Calcium in PDB 3trp: Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin

The structure of Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin, PDB code: 3trp was solved by E.J.Sanchez, K.M.Lewis, G.R.Munske, M.S.Nissen, C.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.86 / 1.88
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	59.122, 144.863, 110.376, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.8

The structure of Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin (pdb code 3trp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin, PDB code: 3trp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin


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 Recombinant Rabbit Skeletal Calsequestrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca358 b:58.5 occ:1.00 O A:HOH435 2.2 30.0 1.0 O A:HOH440 2.3 40.9 1.0 O A:ASP210 2.4 25.0 1.0 OE2 A:GLU217 2.5 27.2 1.0 OE1 A:GLU217 2.6 42.4 1.0 O A:PRO212 2.6 21.6 1.0 O A:HOH436 2.7 30.0 1.0 CD A:GLU217 2.9 36.0 1.0 C A:ASP210 3.6 24.9 1.0 C A:PRO212 3.7 20.6 1.0 CB A:ASP210 4.0 25.8 1.0 O A:HOH736 4.1 43.5 1.0 CA A:ASN213 4.1 22.0 1.0 ND2 A:ASN213 4.1 22.6 1.0 N A:ASN213 4.4 20.3 1.0 CG A:GLU217 4.4 24.1 1.0 CA A:ASP210 4.5 25.9 1.0 C A:LYS211 4.5 29.6 1.0 N A:LYS211 4.6 18.3 1.0 N A:SER214 4.6 19.8 1.0 N A:PRO212 4.6 23.8 1.0 CA A:LYS211 4.6 17.9 1.0 O A:HOH794 4.7 51.1 1.0 O A:LYS211 4.8 28.1 1.0 O A:HOH543 4.8 30.9 1.0 CA A:PRO212 4.8 19.1 1.0 C A:ASN213 4.9 21.1 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin


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 Recombinant Rabbit Skeletal Calsequestrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca359 b:47.8 occ:1.00 OD1 A:ASN17 2.4 41.2 1.0 O A:VAL18 2.4 25.3 1.0 OD1 A:ASP80 2.4 29.8 1.0 O A:LEU74 2.5 20.8 1.0 O A:HOH367 2.7 37.9 1.0 N A:VAL18 3.2 26.6 1.0 C A:VAL18 3.3 31.9 1.0 CG A:ASP80 3.3 36.8 1.0 C A:LEU74 3.5 24.4 1.0 CG A:ASN17 3.5 42.3 1.0 NZ A:LYS79 3.6 41.2 1.0 C A:ASN17 3.6 30.9 1.0 OD2 A:ASP80 3.7 31.6 1.0 CA A:VAL18 3.8 21.3 1.0 CA A:VAL75 3.8 25.3 1.0 N A:ASP76 3.9 25.4 1.0 CA A:ASN17 3.9 26.6 1.0 N A:VAL75 4.1 21.9 1.0 CB A:ASN17 4.4 38.5 1.0 N A:ASN19 4.4 27.6 1.0 O A:ASN17 4.4 28.4 1.0 C A:VAL75 4.4 31.7 1.0 CE A:LYS79 4.4 52.9 1.0 CB A:VAL18 4.4 22.7 1.0 CB A:ASP80 4.5 30.0 1.0 ND2 A:ASN17 4.5 50.2 1.0 CB A:LEU74 4.6 22.4 1.0 CA A:LEU74 4.6 13.5 1.0 CB A:ASP76 4.7 32.2 1.0 CA A:ASN19 4.8 28.0 1.0 CB A:ASN19 4.9 27.0 1.0 CA A:ASP76 4.9 28.5 1.0 CB A:VAL75 5.0 22.0 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin


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 Recombinant Rabbit Skeletal Calsequestrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca360 b:43.6 occ:1.00 OG1 A:THR277 2.4 36.4 1.0 OE2 A:GLU199 2.4 24.0 1.0 OG1 A:THR229 2.4 22.0 1.0 OE1 A:GLU199 2.5 25.3 1.0 O A:THR277 2.5 28.0 1.0 CD A:GLU199 2.8 26.0 1.0 O A:HOH605 3.0 46.2 1.0 O A:HOH732 3.0 43.1 1.0 C A:THR277 3.3 33.8 1.0 CA A:THR277 3.4 28.6 1.0 CB A:THR277 3.5 30.8 1.0 CB A:THR229 3.6 20.2 1.0 N A:THR229 3.9 19.3 1.0 O A:HOH709 4.0 23.6 1.0 O A:HOH508 4.1 30.8 1.0 O A:HOH670 4.2 43.7 1.0 CG A:GLU199 4.3 14.2 1.0 CA A:THR229 4.3 17.0 1.0 CG2 A:THR277 4.5 32.2 1.0 O A:HOH378 4.5 31.2 1.0 N A:ASP278 4.6 27.8 1.0 O A:HOH624 4.7 39.9 1.0 CG2 A:THR229 4.8 22.1 1.0 CE A:MET202 4.8 33.1 1.0 N A:THR277 4.9 24.6 1.0 O A:HOH700 4.9 17.7 1.0 C A:SER228 4.9 22.6 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin


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 Recombinant Rabbit Skeletal Calsequestrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca361 b:61.7 occ:1.00 O A:THR189 2.2 27.7 1.0 O A:HOH792 2.4 43.2 1.0 O A:HOH499 2.4 35.7 1.0 OG1 A:THR189 2.5 34.4 1.0 O A:HOH472 2.6 29.4 1.0 O A:HOH593 3.1 33.8 1.0 CB A:THR189 3.1 35.3 1.0 C A:THR189 3.2 21.4 1.0 CA A:THR189 3.7 21.6 1.0 O A:HOH523 3.9 32.6 1.0 OD2 A:ASP196 3.9 21.0 1.0 O A:HOH622 3.9 48.6 1.0 O A:LEU188 4.1 29.6 1.0 N A:LEU190 4.2 21.4 1.0 O A:HOH379 4.3 39.4 1.0 OE1 A:GLU194 4.3 24.7 1.0 O A:HOH606 4.4 39.1 1.0 CG2 A:THR189 4.5 33.7 1.0 CA A:LEU190 4.6 23.9 1.0 OD1 A:ASP196 4.7 19.6 1.0 CG A:ASP196 4.7 21.0 1.0 N A:THR189 4.8 25.7 1.0 C A:LEU188 4.9 32.7 1.0 OG1 A:THR207 5.0 22.6 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin


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 Recombinant Rabbit Skeletal Calsequestrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca362 b:36.0 occ:0.50 OE1 A:GLU109 2.6 26.5 1.0 O A:ASP291 2.6 15.7 1.0 O A:HOH368 3.1 31.5 1.0 O A:HOH679 3.1 42.7 1.0 O A:HOH580 3.3 35.6 1.0 CD A:GLU109 3.4 26.3 1.0 OE2 A:GLU109 3.4 26.1 1.0 O A:HOH446 3.4 19.9 1.0 O A:HOH486 3.7 28.0 1.0 C A:ASP291 3.8 18.3 1.0 CD1 A:PHE292 3.8 16.8 1.0 CA A:PHE292 3.9 14.1 1.0 CG A:PRO235 4.0 22.4 1.0 CD A:PRO293 4.3 20.1 1.0 CE1 A:PHE292 4.3 20.8 1.0 N A:PHE292 4.3 15.7 1.0 CG A:PHE292 4.3 13.8 1.0 CB A:PRO235 4.4 23.2 1.0 O A:HOH591 4.5 26.7 1.0 O A:HOH497 4.6 29.3 1.0 CB A:PHE292 4.6 15.7 1.0 O A:HOH455 4.7 26.4 1.0 O A:HOH731 4.8 40.3 1.0 CG A:GLU109 4.8 22.6 1.0 O A:HOH680 4.9 40.2 1.0 C A:PHE292 4.9 16.5 1.0 N A:PRO293 5.0 18.5 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Recombinant Rabbit Skeletal Calsequestrin


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 Recombinant Rabbit Skeletal Calsequestrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca363 b:35.3 occ:0.50 OE1 A:GLU236 2.3 39.7 1.0 OD1 A:ASP121 2.5 25.3 1.0 O A:HOH742 2.9 27.3 1.0 O A:HOH441 3.2 31.3 1.0 CA A:PHE118 3.5 14.4 1.0 O A:HOH422 3.5 50.8 1.0 CD A:GLU236 3.5 44.7 1.0 CG A:ASP121 3.7 24.7 1.0 N A:PHE118 3.7 14.2 1.0 O A:GLU117 3.8 16.9 1.0 C A:GLU117 3.8 17.4 1.0 CB A:GLU236 4.1 16.9 1.0 CD1 A:PHE118 4.1 16.8 1.0 CB A:PHE118 4.1 14.3 1.0 O A:HOH438 4.2 30.0 1.0 CB A:ASP121 4.3 18.3 1.0 CG A:GLU236 4.4 25.6 1.0 CB A:GLU117 4.4 21.6 1.0 OE2 A:GLU236 4.4 40.4 1.0 CG A:PHE118 4.6 15.1 1.0 OD2 A:ASP121 4.6 23.4 1.0 C A:PHE118 4.6 17.3 1.0 CA A:GLU117 4.8 21.1 1.0 O A:HOH597 4.8 27.1 1.0 O A:PHE118 4.8 16.1 1.0

E.J.Sanchez, K.M.Lewis, B.R.Danna, C.Kang. High-Capacity CA2+ Binding of Human Skeletal Calsequestrin. J.Biol.Chem. V. 287 11592 2012.
ISSN: ISSN 0021-9258
PubMed: 22337878
DOI: 10.1074/JBC.M111.335075