1.0
O P:GLY354 2.4 15.3 1.0
OD1 P:ASP374 2.4 15.1 1.0
O P:GLY352 2.4 16.1 1.0
OD2 P:ASP374 2.7 15.8 1.0
CG P:ASP374 2.9 15.7 1.0
C P:GLY369 3.4 17.3 1.0
CG P:ASP356 3.5 15.8 1.0
C P:ALA371 3.6 19.0 1.0
C P:GLY354 3.6 15.2 1.0
C P:GLY352 3.6 16.5 1.0
C P:ALA353 3.9 19.2 1.0
C P:GLY370 3.9 17.6 1.0
O P:ALA353 4.0 17.6 1.0
N P:GLY354 4.0 16.8 1.0
N P:ALA371 4.0 16.8 1.0
O P:GLY370 4.1 17.6 1.0
N P:ASP356 4.1 15.5 1.0
CB P:ASP356 4.1 14.4 1.0
CA P:GLY370 4.2 17.9 1.0
N P:GLY370 4.3 18.2 1.0
CA P:ALA353 4.3 17.5 1.0
N P:GLY352 4.3 15.9 1.0
C P:GLY351 4.3 16.2 1.0
CA P:GLY354 4.3 16.1 1.0
CB P:ASP374 4.4 15.2 1.0
CA P:GLY369 4.4 14.1 1.0
OD1 P:ASP356 4.4 13.4 1.0
N P:ALA353 4.4 16.7 1.0
N P:GLY372 4.4 17.6 1.0
CA P:GLY372 4.4 18.3 1.0
CA P:ALA371 4.5 17.8 1.0
CA P:CA486 4.5 28.1 1.0
N P:ASN355 4.6 16.5 1.0
O P:GLY351 4.6 15.7 1.0
CA P:GLY351 4.6 16.2 1.0
CA P:GLY352 4.6 17.0 1.0
C P:GLY372 4.7 16.8 1.0
CA P:ASN355 4.7 16.1 1.0
O P:GLY372 4.7 17.4 1.0
CA P:ASP356 4.8 14.9 1.0
CA P:CA484 4.9 16.2 1.0
C P:ASN355 4.9 15.5 1.0

Calcium binding site 5 out of 8 in 1jiw

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Calcium binding site 5 out of 8 in the Crystal Structure of the Apr-Aprin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Apr-Aprin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca486

b:28.1
occ:1.00
O P:HOH492 2.3 39.7 1.0
OD2 P:ASP374 2.3 15.8 1.0
O P:GLY370 2.4 17.6 1.0
O P:GLY372 2.4 17.4 1.0
O P:HOH533 2.5 17.1 1.0
OD1 P:ASP400 2.6 16.1 1.0
CG P:ASP374 3.4 15.7 1.0
CG P:ASP400 3.4 16.4 1.0
OD2 P:ASP400 3.5 16.7 1.0
C P:GLY370 3.5 17.6 1.0
C P:GLY372 3.5 16.8 1.0
O P:HOH603 3.8 20.8 1.0
C P:ALA371 3.8 19.0 1.0
CB P:ASP374 3.8 15.2 1.0
N P:GLY372 4.0 17.6 1.0
C P:GLY369 4.0 17.3 1.0
N P:ASP374 4.0 16.2 1.0
O P:ALA371 4.0 15.6 1.0
N P:GLY370 4.1 18.2 1.0
O P:GLY369 4.2 16.1 1.0
CA P:GLY369 4.2 14.1 1.0
OE1 P:GLN399 4.3 25.1 1.0
CA P:GLY372 4.3 18.3 1.0
CA P:ALA371 4.3 17.8 1.0
N P:ALA371 4.4 16.8 1.0
OD1 P:ASP374 4.4 15.1 1.0
CA P:CA485 4.5 16.0 1.0
CA P:GLY370 4.5 17.9 1.0
N P:ALA373 4.5 18.5 1.0
CD P:GLN399 4.6 24.1 1.0
CA P:ASP374 4.6 15.1 1.0
CA P:ALA373 4.7 16.9 1.0
C P:ALA373 4.8 15.7 1.0
CB P:ASP400 4.8 16.3 1.0
CG P:GLN399 4.8 23.2 1.0

Calcium binding site 6 out of 8 in 1jiw

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Calcium binding site 6 out of 8 in the Crystal Structure of the Apr-Aprin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Apr-Aprin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca487

b:13.8
occ:1.00
O P:ASN343 2.3 15.2 1.0
OD1 P:ASN347 2.3 13.9 1.0
O P:LEU362 2.3 16.0 1.0
O P:GLY360 2.3 12.8 1.0
O P:VAL345 2.4 14.0 1.0
OD1 P:ASP365 2.4 15.3 1.0
OD2 P:ASP365 3.1 11.6 1.0
CG P:ASP365 3.1 13.1 1.0
CG P:ASN347 3.4 13.8 1.0
C P:ASN343 3.5 13.8 1.0
C P:GLY360 3.5 11.5 1.0
C P:VAL345 3.5 13.8 1.0
C P:LEU362 3.6 16.8 1.0
N P:ASN343 3.9 11.8 1.0
C P:GLY361 4.0 12.0 1.0
N P:LEU362 4.0 13.9 1.0
N P:VAL345 4.1 15.3 1.0
N P:ASN347 4.1 13.2 1.0
C P:ASP344 4.1 15.9 1.0
ND2 P:ASN347 4.2 15.0 1.0
O P:GLY361 4.2 15.5 1.0
CB P:ASN347 4.3 14.8 1.0
CA P:ASN343 4.3 13.1 1.0
CA P:GLY361 4.4 11.3 1.0
N P:GLY361 4.4 11.1 1.0
OD1 P:ASN343 4.4 14.0 1.0
CA P:GLY360 4.4 11.9 1.0
N P:ASP344 4.4 12.8 1.0
CA P:LEU362 4.4 15.1 1.0
CA P:VAL345 4.4 13.9 1.0
N P:ALA346 4.4 14.7 1.0
CA P:ALA346 4.5 14.4 1.0
N P:GLY363 4.5 14.9 1.0
CA P:ASP344 4.5 16.1 1.0
O P:ASP344 4.5 15.5 1.0
C P:GLY342 4.5 12.6 1.0
CA P:GLY363 4.6 15.4 1.0
CB P:ASP365 4.6 12.3 1.0
C P:ALA346 4.6 16.5 1.0
O P:GLY363 4.7 14.5 1.0
CA P:GLY342 4.7 11.3 1.0
CA P:CA488 4.7 14.5 1.0
C P:GLY363 4.8 14.9 1.0
CA P:ASN347 4.8 13.9 1.0

