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Calcium in PDB 1xo5: Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein

Protein crystallography data

The structure of Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein, PDB code: 1xo5 was solved by H.R.Gentry, A.U.Singer, L.Betts, C.Yang, J.D.Ferrara, L.V.Parise, J.Sondek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.32 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.663, 51.009, 77.214, 90.00, 103.12, 90.00
R / Rfree (%) 21.2 / 25.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein (pdb code 1xo5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein, PDB code: 1xo5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1xo5

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Calcium binding site 1 out of 8 in the Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein


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 CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:41.6
occ:1.00
 OD1 A:ASP116 2.2 42.9 1.0
O A:HOH593 2.2 38.8 1.0
O A:THR122 2.3 42.8 1.0
OD1 A:ASP118 2.3 52.8 1.0
OD2 A:ASP120 2.3 49.3 1.0
OD2 A:ASP127 2.5 39.9 1.0
O A:HOH617 2.7 38.4 1.0
CG A:ASP116 3.2 44.2 1.0
CG A:ASP118 3.4 52.2 1.0
CG A:ASP120 3.4 50.3 1.0
C A:THR122 3.5 43.1 1.0
CG A:ASP127 3.6 42.5 1.0
OD2 A:ASP118 3.8 54.1 1.0
OD1 A:ASP127 4.0 41.4 1.0
OD2 A:ASP116 4.0 42.0 1.0
O A:HOH763 4.1 92.1 1.0
CA A:ASP116 4.1 45.6 1.0
OD1 A:ASP120 4.1 51.3 1.0
CB A:ASP116 4.1 45.4 1.0
OG1 A:THR122 4.2 42.0 1.0
N A:THR122 4.2 44.6 1.0
N A:ASP118 4.3 50.1 1.0
C A:ASP116 4.3 46.6 1.0
N A:PHE117 4.4 47.7 1.0
N A:ASP120 4.4 50.5 1.0
CB A:ASP120 4.4 49.8 1.0
CA A:THR122 4.4 43.5 1.0
N A:LEU123 4.4 42.1 1.0
CA A:LEU123 4.5 41.7 1.0
N A:ASN124 4.5 42.1 1.0
ND2 A:ASN124 4.6 43.5 1.0
CB A:ASP118 4.6 51.0 1.0
CG A:ASN124 4.7 43.0 1.0
N A:ASP119 4.7 51.3 1.0
CA A:ASP118 4.8 50.9 1.0
CA A:ASP120 4.8 49.9 1.0
N A:GLY121 4.9 48.0 1.0
OD1 A:ASN124 4.9 43.5 1.0
CB A:ASP127 4.9 42.3 1.0
CB A:THR122 4.9 43.5 1.0
C A:ASP118 5.0 51.2 1.0
O A:ASP116 5.0 46.9 1.0
C A:LEU123 5.0 42.0 1.0

Calcium binding site 2 out of 8 in 1xo5

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Calcium binding site 2 out of 8 in the Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein


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 CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:47.6
occ:1.00
 O A:HOH592 2.3 33.6 1.0
O A:HOH438 2.4 28.2 1.0
O A:HOH731 2.4 38.4 1.0
O A:HOH626 2.4 35.2 1.0
O A:HOH603 2.4 37.1 1.0
O A:HOH633 2.5 30.8 1.0
O A:GLU15 4.2 44.2 1.0
O A:HOH834 4.2 56.4 1.0
O A:HOH495 4.3 27.1 1.0
O A:HOH622 4.5 41.4 1.0
OD2 A:ASP93 4.5 42.1 1.0
OD2 A:ASP18 4.8 49.6 1.0
OE1 A:GLU89 4.8 52.0 1.0
O A:GLN17 4.9 49.1 1.0
OD1 A:ASP93 5.0 43.3 1.0

Calcium binding site 3 out of 8 in 1xo5

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Calcium binding site 3 out of 8 in the Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein


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 CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:40.2
occ:1.00
 OD1 A:ASP165 2.3 41.0 1.0
OD1 A:ASP161 2.3 37.7 1.0
OD1 A:ASP163 2.3 46.6 1.0
O A:THR167 2.4 41.5 1.0
OE1 A:GLU172 2.4 38.5 1.0
O A:HOH589 2.6 40.6 1.0
OE2 A:GLU172 2.8 39.1 1.0
CD A:GLU172 3.0 39.8 1.0
O A:HOH806 3.1 0.0 1.0
CG A:ASP163 3.3 45.1 1.0
CG A:ASP165 3.3 42.7 1.0
CG A:ASP161 3.4 38.9 1.0
C A:THR167 3.5 41.5 1.0
OD2 A:ASP163 3.6 45.9 1.0
OD2 A:ASP165 3.9 44.3 1.0
OG1 A:THR167 4.1 41.2 1.0
OD2 A:ASP161 4.1 39.7 1.0
CA A:ASP161 4.2 38.2 1.0
N A:ASP165 4.3 43.1 1.0
N A:THR167 4.3 41.6 1.0
CB A:ASP161 4.3 38.2 1.0
N A:ILE168 4.3 41.6 1.0
CA A:ILE168 4.3 41.8 1.0
N A:ASN169 4.4 41.9 1.0
CB A:ASP165 4.4 42.9 1.0
CA A:THR167 4.4 41.7 1.0
CG A:GLU172 4.5 39.9 1.0
N A:ASP163 4.5 43.5 1.0
N A:ARG164 4.6 43.9 1.0
C A:ASP161 4.6 39.1 1.0
CB A:ASP163 4.6 44.2 1.0
ND2 A:ASN169 4.6 42.8 1.0
N A:ILE162 4.7 40.4 1.0
CA A:ASP165 4.8 42.6 1.0
C A:ILE168 4.9 41.9 1.0
N A:GLY166 4.9 42.1 1.0
CG A:ASN169 4.9 42.2 1.0
CA A:ASP163 4.9 43.9 1.0
C A:ASP163 4.9 44.0 1.0
CB A:THR167 4.9 41.6 1.0

Calcium binding site 4 out of 8 in 1xo5

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Calcium binding site 4 out of 8 in the Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein


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 CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7

b:43.2
occ:1.00
 O A:HOH596 2.3 28.8 1.0
O A:PHE98 2.4 37.0 1.0
O A:LEU191 2.4 46.9 1.0
OXT A:LEU191 2.4 46.8 1.0
O A:HOH590 2.5 30.4 1.0
O A:HOH404 2.5 29.8 1.0
O A:HOH468 2.5 26.6 1.0
C A:LEU191 2.8 46.9 1.0
C A:PHE98 3.5 37.8 1.0
O A:HOH441 4.0 36.4 1.0
CA A:PHE98 4.0 37.7 1.0
NZ A:LYS107 4.2 41.4 1.0
CB A:PHE98 4.2 38.3 1.0
OD1 A:ASP100 4.3 42.6 1.0
CA A:LEU191 4.4 46.7 1.0
O A:HOH645 4.4 40.4 1.0
O A:HOH584 4.5 27.5 1.0
N A:SER99 4.6 38.1 1.0
O A:LYS188 4.6 45.1 1.0
C A:SER99 4.8 38.6 1.0
CG A:PHE98 4.8 38.7 1.0
CD2 A:PHE98 4.8 40.4 1.0
O A:HOH409 4.8 29.0 1.0
O A:SER99 4.9 37.7 1.0
CA A:SER99 4.9 39.0 1.0
O A:PHE187 5.0 44.0 1.0

Calcium binding site 5 out of 8 in 1xo5

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Calcium binding site 5 out of 8 in the Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein


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 CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:49.9
occ:1.00
 O B:THR122 2.3 43.6 1.0
OD2 B:ASP127 2.4 44.1 1.0
O B:HOH847 2.5 49.2 1.0
OD1 B:ASP120 2.7 44.7 1.0
OD1 B:ASP116 2.8 40.5 1.0
OD1 B:ASP118 2.8 42.6 1.0
OD1 B:ASN124 3.3 43.4 1.0
OD2 B:ASP120 3.3 45.5 1.0
CG B:ASP120 3.3 44.8 1.0
CG B:ASP127 3.5 44.7 1.0
C B:THR122 3.6 43.8 1.0
CG B:ASP118 3.6 43.4 1.0
CG B:ASP116 3.7 41.5 1.0
OD1 B:ASP127 3.9 43.8 1.0
CB B:ASP118 4.0 43.4 1.0
N B:ASN124 4.2 44.2 1.0
CA B:LEU123 4.3 43.9 1.0
CA B:ASP116 4.3 41.4 1.0
N B:ASP118 4.3 43.4 1.0
CG B:ASN124 4.4 44.1 1.0
N B:LEU123 4.4 43.8 1.0
OD2 B:ASP116 4.4 41.9 1.0
CB B:ASP116 4.6 41.3 1.0
C B:ASP116 4.6 42.0 1.0
OD2 B:ASP118 4.6 43.8 1.0
N B:PHE117 4.6 42.7 1.0
CA B:ASP118 4.7 43.4 1.0
N B:THR122 4.7 44.4 1.0
OG1 B:THR122 4.7 43.8 1.0
CA B:THR122 4.7 44.0 1.0
C B:LEU123 4.7 44.0 1.0
CB B:ASP120 4.8 44.4 1.0
CB B:ASP127 4.8 44.8 1.0
N B:ASP120 4.8 44.2 1.0
CB B:ASN124 5.0 44.2 1.0

