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Calcium in PDB 3trq: Crystal Structure of Native Rabbit Skeletal Calsequestrin

Protein crystallography data

The structure of Crystal Structure of Native Rabbit Skeletal Calsequestrin, PDB code: 3trq 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) 30.70 / 1.76
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 59.271, 144.565, 111.170, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.3

Other elements in 3trq:

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

Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Native Rabbit Skeletal Calsequestrin (pdb code 3trq). 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 Native Rabbit Skeletal Calsequestrin, PDB code: 3trq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3trq

Go back to Calcium Binding Sites List in 3trq
Calcium binding site 1 out of 6 in the Crystal Structure of Native 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 Native Rabbit Skeletal Calsequestrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca358

b:44.5
occ:1.00
 O A:ASP210 2.4 23.0 1.0
OE1 A:GLU217 2.4 26.6 1.0
O A:HOH706 2.5 37.7 1.0
OE2 A:GLU217 2.5 39.9 1.0
O A:PRO212 2.6 21.1 1.0
O A:HOH553 2.7 30.0 1.0
CD A:GLU217 2.8 32.2 1.0
C A:ASP210 3.6 22.0 1.0
C A:PRO212 3.7 20.9 1.0
CB A:ASP210 4.0 22.7 1.0
CA A:ASN213 4.0 16.6 1.0
ND2 A:ASN213 4.1 16.7 1.0
N A:ASN213 4.3 17.1 1.0
CG A:GLU217 4.3 24.6 1.0
O A:HOH707 4.4 42.9 1.0
CA A:ASP210 4.4 23.8 1.0
O A:HOH713 4.5 38.5 1.0
N A:SER214 4.5 16.7 1.0
C A:LYS211 4.5 26.3 1.0
N A:LYS211 4.5 18.7 1.0
CA A:LYS211 4.6 16.8 1.0
N A:PRO212 4.6 19.3 1.0
C A:ASN213 4.8 18.0 1.0
CA A:PRO212 4.8 14.5 1.0
O A:HOH665 4.8 28.1 1.0
O A:LYS211 4.9 24.1 1.0
CG A:ASN213 4.9 17.4 1.0
CB A:ASN213 5.0 15.0 1.0

Calcium binding site 2 out of 6 in 3trq

Go back to Calcium Binding Sites List in 3trq
Calcium binding site 2 out of 6 in the Crystal Structure of Native 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 Native Rabbit Skeletal Calsequestrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca359

b:45.4
occ:1.00
 OD1 A:ASN17 2.3 38.5 1.0
OD2 A:ASP80 2.4 25.8 1.0
O A:VAL18 2.5 27.1 1.0
O A:LEU74 2.5 20.7 1.0
O A:HOH606 2.8 35.8 1.0
N A:VAL18 3.2 22.6 1.0
CG A:ASP80 3.3 35.2 1.0
C A:VAL18 3.3 36.2 1.0
C A:LEU74 3.5 21.8 1.0
CG A:ASN17 3.5 52.9 1.0
C A:ASN17 3.6 29.8 1.0
NZ A:LYS79 3.6 38.8 1.0
OD1 A:ASP80 3.8 26.7 1.0
CA A:VAL18 3.8 21.9 1.0
N A:ASP76 3.8 20.0 1.0
CA A:VAL75 3.8 20.7 1.0
CA A:ASN17 3.9 23.8 1.0
N A:VAL75 4.1 18.1 1.0
CE A:LYS79 4.3 66.2 1.0
O A:ASN17 4.3 26.5 1.0
CB A:ASN17 4.3 33.6 1.0
C A:VAL75 4.3 21.6 1.0
N A:ASN19 4.4 23.1 1.0
CB A:ASP80 4.4 24.1 1.0
CB A:VAL18 4.5 22.8 1.0
ND2 A:ASN17 4.5 57.5 1.0
CB A:LEU74 4.5 18.6 1.0
CA A:LEU74 4.6 15.0 1.0
CB A:ASP76 4.6 27.0 1.0
CA A:ASN19 4.8 22.1 1.0
CA A:ASP76 4.9 22.8 1.0
CB A:ASN19 4.9 24.9 1.0
CB A:VAL75 5.0 17.1 1.0

Calcium binding site 3 out of 6 in 3trq

Go back to Calcium Binding Sites List in 3trq
Calcium binding site 3 out of 6 in the Crystal Structure of Native 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 Native Rabbit Skeletal Calsequestrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca360

b:36.2
occ:1.00
 OE2 A:GLU199 2.4 19.8 1.0
OG1 A:THR277 2.4 29.1 1.0
OG1 A:THR229 2.4 17.2 1.0
O A:HOH552 2.4 30.0 1.0
O A:THR277 2.4 26.9 1.0
OE1 A:GLU199 2.4 21.2 1.0
CD A:GLU199 2.7 25.6 1.0
C A:THR277 3.2 32.3 1.0
CA A:THR277 3.4 26.1 1.0
CB A:THR277 3.4 31.5 1.0
O A:HOH481 3.5 48.5 1.0
CB A:THR229 3.6 20.1 1.0
N A:THR229 4.0 13.0 1.0
O A:HOH881 4.1 25.4 1.0
CG A:GLU199 4.2 13.8 1.0
O A:HOH398 4.2 43.5 1.0
O A:HOH612 4.3 30.2 1.0
CA A:THR229 4.4 11.9 1.0
CE A:MET202 4.4 37.3 1.0
CG2 A:THR277 4.5 32.9 1.0
N A:ASP278 4.5 25.1 1.0
O A:HOH617 4.5 28.9 1.0
CG2 A:THR229 4.7 17.1 1.0
O A:HOH888 4.8 16.6 1.0
N A:THR277 4.8 22.8 1.0
C A:SER228 5.0 17.2 1.0

