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Calcium in PDB 3e9t: Crystal Structure of Apo-Form Calx CBD1 Domain

Protein crystallography data

The structure of Crystal Structure of Apo-Form Calx CBD1 Domain, PDB code: 3e9t was solved by M.Wu, L.Zheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.73 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.086, 76.429, 128.918, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Apo-Form Calx CBD1 Domain (pdb code 3e9t). 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 Apo-Form Calx CBD1 Domain, PDB code: 3e9t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3e9t

Go back to Calcium Binding Sites List in 3e9t
Calcium binding site 1 out of 6 in the Crystal Structure of Apo-Form Calx CBD1 Domain


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 Apo-Form Calx CBD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:23.3
occ:1.00
 O A:VAL518 2.2 34.4 1.0
OD2 A:ASP516 2.4 35.0 1.0
OE2 A:GLU455 2.4 25.6 1.0
OD1 A:ASP550 2.4 29.2 1.0
O A:HOH653 2.5 39.5 1.0
OE1 A:GLU455 2.7 26.8 1.0
CD A:GLU455 2.9 23.3 1.0
OE1 A:GLU520 3.0 37.7 1.0
CG A:ASP550 3.2 28.1 1.0
OD2 A:ASP550 3.2 31.4 1.0
C A:VAL518 3.4 34.4 1.0
CG A:ASP516 3.5 32.6 1.0
O A:ASP516 3.6 31.4 1.0
CA A:CA6 3.7 31.2 1.0
N A:VAL518 3.9 33.7 1.0
C A:ASP516 4.0 31.2 1.0
O A:HOH646 4.0 33.8 1.0
CD A:GLU520 4.1 36.5 1.0
OD1 A:ASP516 4.2 34.9 1.0
CA A:VAL518 4.2 34.3 1.0
O A:HOH618 4.2 43.1 1.0
C A:ASP517 4.2 33.5 1.0
N A:PHE519 4.3 34.8 1.0
CG A:GLU455 4.4 22.3 1.0
N A:ASP516 4.5 28.3 1.0
N A:GLU520 4.6 32.6 1.0
CG A:GLU520 4.6 33.6 1.0
CA A:PHE519 4.6 34.8 1.0
CB A:ASP550 4.6 25.2 1.0
CA A:ASP516 4.6 30.3 1.0
N A:ASP517 4.6 31.9 1.0
CB A:ASP516 4.6 30.8 1.0
O A:ASP517 4.6 34.1 1.0
OD1 A:ASP551 4.7 35.6 1.0
C A:PHE519 4.7 33.9 1.0
CA A:ASP517 4.8 33.1 1.0
O A:HOH626 4.8 26.9 1.0
CB A:GLU520 4.8 31.4 1.0
CB A:VAL518 4.9 34.5 1.0

Calcium binding site 2 out of 6 in 3e9t

Go back to Calcium Binding Sites List in 3e9t
Calcium binding site 2 out of 6 in the Crystal Structure of Apo-Form Calx CBD1 Domain


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 Apo-Form Calx CBD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca6

b:31.2
occ:1.00
 OD1 A:ASP551 2.2 35.6 1.0
OD2 A:ASP515 2.3 25.1 1.0
OE2 A:GLU455 2.4 25.6 1.0
O A:ASP516 2.4 31.4 1.0
O A:HOH653 2.7 39.5 1.0
CG A:ASP551 3.2 33.8 1.0
CG A:ASP515 3.4 25.4 1.0
CD A:GLU455 3.5 23.3 1.0
OD2 A:ASP551 3.5 38.7 1.0
C A:ASP516 3.6 31.2 1.0
CA A:CA1 3.7 23.3 1.0
OD1 A:ASP515 3.9 29.5 1.0
N A:ASP516 3.9 28.3 1.0
CG A:GLU455 4.1 22.3 1.0
OE1 A:GLU455 4.4 26.8 1.0
C A:ASP551 4.4 30.9 1.0
CA A:ASP516 4.4 30.3 1.0
CB A:GLU455 4.4 18.9 1.0
N A:ASP551 4.5 28.2 1.0
CB A:ASP551 4.5 31.1 1.0
O A:HOH618 4.5 43.1 1.0
OD2 A:ASP516 4.6 35.0 1.0
N A:ASP517 4.6 31.9 1.0
CB A:ASP515 4.7 25.0 1.0
CA A:ASP517 4.7 33.1 1.0
CA A:ASP551 4.8 30.5 1.0
C A:ASP515 4.8 26.6 1.0
CA A:ASP515 4.8 24.8 1.0

