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Calcium in PDB 1m9i: Crystal Structure of Phosphorylation-Mimicking Mutant T356D of Annexin VI

Protein crystallography data

The structure of Crystal Structure of Phosphorylation-Mimicking Mutant T356D of Annexin VI, PDB code: 1m9i was solved by C.Freye-Minks, R.H.Kretsinger, C.E.Creutz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.21 / 2.65
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 67.970, 67.970, 204.600, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 27.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Phosphorylation-Mimicking Mutant T356D of Annexin VI (pdb code 1m9i). 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 Phosphorylation-Mimicking Mutant T356D of Annexin VI, PDB code: 1m9i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 1m9i

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Calcium binding site 1 out of 5 in the Crystal Structure of Phosphorylation-Mimicking Mutant T356D of Annexin VI


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 Phosphorylation-Mimicking Mutant T356D of Annexin VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:0.3
occ:0.30
 OE2 A:GLU420 1.8 57.8 1.0
O A:GLY380 2.0 43.5 1.0
CD A:GLU420 2.5 61.9 1.0
O A:MET376 2.6 55.2 1.0
OE1 A:GLU420 2.6 62.9 1.0
O A:GLY378 2.9 47.0 1.0
C A:GLY380 3.2 41.2 1.0
O A:LEU379 3.3 48.0 1.0
C A:MET376 3.6 57.0 1.0
CB A:THR381 3.7 52.6 1.0
C A:LEU379 3.8 46.5 1.0
CG A:GLU420 3.8 61.6 1.0
C A:GLY378 3.9 48.3 1.0
CA A:THR381 3.9 40.5 1.0
N A:THR381 3.9 44.0 1.0
CA A:MET376 4.0 48.7 1.0
N A:GLY380 4.3 39.5 1.0
CA A:GLY380 4.3 40.2 1.0
N A:GLY378 4.5 51.1 1.0
OG1 A:THR381 4.5 51.0 1.0
CB A:GLU420 4.5 62.5 1.0
CA A:LEU379 4.6 45.4 1.0
N A:LEU379 4.6 46.8 1.0
CB A:MET376 4.6 51.0 1.0
CA A:GLY378 4.7 48.8 1.0
CG2 A:THR381 4.8 53.3 1.0
N A:LYS377 4.8 68.4 1.0
C A:LYS377 4.9 71.2 1.0

Calcium binding site 2 out of 5 in 1m9i

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Calcium binding site 2 out of 5 in the Crystal Structure of Phosphorylation-Mimicking Mutant T356D of Annexin VI


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 Phosphorylation-Mimicking Mutant T356D of Annexin VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:0.1
occ:0.50
 O A:GLY268 1.6 61.6 1.0
O A:GLY266 2.1 90.1 1.0
OD1 A:ASP308 2.3 77.2 1.0
O A:MET264 2.8 40.2 1.0
C A:GLY268 2.8 60.6 1.0
CG A:ASP308 3.1 76.9 1.0
OD2 A:ASP308 3.2 74.8 1.0
C A:GLY266 3.3 88.8 1.0
C A:MET264 3.4 39.1 1.0
N A:GLY268 3.6 73.0 1.0
CA A:MET264 3.6 32.9 1.0
OG1 A:THR269 3.7 36.8 1.0
CA A:GLY268 3.7 66.5 1.0
N A:THR269 3.8 57.6 1.0
N A:GLY266 3.9 82.3 1.0
C A:LEU267 3.9 93.7 1.0
NH1 A:ARG270 4.0 84.2 1.0
CA A:THR269 4.0 52.6 1.0
CA A:GLY266 4.0 85.8 1.0
N A:LEU267 4.3 97.3 1.0
CB A:MET264 4.3 59.9 1.0
O A:LEU267 4.4 93.9 1.0
N A:LYS265 4.4 0.9 1.0
CB A:ASP308 4.4 74.9 1.0
C A:LYS265 4.5 0.1 1.0
CA A:LEU267 4.5 96.2 1.0
CB A:THR269 4.5 36.2 1.0
O A:ALA263 4.7 29.8 1.0
N A:MET264 4.8 27.5 1.0
CZ A:ARG270 4.9 83.8 1.0
O A:LYS265 5.0 0.5 1.0

Calcium binding site 3 out of 5 in 1m9i

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Calcium binding site 3 out of 5 in the Crystal Structure of Phosphorylation-Mimicking Mutant T356D of Annexin VI


