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Calcium in PDB 2zrs: Crystal Structure of CA2+-Bound Form of DES3-23ALG-2

Protein crystallography data

The structure of Crystal Structure of CA2+-Bound Form of DES3-23ALG-2, PDB code: 2zrs was solved by H.Suzuki, M.Kawasaki, T.Kakiuchi, H.Shibata, S.Wakatsuki, M.Maki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.780, 154.425, 237.676, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 28

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2 (pdb code 2zrs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 25 binding sites of Calcium where determined in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2, PDB code: 2zrs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 25 in 2zrs

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Calcium binding site 1 out of 25 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2


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 CA2+-Bound Form of DES3-23ALG-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca990

b:50.7
occ:1.00
 O A:MET109 2.8 59.2 1.0
OD1 A:ASP103 2.9 48.5 1.0
OE2 A:GLU114 3.0 58.9 1.0
N A:ARG104 3.1 52.2 1.0
N A:ASP105 3.2 53.9 1.0
OD2 A:ASP105 3.4 54.7 1.0
CA A:ASP103 3.5 51.1 1.0
CD A:GLU114 3.6 59.7 1.0
CB A:ASP105 3.7 54.4 1.0
C A:ASP103 3.7 51.6 1.0
CG A:ASP103 3.9 49.9 1.0
CG A:ASP105 3.9 54.5 1.0
C A:MET109 4.0 59.1 1.0
CA A:ASP105 4.0 54.4 1.0
CA A:ARG104 4.0 52.9 1.0
C A:ARG104 4.1 53.3 1.0
CG A:GLU114 4.1 60.1 1.0
CB A:ASP103 4.1 50.9 1.0
N A:ASN106 4.1 55.2 1.0
CB A:ARG104 4.3 53.0 1.0
OE1 A:GLU114 4.4 60.0 1.0
OD2 A:ASP111 4.4 59.5 1.0
C A:ASP105 4.5 54.8 1.0
CA A:ILE110 4.6 59.5 1.0
N A:ASP103 4.7 51.0 1.0
N A:ILE110 4.7 59.3 1.0
N A:MET109 4.8 58.5 1.0
O A:TYR102 4.8 50.8 1.0
N A:SER107 4.9 56.5 1.0
O A:ASP103 4.9 51.5 1.0
CA A:MET109 5.0 58.9 1.0

Calcium binding site 2 out of 25 in 2zrs

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Calcium binding site 2 out of 25 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2


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 CA2+-Bound Form of DES3-23ALG-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca991

b:48.5
occ:1.00
 OE1 A:GLU47 2.2 51.7 1.0
CD A:GLU47 2.6 51.6 1.0
O A:VAL42 2.7 53.5 1.0
N A:GLY41 2.8 55.0 1.0
OE2 A:GLU47 2.9 52.0 1.0
O A:VAL35 3.2 57.4 1.0
CB A:SER40 3.2 55.5 1.0
C A:VAL42 3.4 53.4 1.0
C A:GLY41 3.5 54.4 1.0
CA A:GLY41 3.5 54.5 1.0
N A:VAL42 3.6 54.0 1.0
CG A:GLU47 3.6 50.8 1.0
C A:SER40 3.6 55.3 1.0
CA A:SER40 3.9 55.4 1.0
O A:GLY41 4.0 54.3 1.0
CG2 A:VAL35 4.1 57.6 1.0
N A:ILE43 4.2 53.1 1.0
CA A:VAL42 4.2 53.6 1.0
C A:VAL35 4.2 57.6 1.0
CA A:ILE43 4.3 52.6 1.0
OG A:SER40 4.3 55.7 1.0
CB A:GLU47 4.4 50.1 1.0
N A:SER40 4.5 55.5 1.0
CB A:VAL35 4.5 57.8 1.0
O A:SER40 4.6 55.5 1.0
CG1 A:ILE43 4.7 52.6 1.0
CA A:VAL35 5.0 57.7 1.0

Calcium binding site 3 out of 25 in 2zrs

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Calcium binding site 3 out of 25 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2


