Calcium in PDB 3u1r: Structure Analysis of A New Psychrophilic Marine Protease

The structure of Structure Analysis of A New Psychrophilic Marine Protease, PDB code: 3u1r was solved by S.-C.Zhang, M.Sun, L.Tang, Q.-H.Wang, J.-H.Hao, Y.Han, X.-J.Hu, M.Zhou, S.-X.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.907, 75.195, 115.416, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 21.2

The structure of Structure Analysis of A New Psychrophilic Marine Protease also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Structure Analysis of A New Psychrophilic Marine Protease (pdb code 3u1r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure Analysis of A New Psychrophilic Marine Protease, PDB code: 3u1r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Structure Analysis of A New Psychrophilic Marine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure Analysis of A New Psychrophilic Marine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca700 b:25.2 occ:1.00 OD1 A:ASN74 2.3 24.0 1.0 ND2 A:ASN68 2.3 21.6 1.0 O A:VAL72 2.3 24.4 1.0 OD1 A:ASP70 2.4 24.9 1.0 OD2 A:ASP131 2.4 22.5 1.0 OD1 A:ASP66 2.4 33.3 1.0 CG A:ASP131 3.1 23.9 1.0 OD1 A:ASP131 3.2 21.5 1.0 CG A:ASP70 3.2 29.2 1.0 CG A:ASP66 3.4 36.5 1.0 CG A:ASN68 3.5 27.3 1.0 CG A:ASN74 3.5 24.0 1.0 OD2 A:ASP70 3.5 25.9 1.0 C A:VAL72 3.6 26.9 1.0 N A:ASN74 3.8 20.1 1.0 OD1 A:ASN68 3.9 29.6 1.0 CA A:ASP66 4.2 30.6 1.0 OD2 A:ASP66 4.2 34.0 1.0 N A:ASP70 4.2 31.1 1.0 CB A:ASP66 4.2 30.9 1.0 N A:ASN68 4.2 34.2 1.0 CA A:ILE73 4.3 21.6 1.0 N A:VAL72 4.3 30.2 1.0 CB A:ASN74 4.3 20.1 1.0 N A:ILE73 4.4 24.9 1.0 CB A:ASP70 4.4 27.9 1.0 ND2 A:ASN74 4.4 22.3 1.0 C A:ILE73 4.5 22.9 1.0 CB A:ASP131 4.5 21.0 1.0 C A:ASP66 4.5 32.3 1.0 N A:LEU67 4.5 28.7 1.0 CG2 A:VAL72 4.5 28.1 1.0 CA A:VAL72 4.5 28.1 1.0 N A:GLY69 4.6 34.0 1.0 CA A:ASN74 4.7 22.8 1.0 CB A:ASN68 4.7 28.7 1.0 N A:GLY71 4.7 27.4 1.0 CA A:ASP70 4.7 27.9 1.0 CA A:ASN68 4.8 34.7 1.0 C A:ASN68 4.9 32.9 1.0 C A:ASP70 5.0 29.5 1.0

