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Calcium in PDB 4upu: Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin

Enzymatic activity of Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin

All present enzymatic activity of Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin:
2.7.1.127;

Protein crystallography data

The structure of Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin, PDB code: 4upu was solved by E.Franco-Echevarria, J.I.Banos-Sanz, B.Monterroso, A.Round, J.Sanz-Aparicio, B.Gonzalez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.65 / 2.34
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 159.480, 159.480, 159.480, 90.00, 90.00, 90.00
R / Rfree (%) 18.805 / 21.041

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin (pdb code 4upu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin, PDB code: 4upu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4upu

Go back to Calcium Binding Sites List in 4upu
Calcium binding site 1 out of 5 in the Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin


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 IP3 3-K Calmodulin Binding Region in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1149

b:28.6
occ:1.00
 O A:HOH2011 2.2 29.2 1.0
O A:THR27 2.3 32.2 1.0
OD1 A:ASP21 2.3 28.6 1.0
OD1 A:ASP23 2.3 42.0 1.0
OD1 A:ASP25 2.4 33.2 1.0
OE2 A:GLU32 2.5 33.6 1.0
OE1 A:GLU32 2.6 28.7 1.0
CD A:GLU32 2.9 29.4 1.0
CG A:ASP23 3.3 39.9 1.0
CG A:ASP25 3.3 34.2 1.0
CG A:ASP21 3.4 31.8 1.0
C A:THR27 3.5 32.3 1.0
OD2 A:ASP23 3.5 41.2 1.0
OD2 A:ASP25 3.8 34.6 1.0
OG1 A:THR27 4.0 41.0 1.0
CA A:ASP21 4.1 33.4 1.0
N A:THR27 4.2 31.6 1.0
CB A:ASP21 4.2 31.2 1.0
OD2 A:ASP21 4.3 29.3 1.0
N A:ASP25 4.3 32.7 1.0
CA A:THR27 4.3 33.1 1.0
CG A:GLU32 4.4 28.7 1.0
C A:ASP21 4.4 35.6 1.0
N A:ILE28 4.4 29.7 1.0
CB A:ASP25 4.5 30.6 1.0
N A:ASP23 4.5 35.9 1.0
CA A:ILE28 4.5 27.3 1.0
CB A:ASP23 4.6 36.6 1.0
N A:LYS22 4.6 38.5 1.0
CA A:ASP25 4.7 30.9 1.0
O A:HOH2013 4.8 39.6 1.0
N A:GLY24 4.8 36.2 1.0
CB A:THR27 4.8 34.4 1.0
CA A:ASP23 4.9 36.3 1.0
N A:GLY26 4.9 30.5 1.0
N A:THR29 4.9 26.1 1.0
O A:HOH2010 4.9 42.8 1.0
O A:ASP21 4.9 38.7 1.0
C A:ASP25 4.9 31.0 1.0
C A:ASP23 5.0 37.9 1.0

Calcium binding site 2 out of 5 in 4upu

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Calcium binding site 2 out of 5 in the Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin


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 IP3 3-K Calmodulin Binding Region in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1150

b:36.7
occ:1.00
 OD1 A:ASN61 2.3 42.0 1.0
OD1 A:ASP57 2.3 38.3 1.0
O A:HOH2031 2.4 33.8 1.0
O A:THR63 2.5 34.0 1.0
O A:HOH2030 2.5 34.9 1.0
OD1 A:ASP59 2.5 51.2 1.0
OE1 A:GLU68 2.6 30.2 1.0
OE2 A:GLU68 2.6 32.7 1.0
CD A:GLU68 2.9 29.1 1.0
CG A:ASN61 3.3 43.7 1.0
CG A:ASP57 3.4 40.5 1.0
CG A:ASP59 3.5 48.0 1.0
C A:THR63 3.6 34.8 1.0
ND2 A:ASN61 3.7 46.3 1.0
OD2 A:ASP59 3.8 48.9 1.0
OD2 A:ASP57 4.1 43.0 1.0
CB A:ASP57 4.3 37.8 1.0
N A:THR63 4.3 35.5 1.0
CA A:ASP57 4.4 38.8 1.0
N A:ASP65 4.4 29.4 1.0
OG1 A:THR63 4.4 37.3 1.0
N A:ASN61 4.4 41.3 1.0
CG A:GLU68 4.4 27.2 1.0
CB A:ASN61 4.5 41.4 1.0
CA A:ILE64 4.5 29.1 1.0
OD2 A:ASP65 4.5 41.6 1.0
N A:ILE64 4.5 30.5 1.0
CA A:THR63 4.5 33.1 1.0
N A:ASP59 4.6 39.3 1.0
C A:ASP57 4.7 40.5 1.0
CG A:ASP65 4.7 35.5 1.0
CB A:ASP59 4.8 41.5 1.0
N A:GLY62 4.8 38.5 1.0
C A:ILE64 4.8 29.9 1.0
CA A:ASN61 4.8 40.4 1.0
N A:GLY60 4.9 39.7 1.0
N A:ALA58 5.0 41.9 1.0
CA A:ASP59 5.0 41.9 1.0
C A:ASN61 5.0 40.8 1.0

Calcium binding site 3 out of 5 in 4upu

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Calcium binding site 3 out of 5 in the Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin


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 IP3 3-K Calmodulin Binding Region in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1151

b:22.1
occ:1.00
 OD1 A:ASP94 2.2 23.5 1.0
O A:TYR100 2.2 23.3 1.0
OD1 A:ASN98 2.4 22.6 1.0
O A:HOH2049 2.4 24.3 1.0
OE2 A:GLU105 2.5 22.5 1.0
OD1 A:ASP96 2.5 29.8 1.0
OE1 A:GLU105 2.5 21.2 1.0
CD A:GLU105 2.9 22.4 1.0
CG A:ASP96 3.3 30.6 1.0
CG A:ASN98 3.4 22.3 1.0
CG A:ASP94 3.4 23.9 1.0
C A:TYR100 3.5 24.3 1.0
OD2 A:ASP96 3.5 28.7 1.0
ND2 A:ASN98 4.1 21.2 1.0
N A:TYR100 4.1 23.6 1.0
N A:ASN98 4.2 23.5 1.0
CA A:ASP94 4.2 26.1 1.0
OD2 A:ASP94 4.2 25.4 1.0
CB A:ASP94 4.3 25.3 1.0
CA A:TYR100 4.3 23.4 1.0
CB A:ASN98 4.3 21.0 1.0
CG A:GLU105 4.4 20.9 1.0
N A:ILE101 4.4 24.2 1.0
C A:ASP94 4.5 26.7 1.0
CA A:ILE101 4.5 21.2 1.0
N A:ASP96 4.6 29.8 1.0
CA A:ASN98 4.6 23.6 1.0
N A:LYS95 4.7 27.6 1.0
CB A:ASP96 4.7 29.3 1.0
O A:HOH2048 4.7 24.6 1.0
O2 A:GOL1154 4.7 27.4 1.0
CB A:TYR100 4.8 23.9 1.0
N A:SER102 4.8 21.1 1.0
N A:GLY99 4.8 22.1 1.0
N A:GLY97 4.8 26.9 1.0
C A:ASN98 4.9 23.9 1.0

Calcium binding site 4 out of 5 in 4upu

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Calcium binding site 4 out of 5 in the Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin


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 IP3 3-K Calmodulin Binding Region in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1152

b:24.9
occ:1.00
 OD1 A:ASP130 2.3 24.8 1.0
OD1 A:ASP134 2.3 27.1 1.0
O A:GLN136 2.3 23.4 1.0
OE1 A:GLU141 2.4 29.7 1.0
OD1 A:ASP132 2.4 34.8 1.0
O A:HOH2071 2.4 24.0 1.0
OE2 A:GLU141 2.5 30.3 1.0
CD A:GLU141 2.8 29.0 1.0
CG A:ASP134 3.3 30.1 1.0
CG A:ASP132 3.3 34.7 1.0
CG A:ASP130 3.4 27.2 1.0
C A:GLN136 3.5 23.5 1.0
OD2 A:ASP132 3.6 33.3 1.0
OD2 A:ASP134 3.7 30.2 1.0
N A:ASP134 4.1 28.3 1.0
N A:GLN136 4.2 23.9 1.0
OD2 A:ASP130 4.2 26.3 1.0
CA A:ASP130 4.3 31.7 1.0
N A:VAL137 4.3 23.0 1.0
CA A:VAL137 4.3 22.3 1.0
CG A:GLU141 4.3 26.5 1.0
N A:ASP132 4.3 32.3 1.0
N A:ASN138 4.3 23.6 1.0
CB A:ASP130 4.3 29.0 1.0
CB A:ASP134 4.4 27.1 1.0
CA A:GLN136 4.4 24.1 1.0
C A:ASP130 4.6 33.7 1.0
N A:GLY133 4.6 32.0 1.0
CB A:ASP132 4.6 32.7 1.0
N A:GLY135 4.6 26.5 1.0
CA A:ASP134 4.6 27.6 1.0
N A:ILE131 4.7 35.4 1.0
CA A:ASP132 4.8 31.9 1.0
C A:VAL137 4.8 23.4 1.0
C A:ASP132 4.9 29.9 1.0
C A:ASP134 4.9 28.3 1.0
CB A:GLN136 5.0 24.9 1.0
CG A:ASN138 5.0 25.6 1.0

Calcium binding site 5 out of 5 in 4upu

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Calcium binding site 5 out of 5 in the Crystal Structure of IP3 3-K Calmodulin Binding Region in Complex with Calmodulin


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 IP3 3-K Calmodulin Binding Region in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1153

b:62.6
occ:0.33
 O A:HOH2060 2.3 35.8 1.0
OD2 A:ASP119 2.9 39.4 1.0
CG A:ASP119 3.8 37.7 1.0
OD1 A:ASP119 3.8 38.0 1.0

Reference:

E.Franco-Echevarria, J.I.Banos-Sanz, B.Monterroso, A.Round, J.Sanz-Aparicio, B.Gonzalez. A New Calmodulin Binding Motif For Inositol 1,4,5- Trisphosphate 3-Kinase Regulation. Biochem.J. V. 463 319 2014.
ISSN: ISSN 0264-6021
PubMed: 25101901
DOI: 10.1042/BJ20140757
Page generated: Sat Dec 12 05:09:31 2020

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