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 CA2+-Bound Form of DES3-23ALG-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca990

b:33.8
occ:1.00
 OD1 B:ASP105 2.2 49.6 1.0
OD2 B:ASP105 2.3 50.4 1.0
CG B:ASP105 2.5 50.5 1.0
OD1 B:ASP103 2.5 50.0 1.0
OE1 B:GLU114 2.9 51.5 1.0
O B:MET109 3.0 51.7 1.0
OG B:SER107 3.2 51.7 1.0
CG B:ASP103 3.3 49.2 1.0
OE2 B:GLU114 3.4 51.7 1.0
N B:SER107 3.4 51.5 1.0
CD B:GLU114 3.5 51.6 1.0
N B:ASN106 3.5 51.2 1.0
CB B:SER107 3.8 51.7 1.0
CB B:ASP105 3.8 50.8 1.0
OD2 B:ASP103 3.8 48.9 1.0
C B:ASP105 4.1 51.0 1.0
CA B:ASN106 4.1 51.3 1.0
CA B:SER107 4.2 51.7 1.0
C B:ASN106 4.2 51.4 1.0
C B:MET109 4.2 51.8 1.0
N B:ASP105 4.2 50.5 1.0
CA B:ASP105 4.2 50.8 1.0
O B:ASP103 4.3 49.0 1.0
CA B:ASP103 4.3 48.8 1.0
C B:ASP103 4.3 49.0 1.0
CB B:ASP103 4.4 48.9 1.0
OD2 B:ASP111 4.5 51.8 1.0
CA B:ILE110 4.7 52.0 1.0
C B:SER107 4.9 51.8 1.0
N B:ILE110 5.0 51.8 1.0
CG B:GLU114 5.0 51.6 1.0
N B:MET109 5.0 52.0 1.0
O B:ASP105 5.0 51.2 1.0

Calcium binding site 4 out of 25 in 2zrs

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Calcium binding site 4 out of 25 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2


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 CA2+-Bound Form of DES3-23ALG-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca991

b:66.2
occ:1.00
 OD1 B:ASP171 2.4 57.1 1.0
OD1 B:ASP169 2.9 57.6 1.0
N B:THR170 3.2 57.7 1.0
O B:TRP175 3.4 58.9 1.0
CG B:ASP171 3.4 57.2 1.0
N B:ASP171 3.6 57.8 1.0
OD2 B:ASP171 3.8 56.7 1.0
CG B:ASP169 3.9 57.7 1.0
CB B:THR170 3.9 57.7 1.0
CA B:THR170 3.9 57.7 1.0
C B:ASP169 4.0 57.8 1.0
CA B:ASP169 4.1 57.8 1.0
OD2 B:ASP173 4.1 56.9 1.0
OG1 B:THR170 4.2 57.7 1.0
C B:THR170 4.2 57.8 1.0
CB B:ASP169 4.4 57.7 1.0
CB B:ASP171 4.6 57.6 1.0
C B:TRP175 4.6 58.8 1.0
CA B:ASP171 4.6 57.6 1.0
OD2 B:ASP169 4.8 57.4 1.0
NE1 B:TRP175 4.8 59.0 1.0
CG1 B:ILE176 4.9 58.5 1.0
CD1 B:TRP175 5.0 58.8 1.0
CG B:ASP173 5.0 57.8 1.0

Calcium binding site 5 out of 25 in 2zrs

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Calcium binding site 5 out of 25 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2


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 CA2+-Bound Form of DES3-23ALG-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca992

b:40.6
occ:1.00
 OD2 B:ASP36 2.4 49.5 1.0
O B:VAL42 2.6 50.6 1.0
OE2 B:GLU47 3.1 49.5 1.0
CB B:SER40 3.3 50.9 1.0
OD1 B:ASP38 3.3 50.8 1.0
OE1 B:GLU47 3.5 49.4 1.0
OG B:SER44 3.6 50.4 1.0
CG B:ASP36 3.6 49.5 1.0
CD B:GLU47 3.7 49.4 1.0
OG B:SER40 3.8 50.8 1.0
C B:VAL42 3.9 50.5 1.0
O B:ASP38 4.2 51.1 1.0
N B:SER44 4.2 50.2 1.0
CG B:ASP38 4.2 51.1 1.0
CA B:ASP36 4.3 49.7 1.0
CB B:ASP36 4.5 49.6 1.0
OD1 B:ASP36 4.5 49.1 1.0
CA B:ILE43 4.5 50.3 1.0
N B:LYS37 4.5 50.5 1.0
OD2 B:ASP38 4.6 51.0 1.0
CA B:SER40 4.6 50.9 1.0
N B:ILE43 4.6 50.4 1.0
N B:VAL42 4.7 50.6 1.0
C B:ASP36 4.7 50.0 1.0
C B:ILE43 4.7 50.3 1.0
N B:SER40 4.8 50.9 1.0
CB B:SER44 4.8 50.3 1.0
CA B:VAL42 4.9 50.6 1.0
N B:GLY41 4.9 50.8 1.0
N B:ASP38 5.0 51.0 1.0
C B:SER40 5.0 50.8 1.0

Calcium binding site 6 out of 25 in 2zrs

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Calcium binding site 6 out of 25 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2


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 CA2+-Bound Form of DES3-23ALG-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:31.1
occ:1.00
 ND2 B:ASN106 3.1 50.5 1.0
OD1 C:ASN106 3.2 45.7 1.0
OD1 B:ASN106 3.3 51.0 1.0
CG B:ASN106 3.6 51.1 1.0
O C:ARG100 3.8 42.0 1.0
O C:ASP103 4.1 44.3 1.0
CG C:ASN106 4.3 45.3 1.0
O B:ARG100 4.3 45.0 1.0
CA C:ARG104 4.5 45.1 1.0
CG C:ARG104 4.6 46.2 1.0
C C:ASP103 4.6 44.3 1.0
ND2 C:ASN106 4.7 44.8 1.0
O B:ARG104 4.8 50.2 1.0
N C:ARG104 4.8 44.7 1.0
O B:ASP103 4.9 49.0 1.0
C C:ARG100 5.0 42.1 1.0

Calcium binding site 7 out of 25 in 2zrs

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Calcium binding site 7 out of 25 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2


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 CA2+-Bound Form of DES3-23ALG-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca990

b:33.2
occ:1.00
 O C:VAL42 2.6 43.3 1.0
OD1 C:ASP36 2.9 43.3 1.0
OE2 C:GLU47 3.0 46.5 1.0
OD1 C:ASP38 3.2 44.7 1.0
OD2 C:ASP38 3.2 44.9 1.0
C C:VAL42 3.4 43.5 1.0
CD C:GLU47 3.5 46.1 1.0
CG C:ASP38 3.6 44.5 1.0
CG C:ASP36 3.6 43.5 1.0
CG C:GLU47 3.6 45.1 1.0
CA C:ILE43 3.7 43.3 1.0
N C:SER44 3.8 43.2 1.0
N C:ILE43 4.0 43.4 1.0
OG C:SER44 4.0 43.7 1.0
CB C:ASP36 4.2 43.2 1.0
C C:ILE43 4.3 43.3 1.0
OD2 C:ASP36 4.3 43.9 1.0
OE1 C:GLU47 4.3 46.4 1.0
CB C:GLU47 4.4 44.4 1.0
CB C:SER40 4.5 44.1 1.0
CB C:SER44 4.5 43.4 1.0
CA C:VAL42 4.6 43.5 1.0
CB C:VAL42 4.7 43.5 1.0
CA C:SER44 4.8 43.4 1.0
CA C:ASP36 4.8 43.2 1.0
CB C:ILE43 4.9 43.3 1.0
CG2 C:VAL42 5.0 43.2 1.0
CG2 C:ILE43 5.0 43.3 1.0