Calcium binding site 2 out of 8 in the Structure Analysis of A New Psychrophilic Marine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure Analysis of A New Psychrophilic Marine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:21.6 occ:1.00 O A:ARG267 2.1 21.0 1.0 OD1 A:ASP304 2.3 22.6 1.0 O A:GLY301 2.3 23.2 1.0 O A:GLY269 2.3 23.0 1.0 OD2 A:ASP299 2.4 24.6 1.0 OG1 A:THR271 2.4 19.8 1.0 OD1 A:ASP299 2.5 19.0 1.0 CG A:ASP299 2.8 20.8 1.0 CG A:ASP304 3.1 23.9 1.0 C A:ARG267 3.4 21.2 1.0 OD2 A:ASP304 3.4 23.7 1.0 CB A:THR271 3.5 17.8 1.0 C A:GLY269 3.6 21.9 1.0 C A:GLY301 3.6 24.8 1.0 N A:THR271 3.8 19.5 1.0 C A:ALA268 4.1 27.3 1.0 N A:GLY269 4.1 21.5 1.0 C A:ASP270 4.2 23.1 1.0 N A:ALA268 4.2 20.1 1.0 N A:GLY301 4.2 23.6 1.0 CB A:ARG267 4.3 20.1 1.0 CA A:ALA268 4.3 21.9 1.0 CA A:THR271 4.3 17.4 1.0 CB A:ASP299 4.4 18.2 1.0 CA A:ARG267 4.4 22.4 1.0 CA A:ASP270 4.4 23.3 1.0 CB A:ASP304 4.4 20.8 1.0 N A:ASP270 4.4 22.3 1.0 O A:HOH868 4.4 24.8 1.0 CA A:GLY302 4.4 23.8 1.0 N A:GLY302 4.5 24.4 1.0 CA A:GLY301 4.5 24.8 1.0 O A:ALA268 4.5 25.3 1.0 CA A:GLY269 4.5 25.4 1.0 O A:HOH802 4.6 21.1 1.0 CG2 A:THR271 4.6 17.2 1.0 C A:GLY302 4.7 22.9 1.0 N A:GLY300 4.8 21.1 1.0 OH A:TYR273 4.9 18.4 1.0 O A:GLY302 4.9 23.5 1.0 O A:ASP270 5.0 24.8 1.0

Calcium binding site 3 out of 8 in the Structure Analysis of A New Psychrophilic Marine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure Analysis of A New Psychrophilic Marine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:23.3 occ:1.00 O A:THR341 2.3 23.3 1.0 OD2 A:ASP304 2.4 23.7 1.0 O A:GLY302 2.4 23.5 1.0 O A:HOH815 2.4 21.9 1.0 O A:HOH802 2.4 21.1 1.0 OE2 A:GLU343 2.5 27.1 1.0 OE1 A:GLU343 2.6 25.1 1.0 CD A:GLU343 2.9 26.8 1.0 CG A:ASP304 3.5 23.9 1.0 C A:GLY302 3.5 22.9 1.0 C A:THR341 3.5 22.4 1.0 N A:GLY302 4.0 24.4 1.0 C A:GLY301 4.0 24.8 1.0 CB A:ASP304 4.2 20.8 1.0 N A:ASP304 4.2 22.8 1.0 O A:GLY301 4.3 23.2 1.0 CA A:GLY302 4.3 23.8 1.0 N A:ILE342 4.4 21.3 1.0 CA A:ILE342 4.4 21.0 1.0 N A:ASN303 4.4 24.1 1.0 OD1 A:ASP304 4.4 22.6 1.0 O A:HOH923 4.4 30.9 1.0 CG A:GLU343 4.5 25.0 1.0 CB A:THR341 4.5 26.0 1.0 CA A:THR341 4.5 24.3 1.0 OD1 A:ASP299 4.5 19.0 1.0 CA A:GLY301 4.5 24.8 1.0 CA A:ASN303 4.5 23.8 1.0 O A:HOH825 4.6 36.9 1.0 N A:GLU343 4.8 19.9 1.0 C A:ASN303 4.9 24.8 1.0 N A:THR341 4.9 23.4 1.0 CA A:ASP304 4.9 22.2 1.0 CD1 A:ILE342 4.9 19.4 1.0