Calcium binding site 6 out of 8 in 1xo5

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Calcium binding site 6 out of 8 in the Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein


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 CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:56.7
occ:1.00
 O B:HOH702 2.6 58.7 1.0
OD2 B:ASP93 4.6 41.7 1.0
O B:HOH698 4.7 75.0 1.0
OD2 B:ASP18 4.8 55.2 1.0
O B:GLN17 4.9 55.4 1.0
OD1 B:ASP93 4.9 43.8 1.0
O B:GLU15 5.0 57.2 1.0

Calcium binding site 7 out of 8 in 1xo5

Go back to Calcium Binding Sites List in 1xo5
Calcium binding site 7 out of 8 in the Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein


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 CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca6

b:50.1
occ:1.00
 OD2 B:ASP165 2.3 43.2 1.0
OD1 B:ASP161 2.3 44.2 1.0
OD2 B:ASP163 2.5 43.7 1.0
O B:THR167 2.5 42.8 1.0
O B:HOH690 2.5 59.2 1.0
OE1 B:GLU172 2.7 46.3 1.0
O B:ASP165 2.9 42.9 1.0
OE2 B:GLU172 3.0 46.7 1.0
CD B:GLU172 3.2 46.4 1.0
CG B:ASP161 3.3 44.7 1.0
CG B:ASP163 3.4 44.4 1.0
CG B:ASP165 3.5 43.5 1.0
OD1 B:ASP163 3.5 45.0 1.0
C B:THR167 3.5 42.6 1.0
C B:ASP165 3.9 42.8 1.0
OD2 B:ASP161 3.9 44.5 1.0
N B:ASP165 4.0 43.2 1.0
OG1 B:THR167 4.0 41.6 1.0
ND2 B:ASN169 4.0 44.3 1.0
N B:THR167 4.1 42.1 1.0
OD1 B:ASP165 4.2 43.9 1.0
CA B:ASP161 4.3 44.8 1.0
CB B:ASP161 4.3 44.8 1.0
CA B:ASP165 4.3 43.0 1.0
CA B:THR167 4.4 42.3 1.0
N B:ILE168 4.4 43.1 1.0
CB B:ASP165 4.5 43.0 1.0
CA B:ILE168 4.5 43.3 1.0
N B:ARG164 4.5 44.1 1.0
N B:ASN169 4.7 43.6 1.0
CG B:GLU172 4.7 46.3 1.0
C B:ASP161 4.8 44.7 1.0
CB B:ASP163 4.8 44.5 1.0
N B:ILE162 4.8 44.7 1.0
N B:ASP163 4.8 44.7 1.0
CB B:THR167 4.8 42.1 1.0
CG B:ASN169 4.9 43.7 1.0

Calcium binding site 8 out of 8 in 1xo5

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Calcium binding site 8 out of 8 in the Crystal Structure of CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein


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 CIB1, An Ef-Hand, Integrin and Kinase-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca8

b:50.6
occ:1.00
 O B:HOH513 2.4 48.1 1.0
O B:PHE98 2.4 41.7 1.0
O B:HOH672 2.5 52.4 1.0
O B:HOH742 2.6 51.2 1.0
OXT B:LEU191 2.7 50.6 1.0
O B:LEU191 2.9 50.6 1.0
O B:HOH788 3.1 88.8 1.0
C B:LEU191 3.2 50.7 1.0
C B:PHE98 3.6 41.8 1.0
OD1 B:ASP100 3.9 47.2 1.0
CA B:PHE98 4.2 41.7 1.0
CB B:PHE98 4.4 42.2 1.0
O B:LYS188 4.5 50.6 1.0
NZ B:LYS107 4.6 39.7 1.0
N B:SER99 4.7 42.0 1.0
CA B:LEU191 4.7 50.8 1.0
C B:SER99 4.8 42.8 1.0
N B:ASP100 4.9 43.4 1.0
CG B:PHE98 4.9 43.0 1.0
CA B:SER99 5.0 42.3 1.0
CD2 B:PHE98 5.0 44.0 1.0

Reference:

H.R.Gentry, A.U.Singer, L.Betts, C.Yang, J.D.Ferrara, J.Sondek, L.V.Parise. Structural and Biochemical Characterization of CIB1 Delineates A New Family of Ef-Hand-Containing Proteins J.Biol.Chem. V. 280 8407 2005.
ISSN: ISSN 0021-9258
PubMed: 15574431
DOI: 10.1074/JBC.M411515200
Page generated: Fri Jul 12 07:43:15 2024

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