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

Protein crystallography data

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

Other elements in 3trp:

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

Sodium (Na) 2 atoms

Calcium Binding Sites:

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 3trp

Go back to Calcium Binding Sites List in 3trp
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 3trp

Go back to Calcium Binding Sites List in 3trp
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 3trp

Go back to Calcium Binding Sites List in 3trp
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 3trp

Go back to Calcium Binding Sites List in 3trp
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 3trp

Go back to Calcium Binding Sites List in 3trp
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 3trp

Go back to Calcium Binding Sites List in 3trp
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

Reference:

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
Page generated: Sat Dec 12 04:32:01 2020

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