Calcium binding site 4 out of 8 in the Structure Analysis of A New Psychrophilic Marine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure Analysis of A New Psychrophilic Marine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:24.0 occ:1.00 O A:ALA367 2.3 23.8 1.0 O A:GLY348 2.3 26.7 1.0 O A:GLY350 2.4 21.4 1.0 OD2 A:ASP352 2.4 25.2 1.0 O A:GLY365 2.4 22.1 1.0 OD1 A:ASP370 2.4 21.9 1.0 OD2 A:ASP370 2.9 20.6 1.0 CG A:ASP370 3.0 21.4 1.0 CG A:ASP352 3.3 23.5 1.0 C A:GLY348 3.5 29.5 1.0 C A:GLY365 3.5 21.7 1.0 C A:GLY350 3.6 23.7 1.0 C A:ALA367 3.6 26.2 1.0 N A:GLY350 3.9 23.9 1.0 C A:GLY366 3.9 25.1 1.0 C A:SER349 4.1 28.6 1.0 N A:GLY348 4.1 25.9 1.0 CB A:ASP352 4.1 22.6 1.0 O A:GLY366 4.1 28.0 1.0 OD1 A:ASP352 4.2 22.0 1.0 N A:ALA367 4.2 23.0 1.0 N A:ASP352 4.3 23.2 1.0 CA A:GLY366 4.3 21.7 1.0 N A:SER349 4.4 26.8 1.0 CA A:SER349 4.4 28.1 1.0 N A:GLY366 4.4 22.2 1.0 CA A:GLY350 4.4 23.8 1.0 CA A:GLY348 4.4 24.3 1.0 CA A:GLY365 4.4 23.3 1.0 N A:GLY368 4.5 24.0 1.0 CB A:ASP370 4.5 22.1 1.0 CA A:GLY368 4.5 21.9 1.0 O A:HOH827 4.5 26.9 1.0 CA A:ALA367 4.5 25.1 1.0 O A:SER349 4.6 28.3 1.0 C A:GLY347 4.6 23.8 1.0 N A:ASN351 4.6 24.8 1.0 C A:GLY368 4.6 23.6 1.0 O A:GLY368 4.6 22.5 1.0 CA A:CA704 4.8 23.7 1.0 CA A:ASN351 4.8 25.1 1.0 CA A:GLY347 4.8 22.3 1.0 CA A:ASP352 4.9 20.4 1.0 C A:ASN351 5.0 23.4 1.0

Calcium binding site 5 out of 8 in the Structure Analysis of A New Psychrophilic Marine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure Analysis of A New Psychrophilic Marine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:23.7 occ:1.00 O A:GLY368 2.3 22.5 1.0 O A:GLY383 2.3 22.6 1.0 O A:SER385 2.3 25.4 1.0 OD2 A:ASP370 2.4 20.6 1.0 OD1 A:ASP388 2.4 22.5 1.0 O A:GLY366 2.4 28.0 1.0 OD2 A:ASP388 2.9 24.3 1.0 CG A:ASP388 3.0 26.2 1.0 CG A:ASP370 3.4 21.4 1.0 C A:GLY383 3.4 24.8 1.0 C A:GLY368 3.5 23.6 1.0 C A:SER385 3.6 27.0 1.0 C A:GLY366 3.6 25.1 1.0 C A:GLY384 3.9 25.9 1.0 O A:ALA367 3.9 23.8 1.0 C A:ALA367 3.9 26.2 1.0 N A:ASP370 4.0 21.0 1.0 CB A:ASP370 4.1 22.1 1.0 O A:GLY384 4.1 22.9 1.0 N A:SER385 4.1 27.2 1.0 CA A:GLY384 4.2 25.7 1.0 N A:GLY384 4.3 25.5 1.0 N A:GLY368 4.3 24.0 1.0 CA A:ALA367 4.3 25.1 1.0 N A:GLY366 4.3 22.2 1.0 C A:GLY365 4.3 21.7 1.0 N A:ASN369 4.4 23.9 1.0 CA A:GLY383 4.4 23.2 1.0 OD1 A:ASP370 4.5 21.9 1.0 N A:ALA367 4.5 23.0 1.0 CB A:ASP388 4.5 27.7 1.0 CA A:SER385 4.5 27.8 1.0 CA A:GLY368 4.5 21.9 1.0 CA A:ASN369 4.5 23.8 1.0 N A:GLY386 4.5 26.1 1.0 O A:GLY365 4.5 22.1 1.0 CA A:GLY386 4.6 25.9 1.0 CA A:GLY366 4.6 21.7 1.0 C A:ASN369 4.7 22.6 1.0 CA A:ASP370 4.7 22.2 1.0 CA A:CA703 4.8 24.0 1.0 CA A:GLY365 4.8 23.3 1.0 C A:GLY386 4.8 26.9 1.0 O A:GLY386 5.0 28.0 1.0 CA A:CA707 5.0 43.4 1.0