Calcium binding site 4 out of 6 in 3trq

Go back to Calcium Binding Sites List in 3trq
Calcium binding site 4 out of 6 in the Crystal Structure of Native 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 Native Rabbit Skeletal Calsequestrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca361

b:51.5
occ:1.00
 O A:THR189 2.3 24.7 1.0
O A:HOH554 2.3 30.0 1.0
O A:HOH633 2.4 33.9 1.0
OG1 A:THR189 2.5 32.7 1.0
O A:HOH573 2.7 25.9 1.0
O A:HOH711 2.9 32.2 1.0
CB A:THR189 3.2 38.5 1.0
C A:THR189 3.3 24.5 1.0
O A:HOH651 3.4 37.8 1.0
O A:HOH853 3.6 51.9 1.0
CA A:THR189 3.9 24.8 1.0
OD2 A:ASP196 4.2 23.0 1.0
O A:HOH748 4.3 39.2 1.0
OE1 A:GLU194 4.3 19.7 1.0
O A:LEU188 4.4 26.9 1.0
O A:HOH686 4.4 40.5 1.0
N A:LEU190 4.4 19.6 1.0
CG2 A:THR189 4.5 36.4 1.0
CA A:LEU190 4.8 16.9 1.0
OD1 A:ASP196 4.9 20.4 1.0
OG1 A:THR207 5.0 22.8 1.0
CG A:ASP196 5.0 23.0 1.0

Calcium binding site 5 out of 6 in 3trq

Go back to Calcium Binding Sites List in 3trq
Calcium binding site 5 out of 6 in the Crystal Structure of Native 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 Native Rabbit Skeletal Calsequestrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca362

b:36.2
occ:0.50
 OE1 A:GLU109 2.5 25.4 1.0
O A:ASP291 2.6 14.7 1.0
O A:HOH369 2.7 44.1 1.0
O A:HOH829 3.1 38.7 1.0
OE2 A:GLU109 3.3 23.4 1.0
CD A:GLU109 3.3 24.1 1.0
O A:HOH687 3.4 40.1 1.0
O A:HOH823 3.4 35.4 1.0
O A:HOH560 3.6 18.1 1.0
O A:HOH627 3.6 29.8 1.0
CG A:PRO235 3.8 19.9 1.0
C A:ASP291 3.8 16.4 1.0
O A:HOH915 3.8 38.0 1.0
CD1 A:PHE292 3.8 13.9 1.0
CA A:PHE292 4.0 12.9 1.0
CB A:PRO235 4.3 16.9 1.0
CE1 A:PHE292 4.3 16.7 1.0
CG A:PHE292 4.4 12.6 1.0
N A:PHE292 4.4 13.5 1.0
O A:HOH637 4.5 26.4 1.0
CD A:PRO293 4.5 20.5 1.0
CB A:PHE292 4.7 15.2 1.0
O A:HOH669 4.7 30.6 1.0
CG A:GLU109 4.8 30.1 1.0
O A:HOH619 4.8 25.4 1.0
O A:HOH522 4.9 43.1 1.0
OG1 A:THR114 4.9 20.4 1.0
O A:HOH621 4.9 29.5 1.0

Calcium binding site 6 out of 6 in 3trq

Go back to Calcium Binding Sites List in 3trq
Calcium binding site 6 out of 6 in the Crystal Structure of Native 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 Native Rabbit Skeletal Calsequestrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca363

b:39.2
occ:0.50
 OE1 A:GLU236 2.3 53.4 1.0
OD1 A:ASP121 2.4 24.1 1.0
O A:HOH920 3.0 25.0 1.0
O A:HOH556 3.2 30.0 1.0
CA A:PHE118 3.5 14.0 1.0
O A:HOH438 3.5 46.6 1.0
CG A:ASP121 3.5 23.5 1.0
CD A:GLU236 3.6 55.2 1.0
N A:PHE118 3.7 14.0 1.0
O A:GLU117 3.9 16.6 1.0
C A:GLU117 3.9 15.4 1.0
O A:HOH492 4.0 54.0 1.0
CB A:PHE118 4.1 13.9 1.0
CD1 A:PHE118 4.1 16.4 1.0
CB A:GLU236 4.2 19.7 1.0
CB A:ASP121 4.2 19.3 1.0
OE2 A:GLU236 4.4 34.1 1.0
CG A:GLU236 4.4 27.9 1.0
CB A:GLU117 4.5 18.1 1.0
OD2 A:ASP121 4.5 27.1 1.0
CG A:PHE118 4.6 13.0 1.0
C A:PHE118 4.6 17.3 1.0
O A:PHE118 4.8 17.2 1.0
CA A:GLU117 4.9 21.1 1.0
O A:HOH420 4.9 27.2 1.0

Reference:

E.J.Sanchez, K.M.Lewis, G.R.Munske, M.S.Nissen, C.Kang. Glycosylation of Skeletal Calsequestrin: Implications For Its Function. J.Biol.Chem. V. 287 3042 2012.
ISSN: ISSN 0021-9258
PubMed: 22170046
DOI: 10.1074/JBC.M111.326363
Page generated: Sat Jul 13 19:52:35 2024

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