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Calcium in PDB 3gin: Crystal Structure of E454K-CBD1

Protein crystallography data

The structure of Crystal Structure of E454K-CBD1, PDB code: 3gin was solved by V.Chaptal, G.Mercado-Besserer, J.Abramson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.96 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.858, 91.858, 65.590, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 25.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of E454K-CBD1 (pdb code 3gin). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of E454K-CBD1, PDB code: 3gin:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3gin

Go back to Calcium Binding Sites List in 3gin
Calcium binding site 1 out of 7 in the Crystal Structure of E454K-CBD1


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 E454K-CBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:51.3
occ:1.00
 OD2 A:ASP498 2.0 30.4 1.0
O A:ILE449 2.3 36.6 1.0
OD2 A:ASP500 2.4 29.2 1.0
OD1 A:ASP447 2.5 36.1 1.0
OE1 A:GLU385 2.6 30.2 1.0
CG A:ASP498 2.8 24.9 1.0
OE2 A:GLU385 2.9 30.3 1.0
CD A:GLU385 3.0 30.7 1.0
OD1 A:ASP498 3.0 28.2 1.0
C A:ILE449 3.4 36.5 1.0
CG A:ASP500 3.5 27.6 1.0
CG A:ASP447 3.5 36.8 1.0
OD2 A:ASP447 3.8 40.5 1.0
CA A:CA2 3.9 61.9 1.0
CB A:ASP500 3.9 27.6 1.0
N A:ILE449 4.0 37.6 1.0
CB A:ASP498 4.1 22.7 1.0
N A:PHE450 4.3 36.1 1.0
CA A:ILE449 4.3 37.5 1.0
O A:ASP447 4.4 34.9 1.0
CA A:PHE450 4.4 35.5 1.0
CG A:GLU385 4.4 29.6 1.0
OD1 A:ASP500 4.5 28.3 1.0
C A:ASP447 4.5 34.9 1.0
CA A:ASP498 4.5 22.2 1.0
OD1 A:ASP499 4.6 29.3 1.0
N A:GLU451 4.6 32.8 1.0
N A:ASP500 4.6 26.5 1.0
CA A:CA7 4.6 64.8 1.0
N A:ASP499 4.7 23.2 1.0
C A:ASP448 4.7 37.8 1.0
CG A:GLU451 4.7 33.9 1.0
N A:ASP448 4.8 36.3 1.0
CB A:ASP447 4.9 34.2 1.0
CB A:ILE449 4.9 38.3 1.0
C A:PHE450 4.9 34.4 1.0
CA A:ASP500 4.9 28.1 1.0
CA A:ASP448 4.9 37.8 1.0
OE2 A:GLU451 5.0 42.1 1.0

Calcium binding site 2 out of 7 in 3gin

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Calcium binding site 2 out of 7 in the Crystal Structure of E454K-CBD1


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 E454K-CBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:61.9
occ:1.00
 OD1 A:ASP499 2.3 29.3 1.0
OD2 A:ASP500 2.3 29.2 1.0
O A:ASP447 2.3 34.9 1.0
OE1 A:GLU385 2.7 30.2 1.0
OD1 A:ASP446 2.7 32.3 1.0
OD1 A:ASP500 2.9 28.3 1.0
CG A:ASP500 2.9 27.6 1.0
O A:HOH510 3.1 52.0 1.0
CG A:ASP499 3.3 26.2 1.0
C A:ASP447 3.5 34.9 1.0
OD2 A:ASP499 3.6 32.3 1.0
CD A:GLU385 3.8 30.7 1.0
CG A:ASP446 3.8 31.6 1.0
OD1 A:ASP447 3.8 36.1 1.0
CA A:CA1 3.9 51.3 1.0
N A:ASP447 4.0 32.7 1.0
OD2 A:ASP446 4.2 35.9 1.0
CA A:ASP448 4.2 37.8 1.0
CB A:GLU385 4.3 27.3 1.0
N A:ASP448 4.3 36.3 1.0
CB A:ASP500 4.3 27.6 1.0
CA A:ASP447 4.4 34.1 1.0
N A:ASP500 4.5 26.5 1.0
OE2 A:GLU385 4.5 30.3 1.0
C A:ASP499 4.6 25.1 1.0
CB A:ASP499 4.6 24.7 1.0
N A:ASP499 4.6 23.2 1.0
CG A:GLU385 4.7 29.6 1.0
CA A:ASP500 4.8 28.1 1.0
CA A:ASP499 4.8 24.4 1.0
CG A:ASP447 4.9 36.8 1.0

