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Calcium in PDB 5jdj: Crystal Structure of Domain I10 From Titin in Space Group P212121

Enzymatic activity of Crystal Structure of Domain I10 From Titin in Space Group P212121

All present enzymatic activity of Crystal Structure of Domain I10 From Titin in Space Group P212121:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Domain I10 From Titin in Space Group P212121, PDB code: 5jdj was solved by R.Williams, J.Bogomolovas, S.Labiet, O.Mayans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.65 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.637, 136.239, 140.095, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Domain I10 From Titin in Space Group P212121 (pdb code 5jdj). 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 Domain I10 From Titin in Space Group P212121, PDB code: 5jdj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5jdj

Go back to Calcium Binding Sites List in 5jdj
Calcium binding site 1 out of 6 in the Crystal Structure of Domain I10 From Titin in Space Group P212121


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 Domain I10 From Titin in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca101

b:42.5
occ:1.00
 O A:HOH224 2.4 24.8 1.0
O H:HOH130 2.5 21.8 1.0
OD1 A:ASP82 2.5 24.4 1.0
O A:HOH201 2.5 14.4 1.0
O H:HOH126 2.6 39.2 1.0
O H:HOH112 2.6 29.1 1.0
OD2 A:ASP82 2.9 18.8 1.0
CG A:ASP82 3.0 21.7 1.0
OE1 O:GLU44 3.2 43.5 1.0
O H:HOH207 3.2 36.2 1.0
OE1 H:GLU28 4.2 30.7 1.0
CD O:GLU44 4.2 35.5 1.0
O A:HOH291 4.3 34.5 1.0
CB A:ASP82 4.4 17.7 1.0
O A:HOH278 4.4 36.7 1.0
O H:HOH155 4.6 26.2 1.0
OE2 O:GLU44 4.6 29.8 1.0
O A:GLN83 4.7 19.5 1.0
CB A:ILE8 4.7 17.0 1.0
O H:THR9 4.8 15.2 1.0
O A:ILE8 4.8 16.2 1.0
O O:HOH146 4.8 41.6 1.0
O H:HOH208 5.0 36.3 1.0
OG1 H:THR9 5.0 15.1 1.0

Calcium binding site 2 out of 6 in 5jdj

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Calcium binding site 2 out of 6 in the Crystal Structure of Domain I10 From Titin in Space Group P212121


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 Domain I10 From Titin in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca101

b:33.0
occ:1.00
 O B:GLN83 2.3 21.7 1.0
O N:HOH102 2.3 30.2 1.0
O D:HOH180 2.4 34.0 1.0
O D:HOH155 2.4 36.2 1.0
O B:HOH214 2.8 35.5 1.0
OE2 N:GLU44 3.1 59.9 1.0
C B:GLN83 3.5 25.0 1.0
OD1 B:ASP82 3.9 36.5 1.0
N B:GLN83 4.0 20.3 1.0
CD N:GLU44 4.2 54.3 1.0
CG1 B:VAL84 4.2 23.8 1.0
OE1 D:GLU28 4.2 33.4 1.0
CA B:GLN83 4.3 16.8 1.0
N B:VAL84 4.4 20.3 1.0
CA B:VAL84 4.5 21.8 1.0
O B:HOH231 4.5 30.7 1.0
O D:THR9 4.6 14.7 1.0
OE1 N:GLU44 4.7 49.6 1.0
O B:HOH275 4.7 28.2 1.0
CD D:GLU28 4.8 31.3 1.0
OE2 D:GLU28 4.9 39.3 1.0
CB B:GLN83 5.0 23.7 1.0

Calcium binding site 3 out of 6 in 5jdj

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Calcium binding site 3 out of 6 in the Crystal Structure of Domain I10 From Titin in Space Group P212121


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 Domain I10 From Titin in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:27.0
occ:1.00
 O B:HOH256 2.4 30.3 1.0
O B:HOH232 2.4 29.3 1.0
OG B:SER24 2.4 23.0 1.0
O B:HOH281 2.4 30.6 1.0
OE2 B:GLU26 2.6 29.7 1.0
OE1 B:GLU26 2.6 26.6 1.0
O B:SER24 2.6 21.6 1.0
CD B:GLU26 2.9 28.2 1.0
CB B:SER24 3.4 22.8 1.0
C B:SER24 3.5 21.6 1.0
CA B:SER24 3.9 14.9 1.0
O B:HOH277 4.3 26.2 1.0
N B:SER24 4.4 18.4 1.0
CG B:GLU26 4.4 21.1 1.0
O B:HOH241 4.5 33.1 1.0
N B:PHE25 4.6 17.4 1.0
NE2 B:GLN61 4.6 27.2 1.0
O B:HOH276 4.9 23.5 1.0
O B:HOH298 5.0 35.6 1.0
CA B:PHE25 5.0 18.6 1.0

Calcium binding site 4 out of 6 in 5jdj

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Calcium binding site 4 out of 6 in the Crystal Structure of Domain I10 From Titin in Space Group P212121


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 Domain I10 From Titin in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca101

b:12.1
occ:1.00
 O E:ILE8 2.3 9.3 1.0
O E:THR9 2.3 12.3 1.0
O E:HOH272 2.4 11.0 1.0
O E:HOH244 2.5 12.7 1.0
C E:THR9 3.3 12.6 1.0
C E:ILE8 3.4 9.8 1.0
CA E:THR9 3.7 14.0 1.0
N E:THR9 4.0 12.7 1.0
O E:HOH241 4.0 19.0 1.0
O E:LYS10 4.4 16.3 1.0
N E:LYS10 4.4 14.5 1.0
OD2 E:ASP82 4.5 14.1 1.0
CD2 E:HIS7 4.6 7.1 1.0
CA E:ILE8 4.6 7.7 1.0
C E:LYS10 4.6 16.8 1.0
CB E:ILE8 4.8 10.6 1.0
CA E:LYS10 4.9 15.2 1.0
CG2 E:ILE8 5.0 12.5 1.0
N E:ILE8 5.0 10.0 1.0

Calcium binding site 5 out of 6 in 5jdj

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Calcium binding site 5 out of 6 in the Crystal Structure of Domain I10 From Titin in Space Group P212121


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 Domain I10 From Titin in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca101

b:15.5
occ:1.00
 O I:ILE8 2.3 14.4 1.0
O I:THR9 2.3 16.0 1.0
O I:HOH230 2.3 17.9 1.0
O I:HOH226 2.5 17.1 1.0
C I:THR9 3.3 16.0 1.0
C I:ILE8 3.4 15.3 1.0
CA I:THR9 3.7 14.1 1.0
N I:THR9 4.0 14.7 1.0
O I:HOH236 4.1 25.3 1.0
O I:LYS10 4.4 17.2 1.0
N I:LYS10 4.4 17.6 1.0
OD2 I:ASP82 4.5 15.6 1.0
CA I:ILE8 4.6 13.8 1.0
ND1 I:HIS7 4.7 13.9 1.0
C I:LYS10 4.7 20.0 1.0
CB I:ILE8 4.8 14.8 1.0
CA I:LYS10 4.9 19.1 1.0

Calcium binding site 6 out of 6 in 5jdj

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Calcium binding site 6 out of 6 in the Crystal Structure of Domain I10 From Titin in Space Group P212121


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 Domain I10 From Titin in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca101

b:10.6
occ:1.00
 O L:ILE8 2.3 10.7 1.0
O L:THR9 2.3 10.6 1.0
O L:HOH237 2.4 10.0 1.0
O L:HOH251 2.4 11.8 1.0
C L:THR9 3.2 12.7 1.0
C L:ILE8 3.4 13.6 1.0
CA L:THR9 3.7 13.5 1.0
N L:THR9 3.9 10.7 1.0
O L:HOH225 4.1 16.2 1.0
O L:LYS10 4.4 15.4 1.0
N L:LYS10 4.4 13.5 1.0
OD2 L:ASP82 4.6 11.9 1.0
C L:LYS10 4.6 13.8 1.0
CA L:ILE8 4.6 11.3 1.0
ND1 L:HIS7 4.7 11.4 1.0
CB L:ILE8 4.8 10.3 1.0
CA L:LYS10 4.9 14.1 1.0
N L:ILE8 5.0 10.3 1.0

Reference:

J.Bogomolovas, J.R.Fleming, B.R.Anderson, R.Williams, S.Lange, B.Simon, M.M.Khan, R.Rudolf, B.Franke, B.Bullard, D.J.Rigden, H.Granzier, S.Labeit, O.Mayans. Exploration of Pathomechanisms Triggered By A Single-Nucleotide Polymorphism in Titin'S I-Band: the Cardiomyopathy-Linked Mutation T2580I. Open Biology V. 6 2016.
ISSN: ESSN 2046-2441
PubMed: 27683155
DOI: 10.1098/RSOB.160114
Page generated: Mon Jul 15 06:26:44 2024

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