Calcium binding site 7 out of 8 in 1jiw

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Calcium binding site 7 out of 8 in the Crystal Structure of the Apr-Aprin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Apr-Aprin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca488

b:14.5
occ:1.00
O P:HOH495 2.3 12.7 1.0
OD2 P:ASP365 2.3 11.6 1.0
O P:GLU383 2.3 14.7 1.0
O P:GLY363 2.3 14.5 1.0
O P:GLY361 2.4 15.5 1.0
OD1 P:ASP390 2.5 16.4 1.0
CG P:ASP390 3.3 14.2 1.0
OD2 P:ASP390 3.3 18.5 1.0
CG P:ASP365 3.4 13.1 1.0
C P:GLU383 3.5 15.9 1.0
C P:GLY361 3.5 12.0 1.0
C P:GLY363 3.5 14.9 1.0
C P:LEU362 3.9 16.8 1.0
O P:LEU362 3.9 16.0 1.0
N P:ASP365 4.0 14.2 1.0
C P:GLY360 4.1 11.5 1.0
N P:GLY363 4.1 14.9 1.0
N P:GLY361 4.1 11.1 1.0
CB P:ASP365 4.1 12.3 1.0
CA P:GLU383 4.2 15.5 1.0
CB P:GLU383 4.3 16.6 1.0
CA P:LEU362 4.3 15.1 1.0
O P:GLY360 4.4 12.8 1.0
OD1 P:ASP365 4.4 15.3 1.0
N P:LEU362 4.4 13.9 1.0
CA P:GLY363 4.4 15.4 1.0
CA P:GLY360 4.4 11.9 1.0
CA P:GLY361 4.5 11.3 1.0
N P:ALA364 4.5 14.8 1.0
N P:SER384 4.5 17.2 1.0
CA P:ALA364 4.6 14.3 1.0
CB P:ASP390 4.7 15.3 1.0
CA P:CA487 4.7 13.8 1.0
O P:HOH505 4.8 14.6 1.0
CA P:SER384 4.8 18.4 1.0
CA P:ASP365 4.8 15.2 1.0
C P:ALA364 4.8 17.7 1.0
CB P:SER384 4.9 17.4 1.0

Calcium binding site 8 out of 8 in 1jiw

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Calcium binding site 8 out of 8 in the Crystal Structure of the Apr-Aprin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Apr-Aprin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca489

b:1.0
occ:1.00
O P:HIS452 2.2 28.4 1.0
OD2 P:ASP454 2.3 30.5 1.0
OD1 P:ASP450 2.3 38.6 1.0
OG P:SER448 2.4 28.4 1.0
OD1 P:ASP446 2.5 27.1 1.0
CG P:ASP454 3.2 32.8 1.0
CG P:ASP450 3.3 36.8 1.0
C P:HIS452 3.4 31.0 1.0
CB P:SER448 3.6 29.7 1.0
CG P:ASP446 3.6 27.4 1.0
CB P:ASP454 3.8 30.4 1.0
OD2 P:ASP450 3.9 38.1 1.0
N P:SER448 3.9 30.0 1.0
N P:HIS452 4.1 33.9 1.0
CA P:HIS452 4.1 33.6 1.0
N P:ASP454 4.1 29.3 1.0
CA P:ASP446 4.2 25.1 1.0
OD1 P:ASP454 4.2 34.5 1.0
CB P:HIS452 4.2 37.6 1.0
CA P:SER448 4.3 30.5 1.0
N P:ASP450 4.3 36.7 1.0
CB P:ASP446 4.3 26.6 1.0
N P:GLY449 4.3 32.5 1.0
C P:ALA453 4.3 31.0 1.0
N P:PHE447 4.4 25.7 1.0
N P:ALA453 4.5 30.4 1.0
CB P:ASP450 4.5 36.9 1.0
C P:ASP446 4.5 25.6 1.0
OD2 P:ASP446 4.5 31.0 1.0
CA P:ASP454 4.5 29.7 1.0
CA P:ALA453 4.7 31.2 1.0
C P:SER448 4.7 31.4 1.0
O P:ALA453 4.8 32.5 1.0
CA P:ASP450 4.8 36.4 1.0

Reference:

T.Hege, R.E.Feltzer, R.D.Gray, U.Baumann. Crystal Structure of A Complex Between Pseudomonas Aeruginosa Alkaline Protease and Its Cognate Inhibitor: Inhibition By A Zinc-NH2 Coordinative Bond J.Biol.Chem. V. 276 35087 2001.
ISSN: ISSN 0021-9258
PubMed: 11445573
DOI: 10.1074/JBC.M104020200
Page generated: Sat Dec 12 03:02:20 2020

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