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 Phosphorylation-Mimicking Mutant T356D of Annexin VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:83.6
occ:1.00
 OD1 A:ASP656 2.4 37.6 1.0
O A:GLY616 2.6 54.8 1.0
O A:MET612 2.8 48.9 1.0
O A:HOH770 2.9 45.8 1.0
C A:MET612 3.4 47.2 1.0
O A:ALA615 3.4 89.1 1.0
CG A:ASP656 3.5 37.2 1.0
C A:GLY616 3.5 52.8 1.0
O A:GLY614 3.7 74.2 1.0
C A:ALA615 3.9 88.7 1.0
OD2 A:ASP656 3.9 40.6 1.0
CA A:MET612 4.1 41.2 1.0
C A:GLY614 4.1 73.7 1.0
CA A:GLY616 4.1 61.9 1.0
N A:LYS613 4.2 47.9 1.0
N A:GLY614 4.2 62.3 1.0
N A:GLY616 4.2 69.5 1.0
C A:LYS613 4.3 57.4 1.0
OG1 A:THR617 4.3 30.6 1.0
CA A:LYS613 4.5 53.9 1.0
N A:THR617 4.5 26.9 1.0
N A:ALA615 4.6 92.0 1.0
O A:HOH852 4.6 45.8 1.0
O A:LYS613 4.7 57.5 1.0
CA A:GLY614 4.7 68.4 1.0
CB A:MET612 4.7 33.0 1.0
CA A:ALA615 4.8 93.2 1.0
CB A:ASP656 4.8 29.4 1.0
CA A:THR617 4.8 22.2 1.0

Calcium binding site 4 out of 5 in 1m9i

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Calcium binding site 4 out of 5 in the Crystal Structure of Phosphorylation-Mimicking Mutant T356D of Annexin VI


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 Phosphorylation-Mimicking Mutant T356D of Annexin VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:0.1
occ:0.50
 O A:MET448 1.6 52.1 1.0
O A:GLY450 1.9 32.6 1.0
OD1 A:ASP492 2.5 81.2 1.0
C A:MET448 2.7 53.8 1.0
O A:GLY452 2.8 35.3 1.0
C A:GLY450 3.0 31.4 1.0
N A:GLY450 3.3 34.5 1.0
C A:GLU449 3.4 73.8 1.0
CG A:ASP492 3.5 79.0 1.0
N A:GLU449 3.6 71.1 1.0
CA A:MET448 3.6 52.8 1.0
CA A:GLY450 3.7 33.1 1.0
CA A:GLU449 3.8 73.9 1.0
O A:GLU449 3.9 75.2 1.0
OD2 A:ASP492 3.9 80.2 1.0
C A:GLY452 4.0 33.0 1.0
N A:ALA451 4.1 33.5 1.0
N A:GLY452 4.2 29.8 1.0
O A:HOH724 4.2 41.5 1.0
C A:ALA451 4.2 34.2 1.0
CA A:ALA451 4.4 33.5 1.0
N A:MET448 4.6 53.6 1.0
O A:ALA447 4.6 52.7 1.0
CB A:MET448 4.6 40.2 1.0
CA A:GLY452 4.7 29.5 1.0
CB A:ASP492 4.7 69.5 1.0
O A:ALA451 4.7 35.3 1.0
N A:THR453 5.0 40.1 1.0
C A:ALA447 5.0 53.6 1.0

Calcium binding site 5 out of 5 in 1m9i

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Calcium binding site 5 out of 5 in the Crystal Structure of Phosphorylation-Mimicking Mutant T356D of Annexin VI


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 Phosphorylation-Mimicking Mutant T356D of Annexin VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:0.5
occ:0.50
 O A:HOH706 0.4 44.0 1.0
O A:GLY35 2.1 42.5 1.0
O A:MET33 2.4 60.7 1.0
OE1 A:GLU77 2.7 52.2 1.0
O A:GLY37 2.8 31.6 1.0
C A:MET33 3.3 56.3 1.0
C A:GLY35 3.3 40.6 1.0
CD A:GLU77 3.6 51.8 1.0
C A:LYS34 3.6 48.1 1.0
N A:GLY35 3.8 37.4 1.0
O A:LYS34 3.8 49.3 1.0
C A:GLY37 3.9 30.5 1.0
OE2 A:GLU77 4.0 47.2 1.0
N A:GLY37 4.0 34.8 1.0
N A:LYS34 4.0 43.3 1.0
CA A:LYS34 4.0 46.4 1.0
CA A:GLY35 4.2 38.3 1.0
C A:PHE36 4.2 36.8 1.0
CA A:MET33 4.2 47.7 1.0
N A:PHE36 4.3 36.1 1.0
CA A:PHE36 4.3 37.5 1.0
O A:HOH762 4.4 42.3 1.0
CA A:GLY37 4.5 32.8 1.0
CG A:GLU77 4.7 53.2 1.0
O A:PHE36 4.8 38.5 1.0
CB A:MET33 4.8 40.1 1.0
N A:SER38 4.9 42.4 1.0

Reference:

C.Freye-Minks, R.H.Kretsinger, C.E.Creutz. Structural and Dynamic Changes in Human Annexin VI Induced By A Phosphorylation-Mimicking Mutation, T356D Biochemistry V. 42 620 2003.
ISSN: ISSN 0006-2960
PubMed: 12534274
DOI: 10.1021/BI026742H
Page generated: Thu Jul 11 12:29:14 2024

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