Calcium binding site 3 out of 6 in 3e9t

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Calcium binding site 3 out of 6 in the Crystal Structure of Apo-Form Calx CBD1 Domain


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 Apo-Form Calx CBD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:30.8
occ:1.00
 O B:HOH613 2.1 38.2 1.0
O B:HOH647 2.3 39.5 1.0
OD2 B:ASP490 2.5 19.8 1.0
OE2 B:GLU520 2.5 31.2 1.0
OE1 B:GLU523 2.5 26.2 1.0
OD1 B:ASP490 2.9 16.6 1.0
CG B:ASP490 3.0 17.7 1.0
CD B:GLU523 3.4 22.3 1.0
OE2 B:GLU523 3.5 26.8 1.0
CD B:GLU520 3.6 30.6 1.0
O B:HOH584 4.1 27.2 1.0
CA B:CA5 4.1 23.9 1.0
CG B:GLU520 4.3 28.1 1.0
OG1 B:THR489 4.5 23.3 1.0
O B:HOH657 4.5 36.8 1.0
CB B:ASP490 4.5 16.2 1.0
OE1 B:GLU520 4.6 31.3 1.0
O B:THR484 4.8 18.8 1.0
CG B:GLU523 4.8 20.9 1.0
CB B:GLU520 4.9 26.1 1.0

Calcium binding site 4 out of 6 in 3e9t

Go back to Calcium Binding Sites List in 3e9t
Calcium binding site 4 out of 6 in the Crystal Structure of Apo-Form Calx CBD1 Domain


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 Apo-Form Calx CBD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:24.3
occ:1.00
 OD2 B:ASP515 2.2 23.2 1.0
O B:ASP516 2.2 24.3 1.0
OD1 B:ASP552 2.4 36.8 1.0
OD1 B:ASP551 2.4 34.7 1.0
OE2 B:GLU455 2.6 22.4 1.0
OD2 B:ASP552 2.8 37.4 1.0
CG B:ASP552 2.9 35.8 1.0
CG B:ASP551 3.2 32.4 1.0
OD2 B:ASP551 3.2 33.9 1.0
CG B:ASP515 3.3 21.8 1.0
C B:ASP516 3.4 24.9 1.0
N B:ASP516 3.7 23.2 1.0
CD B:GLU455 3.7 23.1 1.0
OD1 B:ASP515 3.8 22.4 1.0
CA B:CA4 3.9 20.8 1.0
CA B:ASP516 4.1 24.5 1.0
CG B:GLU455 4.3 21.2 1.0
CB B:ASP552 4.4 34.9 1.0
N B:ASP517 4.4 25.4 1.0
C B:ASP515 4.5 21.8 1.0
CB B:ASP515 4.5 20.8 1.0
OD2 B:ASP516 4.5 28.4 1.0
N B:ASP552 4.5 33.3 1.0
CA B:ASP515 4.6 20.8 1.0
CB B:GLU455 4.6 17.8 1.0
CB B:ASP551 4.6 30.8 1.0
OE1 B:GLU455 4.6 26.6 1.0
CA B:ASP517 4.7 26.8 1.0
N B:ASP551 4.8 27.7 1.0
C B:ASP551 4.9 31.9 1.0
CA B:ASP552 4.9 34.6 1.0
CA B:ASP551 5.0 30.5 1.0

Calcium binding site 5 out of 6 in 3e9t

Go back to Calcium Binding Sites List in 3e9t
Calcium binding site 5 out of 6 in the Crystal Structure of Apo-Form Calx CBD1 Domain