Calcium binding site 6 out of 8 in the Structure Analysis of A New Psychrophilic Marine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure Analysis of A New Psychrophilic Marine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:22.7 occ:1.00 O A:GLY376 2.3 23.8 1.0 OD1 A:ASN361 2.3 24.1 1.0 O A:ALA359 2.3 22.9 1.0 O A:GLY374 2.3 20.7 1.0 OD1 A:ASP379 2.4 24.9 1.0 O A:ASN357 2.5 24.8 1.0 OD2 A:ASP379 3.0 23.5 1.0 CG A:ASP379 3.0 24.6 1.0 CG A:ASN361 3.4 26.4 1.0 C A:GLY374 3.5 23.9 1.0 C A:GLY376 3.5 25.2 1.0 C A:ALA359 3.6 25.4 1.0 C A:ASN357 3.6 23.2 1.0 N A:ASN357 3.9 21.9 1.0 C A:GLY375 3.9 25.2 1.0 N A:GLY376 4.0 21.5 1.0 N A:ASN361 4.1 25.1 1.0 O A:GLY375 4.1 21.7 1.0 C A:ALA358 4.1 27.1 1.0 N A:ALA359 4.2 24.6 1.0 CB A:ASN361 4.3 22.7 1.0 CA A:GLY376 4.3 23.4 1.0 OD1 A:ASN357 4.3 21.2 1.0 ND2 A:ASN361 4.3 23.3 1.0 N A:GLY375 4.3 25.3 1.0 CA A:ASN357 4.4 22.4 1.0 CA A:GLY374 4.4 20.1 1.0 O A:ALA358 4.4 26.8 1.0 CA A:GLY375 4.4 21.3 1.0 N A:SER360 4.4 29.1 1.0 CA A:SER360 4.5 28.0 1.0 N A:ALA358 4.5 23.8 1.0 CB A:ASP379 4.5 23.1 1.0 CA A:ALA359 4.5 25.2 1.0 CA A:CA706 4.5 22.1 1.0 CA A:ALA358 4.5 26.0 1.0 O A:GLY377 4.5 22.9 1.0 N A:GLY377 4.5 24.4 1.0 C A:GLY356 4.6 22.9 1.0 C A:SER360 4.7 27.9 1.0 CA A:GLY377 4.7 22.3 1.0 CA A:GLY356 4.7 21.8 1.0 C A:GLY377 4.8 25.7 1.0 CA A:ASN361 4.8 22.1 1.0

