Atomistry » Calcium » PDB 2dcj-2dw0 » 2dpk
Atomistry »
  Calcium »
    PDB 2dcj-2dw0 »
      2dpk »

Calcium in PDB 2dpk: The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger

Protein crystallography data

The structure of The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger, PDB code: 2dpk was solved by J.Abramson, M.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.26 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 59.624, 45.524, 57.269, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 28.4

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger (pdb code 2dpk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger, PDB code: 2dpk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2dpk

Go back to Calcium Binding Sites List in 2dpk
Calcium binding site 1 out of 4 in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:62.2
occ:1.00
OE2 A:GLU451 2.5 45.6 1.0
OE2 A:GLU454 2.6 49.2 1.0
OD2 A:ASP421 2.7 43.0 1.0
OD1 A:ASP421 2.8 40.1 1.0
OE1 A:GLU454 2.9 50.6 1.0
CD A:GLU454 3.1 48.7 1.0
CG A:ASP421 3.1 42.1 1.0
CD A:GLU451 3.5 47.7 1.0
O A:HOH5 4.0 29.5 1.0
CA A:CA2001 4.3 59.3 1.0
OE1 A:GLU451 4.3 52.6 1.0
CG A:GLU451 4.4 44.9 1.0
CG A:GLU454 4.6 45.5 1.0
CB A:ASP421 4.6 41.2 1.0
OG A:SER420 4.7 51.3 1.0
O A:HOH15 4.7 46.1 1.0
O A:THR415 4.8 34.7 1.0
CB A:GLU451 4.9 45.0 1.0
ND2 A:ASN417 4.9 37.1 1.0

Calcium binding site 2 out of 4 in 2dpk

Go back to Calcium Binding Sites List in 2dpk
Calcium binding site 2 out of 4 in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:59.3
occ:1.00
O A:HOH16 2.3 47.0 1.0
O A:HOH1 2.3 63.1 1.0
O A:HOH15 2.5 46.1 1.0
OD2 A:ASP421 2.5 43.0 1.0
OE1 A:GLU451 2.7 52.6 1.0
OE2 A:GLU451 2.9 45.6 1.0
CD A:GLU451 3.1 47.7 1.0
CD A:GLU385 3.4 47.5 1.0
OE2 A:GLU385 3.4 46.0 1.0
OE1 A:GLU385 3.5 55.3 1.0
CG A:ASP421 3.6 42.1 1.0
CB A:ASP421 4.1 41.2 1.0
CG A:GLU385 4.2 48.6 1.0
CA A:ASP421 4.2 41.7 1.0
O A:ILE445 4.2 41.8 1.0
OE1 A:GLU454 4.2 50.6 1.0
CA A:CA1001 4.3 62.2 1.0
CA A:CA3001 4.3 55.5 1.0
OD1 A:ASP447 4.4 42.4 1.0
O A:HOH14 4.4 35.2 1.0
CG A:GLU451 4.6 44.9 1.0
O A:SER420 4.6 45.4 1.0
OD1 A:ASP421 4.6 40.1 1.0
CG2 A:ILE496 4.7 35.5 1.0
OD2 A:ASP447 4.8 41.7 1.0
O A:ASP421 4.8 40.8 1.0
CG A:ASP447 4.9 44.6 1.0
OD1 A:ASP498 4.9 55.7 1.0

Calcium binding site 3 out of 4 in 2dpk

Go back to Calcium Binding Sites List in 2dpk
Calcium binding site 3 out of 4 in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3001