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 Apo-Form Calx CBD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:20.8
occ:1.00
 OD2 B:ASP552 2.1 37.4 1.0
O B:VAL518 2.2 26.9 1.0
OD2 B:ASP516 2.3 28.4 1.0
OD1 B:ASP550 2.3 26.4 1.0
OE2 B:GLU455 2.4 22.4 1.0
OE1 B:GLU520 2.5 31.3 1.0
OE1 B:GLU455 2.8 26.6 1.0
CD B:GLU455 2.9 23.1 1.0
CG B:ASP550 3.3 25.0 1.0
C B:VAL518 3.3 28.0 1.0
CG B:ASP552 3.4 35.8 1.0
CG B:ASP516 3.5 26.7 1.0
OD2 B:ASP550 3.5 28.3 1.0
CD B:GLU520 3.7 30.6 1.0
CA B:CA3 3.9 24.3 1.0
O B:ASP516 3.9 24.3 1.0
N B:VAL518 3.9 27.4 1.0
O B:HOH608 4.0 31.5 1.0
CA B:VAL518 4.1 28.0 1.0
OD1 B:ASP516 4.1 29.8 1.0
C B:ASP516 4.1 24.9 1.0
CG B:GLU520 4.2 28.1 1.0
CB B:ASP552 4.2 34.9 1.0
OD1 B:ASP552 4.2 36.8 1.0
N B:PHE519 4.3 28.2 1.0
N B:ASP516 4.4 23.2 1.0
CA B:CA5 4.4 23.9 1.0
CG B:GLU455 4.4 21.2 1.0
N B:GLU520 4.5 26.5 1.0
CA B:PHE519 4.5 28.6 1.0
CA B:ASP516 4.5 24.5 1.0
CB B:ASP516 4.6 24.9 1.0
CB B:VAL518 4.6 28.3 1.0
O B:HOH657 4.6 36.8 1.0
C B:PHE519 4.6 27.7 1.0
CB B:ASP550 4.7 23.0 1.0
C B:ASP517 4.7 27.1 1.0
OD1 B:ASP551 4.7 34.7 1.0
N B:ASP517 4.7 25.4 1.0
OE2 B:GLU520 4.7 31.2 1.0
CB B:GLU520 4.7 26.1 1.0
CB B:GLU455 5.0 17.8 1.0

Calcium binding site 6 out of 6 in 3e9t

Go back to Calcium Binding Sites List in 3e9t
Calcium binding site 6 out of 6 in the Crystal Structure of Apo-Form Calx CBD1 Domain


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 Apo-Form Calx CBD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5

b:23.9
occ:1.00
 O B:HOH657 2.3 36.8 1.0
OE1 B:GLU455 2.4 26.6 1.0
OE2 B:GLU520 2.5 31.2 1.0
OD2 B:ASP490 2.6 19.8 1.0
O B:HOH584 2.7 27.2 1.0
O B:HOH575 2.7 21.9 1.0
OE1 B:GLU520 2.7 31.3 1.0
O B:HOH608 2.8 31.5 1.0
CD B:GLU520 2.9 30.6 1.0
CD B:GLU455 3.4 23.1 1.0
CG B:ASP490 3.7 17.7 1.0
CG B:GLU455 4.0 21.2 1.0
CB B:ASP490 4.1 16.2 1.0
CA B:CA2 4.1 30.8 1.0
CA B:ASP490 4.3 16.5 1.0
CG B:GLU520 4.3 28.1 1.0
O B:ILE514 4.3 18.7 1.0
O B:HOH567 4.4 19.0 1.0
CA B:CA4 4.4 20.8 1.0
OD1 B:ASP550 4.4 26.4 1.0
OE2 B:GLU455 4.4 22.4 1.0
OD1 B:ASP516 4.5 29.8 1.0
OE1 B:GLU523 4.6 26.2 1.0
CG2 B:ILE548 4.7 14.4 1.0
CB B:GLU520 4.7 26.1 1.0
OD1 B:ASP490 4.8 16.6 1.0
OD2 B:ASP516 4.8 28.4 1.0
O B:THR489 4.8 17.9 1.0
CB B:GLU455 4.9 17.8 1.0
CG B:ASP516 5.0 26.7 1.0

Reference:

M.Wu, L.Zheng. Crystal Structure of Apo-Form of Calx CBD1 Domain To Be Published.
Page generated: Tue Jul 8 11:48:55 2025

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