Calcium binding site 3 out of 7 in 3gin

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Calcium binding site 3 out of 7 in the Crystal Structure of E454K-CBD1


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 E454K-CBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:37.0
occ:0.80
 O A:HOH46 2.0 27.0 1.0
O A:HOH22 2.2 24.0 1.0
O A:HOH48 2.2 21.4 1.0
O A:HOH45 2.3 24.2 1.0
O A:HOH44 2.3 25.1 1.0
O A:HOH47 4.0 27.4 1.0
O A:HOH94 4.0 33.8 1.0
O A:HOH78 4.2 32.0 1.0
OD1 A:ASP453 4.2 20.7 1.0
OD2 A:ASP453 4.3 23.2 1.0
O A:HOH77 4.4 33.9 1.0
O A:ASP498 4.5 20.7 1.0
CG A:ASP453 4.7 22.9 1.0
O A:HOH49 4.8 31.2 1.0
CD2 A:PHE497 4.8 19.0 1.0

Calcium binding site 4 out of 7 in 3gin

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Calcium binding site 4 out of 7 in the Crystal Structure of E454K-CBD1


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 E454K-CBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7

b:64.8
occ:1.00
 OD2 A:ASP447 2.4 40.5 1.0
OE2 A:GLU385 2.6 30.3 1.0
OD1 A:ASP421 3.2 30.1 1.0
CG A:ASP447 3.3 36.8 1.0
OE2 A:GLU451 3.4 42.1 1.0
CD A:GLU385 3.8 30.7 1.0
OD1 A:ASP447 3.9 36.1 1.0
O A:HOH3 4.1 22.3 1.0
CB A:ASP447 4.3 34.2 1.0
CG A:ASP421 4.4 27.8 1.0
CD A:GLU451 4.4 35.9 1.0
CG A:GLU385 4.5 29.6 1.0
O A:ILE445 4.5 24.4 1.0
CA A:CA1 4.6 51.3 1.0
O A:SER420 4.8 27.1 1.0
NZ A:LYS454 4.8 30.2 1.0
CG A:GLU451 4.8 33.9 1.0
CB A:ASP421 4.8 26.1 1.0
OE1 A:GLU385 4.9 30.2 1.0
CA A:ASP421 4.9 26.1 1.0
O A:HOH4 4.9 17.1 1.0
N A:ASP447 5.0 32.7 1.0

Calcium binding site 5 out of 7 in 3gin

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Calcium binding site 5 out of 7 in the Crystal Structure of E454K-CBD1


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 E454K-CBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:49.4
occ:1.00
 O B:ASP447 2.3 31.1 1.0
OD2 B:ASP500 2.4 34.1 1.0
OD1 B:ASP499 2.4 29.0 1.0
OE1 B:GLU385 2.5 29.4 1.0
OD1 B:ASP446 2.6 25.4 1.0
OD1 B:ASP500 2.9 31.4 1.0
CG B:ASP500 2.9 31.1 1.0
O B:HOH2 3.0 39.8 1.0
CA B:CA4 3.4 51.5 1.0
C B:ASP447 3.4 31.5 1.0
CD B:GLU385 3.5 33.0 1.0
CG B:ASP499 3.5 27.6 1.0
CG B:ASP446 3.6 26.3 1.0
OD1 B:ASP447 3.7 36.0 1.0
N B:ASP447 3.8 29.8 1.0
OD2 B:ASP446 4.0 24.2 1.0
OD2 B:ASP499 4.0 31.1 1.0
CA B:ASP447 4.2 31.1 1.0
CG B:GLU385 4.3 30.1 1.0
N B:ASP448 4.3 33.9 1.0
CB B:ASP500 4.3 30.4 1.0
OE2 B:GLU385 4.4 36.2 1.0
CB B:GLU385 4.4 26.2 1.0
CA B:ASP448 4.4 34.9 1.0
N B:ASP499 4.5 24.7 1.0
N B:ASP500 4.6 28.8 1.0
CG B:ASP447 4.6 33.3 1.0
C B:ASP448 4.7 34.4 1.0
C B:ASP499 4.7 27.6 1.0
CB B:ASP499 4.8 26.8 1.0
C B:ASP446 4.8 28.0 1.0
CB B:ASP446 4.8 26.3 1.0
N B:ILE449 4.8 34.0 1.0
CA B:ASP499 4.9 26.3 1.0
O B:ILE449 4.9 33.1 1.0
CA B:ASP500 4.9 30.6 1.0
CA B:ASP446 4.9 26.6 1.0