b:55.5
occ:1.00
O A:ILE449 2.4 42.2 1.0
OD2 A:ASP500 2.4 60.5 1.0
OD2 A:ASP447 2.4 41.7 1.0
OD1 A:ASP498 2.4 55.7 1.0
OE1 A:GLU451 2.6 52.6 1.0
OE1 A:GLU385 2.7 55.3 1.0
OE2 A:GLU385 2.7 46.0 1.0
CD A:GLU385 3.0 47.5 1.0
CD A:GLU451 3.5 47.7 1.0
CG A:ASP447 3.5 44.6 1.0
C A:ILE449 3.5 48.8 1.0
CG A:ASP500 3.5 57.6 1.0
CG A:ASP498 3.6 62.5 1.0
CG A:GLU451 3.7 44.9 1.0
CD1 A:ILE449 3.9 62.9 1.0
CA A:CA4001 3.9 57.7 1.0
N A:ILE449 3.9 51.4 1.0
OD1 A:ASP447 4.0 42.4 1.0
O A:ASP447 4.2 41.8 1.0
OD2 A:ASP498 4.2 65.9 1.0
O A:HOH1 4.2 63.1 1.0
CA A:ILE449 4.3 51.6 1.0
CA A:CA2001 4.3 59.3 1.0
CB A:ASP500 4.3 62.5 1.0
OD1 A:ASP500 4.4 53.8 1.0
C A:ASP447 4.4 49.4 1.0
CB A:GLU451 4.5 45.0 1.0
CG A:GLU385 4.5 48.6 1.0
OE2 A:GLU451 4.6 45.6 1.0
N A:PHE450 4.6 48.4 1.0
CG1 A:ILE449 4.6 58.3 1.0
OD1 A:ASP499 4.7 73.8 1.0
N A:GLU451 4.7 42.1 1.0
N A:ASP447 4.8 43.0 1.0
CB A:ASP447 4.8 46.2 1.0
O A:HOH15 4.8 46.1 1.0
CB A:ASP498 4.8 63.6 1.0
C A:PHE450 4.8 46.9 1.0
CA A:PHE450 4.8 45.9 1.0
C A:ASP448 4.9 56.7 1.0
CA A:ASP447 4.9 47.5 1.0
N A:ASP448 4.9 54.1 1.0

Calcium binding site 4 out of 4 in 2dpk

Go back to Calcium Binding Sites List in 2dpk
Calcium binding site 4 out of 4 in the The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4001

b:57.7
occ:1.00
OD1 A:ASP499 2.3 73.8 1.0
O A:ASP447 2.3 41.8 1.0
OD2 A:ASP446 2.3 50.8 1.0
OD1 A:ASP500 2.5 53.8 1.0
OD2 A:ASP500 2.8 60.5 1.0
CG A:ASP500 3.0 57.6 1.0
CG A:ASP499 3.2 73.3 1.0
OE2 A:GLU385 3.4 46.0 1.0
C A:ASP447 3.5 49.4 1.0
O A:HOH8 3.5 38.9 1.0
CG A:ASP446 3.5 49.0 1.0
CD A:GLU385 3.5 47.5 1.0
OD2 A:ASP499 3.6 77.2 1.0
N A:ASP447 3.7 43.0 1.0
OE1 A:GLU385 3.9 55.3 1.0
CA A:CA3001 3.9 55.5 1.0
CG A:GLU385 4.0 48.6 1.0
OD1 A:ASP446 4.1 43.7 1.0
OD2 A:ASP447 4.1 41.7 1.0
CA A:ASP447 4.3 47.5 1.0
CB A:GLU385 4.3 45.1 1.0
N A:ASP448 4.4 54.1 1.0
O A:ASP499 4.5 74.0 1.0
C A:ASP499 4.5 69.8 1.0
C A:ASP446 4.5 44.1 1.0
CB A:ASP500 4.5 62.5 1.0
CB A:ASP499 4.6 71.3 1.0
CA A:ASP448 4.6 57.9 1.0
CA A:ASP446 4.6 42.9 1.0
CB A:ASP446 4.7 45.1 1.0
N A:ASP499 4.7 66.8 1.0
N A:ASP500 4.8 69.1 1.0
CA A:ASP499 4.9 69.3 1.0
OD1 A:ASP498 4.9 55.7 1.0

Reference:

D.A.Nicoll, M.Sawaya, S.Kwon, D.Cascio, K.D.Philipson, J.Abramson. The Crystal Structure of the Primary CA2+ Sensor of the Na+/CA2+ Exchanger Reveals A Novel CA2+ Binding Motif. J.Biol.Chem. V. 281 21577 2006.
ISSN: ISSN 0021-9258
PubMed: 16774926
DOI: 10.1074/JBC.C600117200
Page generated: Sat Dec 12 03:35:14 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy