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Calcium in PDB 3e3r: Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family

Protein crystallography data

The structure of Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family, PDB code: 3e3r was solved by H.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.593, 130.411, 46.199, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 27.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family (pdb code 3e3r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family, PDB code: 3e3r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 3e3r

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Calcium binding site 1 out of 9 in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca192

b:36.3
occ:1.00
OD1 A:ASN72 2.1 33.5 1.0
OD1 A:ASP70 2.3 32.7 1.0
OE1 A:GLU81 2.4 29.1 1.0
O A:THR76 2.5 29.5 1.0
OG A:SER74 2.5 28.8 1.0
OE2 A:GLU81 2.7 29.0 1.0
CD A:GLU81 2.9 28.6 1.0
CG A:ASN72 3.2 31.2 1.0
CG A:ASP70 3.4 30.2 1.0
CB A:SER74 3.5 29.0 1.0
C A:THR76 3.7 29.7 1.0
ND2 A:ASN72 3.8 31.2 1.0
N A:SER74 4.0 28.4 1.0
CB A:ASP70 4.2 29.8 1.0
OD1 A:ASP78 4.3 29.9 1.0
CA A:ASP70 4.3 29.7 1.0
OD2 A:ASP70 4.3 29.0 1.0
CA A:SER74 4.3 28.6 1.0
N A:THR76 4.3 29.6 1.0
CG A:GLU81 4.4 29.3 1.0
OG1 A:THR76 4.4 30.3 1.0
N A:ASN72 4.4 29.5 1.0
N A:GLY73 4.5 29.0 1.0
CB A:ASN72 4.5 29.5 1.0
N A:ASP78 4.5 29.8 1.0
CA A:THR76 4.5 29.8 1.0
N A:LEU77 4.6 29.7 1.0
C A:ASP70 4.6 29.7 1.0
CA A:LEU77 4.6 29.6 1.0
CG A:ASP78 4.7 30.1 1.0
CA A:ASN72 4.7 29.5 1.0
N A:ARG71 4.7 29.7 1.0
C A:ASN72 4.9 29.3 1.0
C A:SER74 4.9 28.7 1.0
N A:GLY75 4.9 28.7 1.0

Calcium binding site 2 out of 9 in 3e3r

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Calcium binding site 2 out of 9 in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca194

b:36.0
occ:1.00
OD1 A:ASP154 2.4 36.6 1.0
O A:GLN156 2.4 31.6 1.0
OE2 A:GLU161 2.5 32.1 1.0
OD2 A:ASP149 2.5 31.4 1.0
OE1 A:GLU161 2.6 30.9 1.0
CD A:GLU161 2.9 30.9 1.0
CG A:ASP154 3.2 35.3 1.0
OD2 A:ASP154 3.3 33.7 1.0
CG A:ASP149 3.4 32.1 1.0
OD1 A:ASP149 3.6 31.2 1.0
C A:GLN156 3.6 31.5 1.0
CB A:GLN156 4.2 32.8 1.0
O A:GLU152 4.4 39.7 1.0
CA A:GLN156 4.4 32.5 1.0
CG A:GLU161 4.4 28.3 1.0
N A:VAL157 4.5 30.1 1.0
CA A:VAL157 4.6 29.1 1.0
N A:SER150 4.6 34.6 1.0
N A:GLN156 4.6 32.7 1.0
CB A:ASP154 4.6 35.4 1.0
CB A:SER150 4.7 35.4 1.0
CB A:ASP149 4.8 32.2 1.0
N A:ASP154 4.9 36.0 1.0

Calcium binding site 3 out of 9 in 3e3r

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Calcium binding site 3 out of 9 in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca195

b:35.6
occ:1.00
OE1 A:GLU137 4.2 26.1 1.0
OD1 A:ASP138 4.5 24.8 1.0
NE A:ARG119 4.5 26.3 1.0
OD2 A:ASP138 4.8 24.8 1.0
CG A:ASP138 4.9 23.9 1.0
CD A:ARG119 4.9 25.5 1.0

Calcium binding site 4 out of 9 in 3e3r

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Calcium binding site 4 out of 9 in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca197

b:40.8
occ:1.00
OE1 A:GLU45 2.2 45.4 1.0
OD2 A:ASP36 2.4 48.0 1.0
O A:SER40 2.5 39.7 1.0
OG A:SER38 2.5 42.0 1.0
OD1 A:ASP34 2.7 45.6 1.0
CD A:GLU45 2.8 46.6 1.0
OE2 A:GLU45 3.0 48.4 1.0
CG A:ASP36 3.4 47.9 1.0
OD2 A:ASP42 3.6 43.3 1.0
CB A:SER38 3.7 43.1 1.0
C A:SER40 3.7 40.0 1.0
OD1 A:ASP36 3.7 48.9 1.0
CG A:ASP34 4.0 46.7 1.0
N A:ASP42 4.0 39.8 1.0
CA A:LEU41 4.1 39.5 1.0
CG A:ASP42 4.1 42.1 1.0
CG A:GLU45 4.1 44.7 1.0
N A:LEU41 4.3 39.7 1.0
N A:SER38 4.4 43.7 1.0
OD1 A:ASP42 4.4 43.5 1.0
C A:LEU41 4.5 39.6 1.0
N A:ASP36 4.6 47.1 1.0
CA A:SER38 4.6 43.2 1.0
CB A:ASP36 4.6 47.2 1.0
CA A:ASP34 4.7 47.5 1.0
OD2 A:ASP34 4.8 45.6 1.0
CD2 A:LEU41 4.8 38.9 1.0
CB A:GLU45 4.8 43.8 1.0
N A:SER40 4.8 41.0 1.0
CB A:ASP34 4.9 47.4 1.0
CB A:ASP42 4.9 40.5 1.0
CA A:SER40 4.9 40.4 1.0
N A:ARG35 4.9 47.7 1.0
CA A:ASP36 5.0 47.0 1.0
C A:ASP34 5.0 47.6 1.0
OG A:SER40 5.0 40.8 1.0

Calcium binding site 5 out of 9 in 3e3r

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Calcium binding site 5 out of 9 in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca196

b:37.8
occ:1.00
O A:VAL112 2.4 25.0 1.0
OD1 A:ASP106 2.5 25.3 1.0
OD2 A:ASP117 2.5 23.0 1.0
OG A:SER108 2.5 30.1 1.0
O A:HOH222 2.7 34.6 1.0
OD2 A:ASP110 2.7 33.8 1.0
OD1 A:ASP117 2.9 24.6 1.0
CG A:ASP117 3.1 24.4 1.0
CG A:ASP110 3.3 31.5 1.0
CB A:SER108 3.5 29.1 1.0
OD1 A:ASP110 3.6 31.3 1.0
CG A:ASP106 3.6 25.5 1.0
C A:VAL112 3.6 25.2 1.0
N A:SER108 3.9 27.6 1.0
N A:ASP110 4.0 29.6 1.0
N A:GLY109 4.2 28.6 1.0
CA A:SER108 4.2 28.3 1.0
N A:VAL112 4.3 25.9 1.0
OD2 A:ASP106 4.3 24.9 1.0
CB A:ASP110 4.3 29.8 1.0
CA A:ASP106 4.4 24.8 1.0
CG2 A:VAL112 4.4 25.8 1.0
C A:SER108 4.5 28.4 1.0
CA A:VAL112 4.5 25.6 1.0
CB A:ASP106 4.5 25.1 1.0
N A:VAL113 4.5 24.9 1.0
C A:ASP106 4.6 25.4 1.0
CA A:VAL113 4.6 25.0 1.0
CB A:ASP117 4.6 24.6 1.0
CA A:ASP110 4.6 29.0 1.0
N A:ARG107 4.7 26.4 1.0
OG1 A:THR114 4.7 23.1 1.0
N A:THR114 4.8 24.6 1.0
N A:GLY111 4.8 27.6 1.0
C A:ASP110 5.0 28.4 1.0

Calcium binding site 6 out of 9 in 3e3r

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Calcium binding site 6 out of 9 in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca192

b:32.1
occ:1.00
OG B:SER74 2.4 35.5 1.0
OD2 B:ASP70 2.4 40.5 1.0
OD1 B:ASN72 2.4 37.0 1.0
O B:THR76 2.4 29.7 1.0
OE1 B:GLU81 2.6 28.5 1.0
OE2 B:GLU81 2.6 27.4 1.0
CD B:GLU81 3.0 27.6 1.0
CG B:ASN72 3.3 38.4 1.0
CG B:ASP70 3.4 40.2 1.0
CB B:SER74 3.4 35.0 1.0
C B:THR76 3.6 29.4 1.0
ND2 B:ASN72 3.7 38.2 1.0
N B:SER74 4.0 35.8 1.0
OD1 B:ASP70 4.1 39.8 1.0
CB B:ASP70 4.2 40.3 1.0
CA B:SER74 4.3 35.0 1.0
CA B:ASP70 4.3 40.4 1.0
OG1 B:THR76 4.3 29.5 1.0
N B:THR76 4.4 31.1 1.0
N B:ASN72 4.4 38.5 1.0
N B:ASP78 4.5 25.8 1.0
CG B:GLU81 4.5 26.0 1.0
CA B:THR76 4.5 30.0 1.0
N B:LEU77 4.5 28.2 1.0
CA B:LEU77 4.6 26.8 1.0
N B:ARG71 4.6 39.9 1.0
CB B:ASN72 4.6 38.1 1.0
C B:ASP70 4.7 40.4 1.0
CA B:ASN72 4.8 38.1 1.0
N B:GLY73 4.8 37.7 1.0
C B:ASN72 4.8 37.8 1.0
OD1 B:ASP78 4.8 26.9 1.0
C B:SER74 4.8 34.0 1.0
C B:LEU77 5.0 26.5 1.0
N B:GLY75 5.0 32.9 1.0

Calcium binding site 7 out of 9 in 3e3r

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Calcium binding site 7 out of 9 in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca193

b:38.9
occ:1.00
OD2 B:ASP149 2.3 28.4 1.0
OE1 B:GLU161 2.5 26.0 1.0
O B:GLN156 2.5 30.2 1.0
OD1 B:ASP154 2.5 35.4 1.0
OE2 B:GLU161 2.6 28.5 1.0
CD B:GLU161 2.9 27.6 1.0
CG B:ASP149 3.2 31.5 1.0
OD1 B:ASP149 3.3 30.4 1.0
CG B:ASP154 3.5 33.5 1.0
C B:GLN156 3.6 29.9 1.0
OD2 B:ASP154 3.8 31.1 1.0
CG B:GLU161 4.4 26.0 1.0
CB B:GLN156 4.4 30.1 1.0
CA B:GLN156 4.4 30.0 1.0
N B:VAL157 4.5 29.6 1.0
N B:GLN156 4.5 30.6 1.0
CA B:VAL157 4.5 28.6 1.0
CB B:ASP149 4.7 32.9 1.0
N B:SER150 4.7 35.8 1.0
N B:ASP154 4.8 35.3 1.0
CB B:ASP154 4.8 34.0 1.0
N B:THR158 4.9 27.4 1.0
CB B:SER150 4.9 37.2 1.0
OG B:SER150 4.9 38.8 1.0