Calcium binding site 8 out of 25 in 2zrs

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Calcium binding site 8 out of 25 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of CA2+-Bound Form of DES3-23ALG-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca991

b:52.4
occ:1.00
 OG C:SER107 2.3 44.9 1.0
CB C:SER107 3.1 44.9 1.0
OD1 C:ASP105 3.2 44.4 1.0
N C:MET109 3.3 44.2 1.0
O C:MET109 3.3 43.7 1.0
CB C:MET109 3.7 43.9 1.0
C C:SER107 3.7 44.8 1.0
CA C:MET109 3.8 43.9 1.0
N C:GLY108 3.9 44.8 1.0
CA C:SER107 3.9 44.9 1.0
C C:MET109 3.9 43.8 1.0
O C:SER107 4.0 44.7 1.0
OD2 C:ASP103 4.0 42.5 1.0
CG C:ASP105 4.3 44.6 1.0
OE1 C:GLN145 4.4 33.5 1.0
C C:GLY108 4.4 44.4 1.0
N C:SER107 4.4 45.0 1.0
CA C:GLY108 4.6 44.6 1.0
CG C:MET109 4.6 43.7 1.0
OE1 C:GLU114 4.7 40.8 1.0

Calcium binding site 9 out of 25 in 2zrs

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Calcium binding site 9 out of 25 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of CA2+-Bound Form of DES3-23ALG-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca992

b:51.4
occ:1.00
 OD2 C:ASP173 2.8 45.1 1.0
CB C:ASP173 2.9 45.0 1.0
OD1 C:ASP169 3.1 43.3 1.0
CG C:ASP173 3.2 45.4 1.0
O C:TRP175 3.4 45.5 1.0
CG C:ASP169 3.8 43.0 1.0
N C:THR170 4.2 43.0 1.0
CA C:ASP173 4.2 45.0 1.0
OD1 C:ASP173 4.3 46.1 1.0
OD2 C:ASP169 4.4 43.5 1.0
N C:ASP173 4.4 44.6 1.0
CA C:ASP169 4.5 42.7 1.0
C C:TRP175 4.6 45.5 1.0
N C:ASP171 4.6 43.6 1.0
CB C:ASP169 4.7 42.7 1.0
C C:ASP169 4.8 42.8 1.0
C C:ASP173 4.9 45.2 1.0
N C:GLY174 5.0 45.3 1.0
OG1 C:THR170 5.0 43.0 1.0

Calcium binding site 10 out of 25 in 2zrs

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Calcium binding site 10 out of 25 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of CA2+-Bound Form of DES3-23ALG-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca990

b:13.4
occ:1.00
 OE1 D:GLU47 2.0 16.5 1.0
OE2 D:GLU47 2.5 17.0 1.0
CD D:GLU47 2.6 17.6 1.0
OD2 D:ASP38 2.8 24.8 1.0
O D:VAL42 2.8 26.6 1.0
OG D:SER40 2.9 27.1 1.0
OG D:SER44 3.1 25.7 1.0
OD1 D:ASP36 3.3 25.2 1.0
OD1 D:ASP38 3.4 25.8 1.0
N D:SER44 3.5 25.5 1.0
CG D:ASP38 3.5 25.6 1.0
C D:VAL42 3.9 26.5 1.0
CB D:SER40 4.0 27.3 1.0
CB D:SER44 4.0 25.4 1.0
CG D:GLU47 4.0 19.1 1.0
CA D:ILE43 4.1 25.9 1.0
C D:ILE43 4.2 25.8 1.0
CA D:SER44 4.3 25.3 1.0
N D:ILE43 4.5 26.1 1.0
CG D:ASP36 4.5 25.0 1.0
CA D:ASP36 4.5 24.7 1.0
N D:SER40 4.7 27.1 1.0
CB D:GLU47 4.7 19.9 1.0
N D:LYS37 4.8 24.9 1.0
C D:ASP36 4.9 24.7 1.0
CA D:SER40 4.9 27.2 1.0
N D:ASP38 4.9 25.7 1.0
CB D:ASP38 5.0 26.0 1.0
O D:VAL35 5.0 24.3 1.0

Reference:

H.Suzuki, M.Kawasaki, T.Kakiuchi, H.Shibata, S.Wakatsuki, M.Maki. Crystallization and X-Ray Diffraction Analysis of N-Terminally Truncated Human Alg-2 Acta Crystallogr.,Sect.F V. 64 974 2008.
ISSN: ESSN 1744-3091
PubMed: 18997320
DOI: 10.1107/S1744309108030297
Page generated: Sat Jul 13 06:51:14 2024

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