Calcium binding site 6 out of 7 in 3gin

Go back to Calcium Binding Sites List in 3gin
Calcium binding site 6 out of 7 in the Crystal Structure of E454K-CBD1


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 E454K-CBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:51.5
occ:1.00
 OD2 B:ASP500 2.2 34.1 1.0
OD1 B:ASP498 2.2 32.5 1.0
O B:ILE449 2.2 33.1 1.0
OD1 B:ASP447 2.2 36.0 1.0
OE1 B:GLU385 2.4 29.4 1.0
CG B:ASP498 2.9 24.5 1.0
OE2 B:GLU385 2.9 36.2 1.0
CD B:GLU385 3.0 33.0 1.0
OD2 B:ASP498 3.1 24.4 1.0
CG B:ASP447 3.3 33.3 1.0
CG B:ASP500 3.3 31.1 1.0
C B:ILE449 3.4 32.5 1.0
CA B:CA3 3.4 49.4 1.0
OD2 B:ASP447 3.7 36.4 1.0
N B:ILE449 3.9 34.0 1.0
CB B:ASP500 4.0 30.4 1.0
O B:ASP447 4.1 31.1 1.0
CB B:ASP498 4.2 22.4 1.0
CA B:ILE449 4.2 33.8 1.0
OD1 B:ASP500 4.3 31.4 1.0
O B:HOH51 4.3 34.1 1.0
N B:PHE450 4.3 31.5 1.0
C B:ASP447 4.4 31.5 1.0
CA B:ASP498 4.5 22.2 1.0
CG B:GLU385 4.5 30.1 1.0
CA B:PHE450 4.5 31.5 1.0
C B:ASP448 4.6 34.4 1.0
CB B:ASP447 4.6 31.6 1.0
N B:ASP500 4.6 28.8 1.0
OD1 B:ASP499 4.6 29.0 1.0
N B:ASP499 4.6 24.7 1.0
N B:GLU451 4.7 30.1 1.0
CB B:ILE449 4.8 33.9 1.0
N B:ASP447 4.9 29.8 1.0
CA B:ASP447 4.9 31.1 1.0
OE1 B:GLU451 4.9 35.1 1.0
CA B:CA6 5.0 63.0 0.8
CA B:ASP500 5.0 30.6 1.0
N B:ASP448 5.0 33.9 1.0

Calcium binding site 7 out of 7 in 3gin

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Calcium binding site 7 out of 7 in the Crystal Structure of E454K-CBD1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of E454K-CBD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca6

b:63.0
occ:0.80
 OD2 B:ASP447 2.3 36.4 1.0
O B:HOH95 2.6 40.0 1.0
OD1 B:ASP421 2.7 26.4 1.0
OE1 B:GLU451 3.1 35.1 1.0
OE2 B:GLU385 3.1 36.2 1.0
CG B:ASP447 3.5 33.3 1.0
CG B:ASP421 3.8 23.6 1.0
O B:HOH51 4.1 34.1 1.0
NZ B:LYS454 4.1 26.3 1.0
OD1 B:ASP447 4.2 36.0 1.0
O B:HOH52 4.3 23.3 1.0
CD B:GLU451 4.3 31.9 1.0
CD B:GLU385 4.4 33.0 1.0
CD B:LYS454 4.4 23.4 1.0
CB B:ASP447 4.5 31.6 1.0
CB B:ASP421 4.6 23.8 1.0
OD2 B:ASP421 4.6 25.1 1.0
CA B:ASP421 4.8 23.4 1.0
O B:HOH56 4.8 33.6 1.0
OE2 B:GLU451 4.8 35.6 1.0
O B:SER420 4.9 23.9 1.0
CE B:LYS454 4.9 24.1 1.0
CA B:CA4 5.0 51.5 1.0

Reference:

V.Chaptal, M.Ottolia, G.Mercado-Besserer, D.A.Nicoll, K.D.Philipson, J.Abramson. Structure and Functional Analysis of A CA2+ Sensor Mutant of the Na+/CA2+ Exchanger J.Biol.Chem. V. 284 14688 2009.
ISSN: ISSN 0021-9258
PubMed: 19332552
DOI: 10.1074/JBC.C900037200
Page generated: Sat Jul 13 10:41:03 2024

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