Calcium binding site 8 out of 9 in 3e3r

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Calcium binding site 8 out of 9 in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca194

b:27.9
occ:1.00
OD1 B:ASP106 2.2 29.9 1.0
OD1 B:ASP110 2.5 25.7 1.0
OD2 B:ASP117 2.5 34.2 1.0
O B:VAL112 2.5 19.6 1.0
OD1 B:ASP117 2.8 28.6 1.0
OG B:SER108 2.9 21.3 1.0
CG B:ASP117 3.0 31.8 1.0
O B:HOH197 3.1 35.7 1.0
CG B:ASP106 3.3 25.4 1.0
CB B:SER108 3.4 20.9 1.0
CG B:ASP110 3.4 21.7 1.0
C B:VAL112 3.7 19.8 1.0
N B:GLY109 3.9 20.8 1.0
OD2 B:ASP106 3.9 27.4 1.0
N B:ASP110 4.0 20.4 1.0
OD2 B:ASP110 4.0 21.8 1.0
CA B:SER108 4.1 21.2 1.0
O B:HOH201 4.1 14.6 1.0
N B:SER108 4.2 21.4 1.0
C B:SER108 4.2 20.9 1.0
CB B:ASP110 4.4 19.9 1.0
N B:VAL112 4.5 19.7 1.0
CB B:ASP106 4.5 23.0 1.0
CB B:ASP117 4.5 31.8 1.0
CA B:VAL113 4.5 21.9 1.0
N B:VAL113 4.6 20.6 1.0
CA B:ASP106 4.6 22.4 1.0
OG1 B:THR114 4.7 26.0 1.0
CA B:ASP110 4.7 20.3 1.0
O B:ASP106 4.7 21.2 1.0
C B:ASP106 4.7 21.9 1.0
CA B:VAL112 4.7 19.0 1.0
N B:THR114 4.8 24.6 1.0
CA B:GLY109 4.8 20.7 1.0
N B:GLY111 4.8 19.8 1.0
CG2 B:VAL112 4.8 17.4 1.0
C B:GLY109 4.9 20.7 1.0

Calcium binding site 9 out of 9 in 3e3r

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Calcium binding site 9 out of 9 in the Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca195

b:30.9
occ:1.00
OE2 B:GLU45 2.2 42.8 1.0
OD2 B:ASP34 2.4 34.7 1.0
OD1 B:ASP36 2.4 36.7 1.0
O B:SER40 2.4 30.8 1.0
OG B:SER38 2.5 31.8 1.0
CD B:GLU45 2.9 43.1 1.0
OE1 B:GLU45 3.0 44.0 1.0
CG B:ASP36 3.2 35.5 1.0
OD2 B:ASP36 3.3 36.9 1.0
OD1 B:ASP42 3.4 39.2 1.0
CG B:ASP34 3.6 36.9 1.0
C B:SER40 3.6 31.3 1.0
CB B:SER38 3.7 31.4 1.0
N B:SER38 4.2 31.8 1.0
CG B:GLU45 4.3 42.1 1.0
CA B:LEU41 4.4 32.2 1.0
OD1 B:ASP34 4.4 38.9 1.0
CA B:SER38 4.4 31.6 1.0
N B:LEU41 4.5 31.8 1.0
N B:SER40 4.5 31.6 1.0
CA B:ASP34 4.5 36.5 1.0
CB B:ASP34 4.5 36.5 1.0
N B:ASP42 4.6 33.9 1.0
CB B:ASP36 4.6 34.7 1.0
CA B:SER40 4.6 31.5 1.0
CG B:ASP42 4.7 36.5 1.0
N B:ASP36 4.7 35.1 1.0
OG B:SER40 4.9 31.9 1.0
N B:GLY37 4.9 33.1 1.0
C B:ASP34 4.9 36.6 1.0
CB B:GLU45 4.9 40.9 1.0
C B:LEU41 4.9 32.9 1.0
C B:SER38 4.9 31.7 1.0
N B:ARG39 5.0 31.6 1.0

Reference:

H.Dong, X.Li, Z.Lou, X.Xu, D.Su, X.Zhou, W.Zhou, M.Bartlam, Z.Rao. Crystal-Structure and Biochemical Characterization of Recombinant Human Calcyphosine Delineates A Novel Ef-Hand-Containing Protein Family J.Mol.Biol. V. 383 455 2008.
ISSN: ISSN 0022-2836
PubMed: 18775726
DOI: 10.1016/J.JMB.2008.08.048
Page generated: Sat Dec 12 04:09:36 2020

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