Calcium binding site 7 out of 8 in the Structure Analysis of A New Psychrophilic Marine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure Analysis of A New Psychrophilic Marine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:22.1 occ:1.00 O A:GLY377 2.2 22.9 1.0 O A:HOH929 2.3 20.6 1.0 OD2 A:ASP379 2.3 23.5 1.0 O A:GLY375 2.3 21.7 1.0 O A:ASP397 2.4 23.8 1.0 OD1 A:ASP404 2.5 21.8 1.0 CG A:ASP379 3.4 24.6 1.0 C A:GLY377 3.4 25.7 1.0 CG A:ASP404 3.4 24.7 1.0 C A:GLY375 3.5 25.2 1.0 C A:ASP397 3.5 26.1 1.0 OD2 A:ASP404 3.7 25.4 1.0 O A:GLY376 3.7 23.8 1.0 C A:GLY376 3.8 25.2 1.0 N A:GLY377 4.0 24.4 1.0 C A:GLY374 4.0 23.9 1.0 N A:ASP379 4.0 26.0 1.0 CA A:ASP397 4.1 23.5 1.0 CB A:ASP379 4.1 23.1 1.0 N A:GLY375 4.1 25.3 1.0 O A:GLY374 4.2 20.7 1.0 CA A:GLY377 4.3 22.3 1.0 OD1 A:ASP379 4.3 24.9 1.0 CA A:GLY374 4.3 20.1 1.0 N A:GLY376 4.3 21.5 1.0 CA A:GLY376 4.4 23.4 1.0 CB A:ASP397 4.4 23.7 1.0 N A:ALA378 4.4 25.4 1.0 O A:HOH853 4.4 32.3 1.0 CA A:GLY375 4.4 21.3 1.0 CA A:CA705 4.5 22.7 1.0 N A:SER398 4.6 22.6 1.0 CA A:ALA378 4.6 27.6 1.0 C A:ALA378 4.6 28.4 1.0 CA A:ASP379 4.8 25.7 1.0 CA A:SER398 4.8 20.4 1.0 CB A:ASP404 4.9 23.0 1.0 O A:HOH918 4.9 26.0 1.0 CB A:SER398 5.0 18.2 1.0

Calcium binding site 8 out of 8 in the Structure Analysis of A New Psychrophilic Marine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure Analysis of A New Psychrophilic Marine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:43.4 occ:1.00 OE1 A:GLN410 2.2 47.3 1.0 O A:HOH803 2.4 25.6 1.0 OD2 A:ASP388 2.4 24.3 1.0 O A:GLY384 2.6 22.9 1.0 OD1 A:ASP414 2.7 26.1 1.0 O A:GLY386 2.7 28.0 1.0 OD2 A:ASP414 3.3 30.8 1.0 CG A:ASP414 3.4 30.1 1.0 CD A:GLN410 3.4 51.7 1.0 CG A:ASP388 3.5 26.2 1.0 C A:GLY384 3.8 25.9 1.0 C A:GLY386 3.8 26.9 1.0 CB A:ASP388 4.0 27.7 1.0 C A:SER385 4.0 27.0 1.0 O A:SER385 4.1 25.4 1.0 N A:ASP388 4.2 24.1 1.0 N A:GLY386 4.3 26.1 1.0 NE2 A:GLN410 4.3 54.4 1.0 C A:GLY383 4.3 24.8 1.0 CA A:SER385 4.4 27.8 1.0 CG A:GLN410 4.4 40.1 1.0 N A:GLY384 4.4 25.5 1.0 CA A:GLY383 4.5 23.2 1.0 OD1 A:ASP388 4.5 22.5 1.0 N A:SER385 4.6 27.2 1.0 CD2 A:LEU413 4.7 32.2 1.0 CA A:GLY386 4.7 25.9 1.0 CB A:GLN410 4.7 32.6 1.0 N A:SER387 4.7 26.9 1.0 O A:GLY383 4.8 22.6 1.0 CA A:SER387 4.8 27.4 1.0 CA A:GLY384 4.8 25.7 1.0 CA A:ASP388 4.8 26.7 1.0 O A:ASP408 4.8 27.1 1.0 CB A:ASP414 4.9 29.7 1.0 C A:SER387 4.9 26.2 1.0 CG A:LEU413 5.0 37.4 1.0 CA A:CA704 5.0 23.7 1.0

S.C.Zhang, M.Sun, T.Li, Q.H.Wang, J.H.Hao, Y.Han, X.J.Hu, M.Zhou, S.X.Lin. Structure Analysis of A New Psychrophilic Marine Protease. Plos One V. 6 26939 2011.
ISSN: ESSN 1932-6203
PubMed: 22132082
DOI: 10.1371/JOURNAL.PONE.0026939