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Calcium in PDB 1a8a: Rat Annexin V Complexed with Glycerophosphoserine

Protein crystallography data

The structure of Rat Annexin V Complexed with Glycerophosphoserine, PDB code: 1a8a was solved by M.A.Swairjo, N.O.Concha, M.A.Kaetzel, J.R.Dedman, B.A.Seaton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.90
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 157.270, 157.270, 37.450, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Rat Annexin V Complexed with Glycerophosphoserine (pdb code 1a8a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Rat Annexin V Complexed with Glycerophosphoserine, PDB code: 1a8a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1a8a

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Calcium binding site 1 out of 10 in the Rat Annexin V Complexed with Glycerophosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rat Annexin V Complexed with Glycerophosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:20.0
occ:0.84
 O A:MET26 2.3 28.0 1.0
O A:GLY30 2.4 25.3 1.0
O A:GLY28 2.4 56.7 1.0
OE1 A:GLU70 2.5 33.7 1.0
O A:HOH636 2.5 40.4 1.0
OE2 A:GLU70 2.6 37.7 1.0
O A:HOH635 2.6 37.7 1.0
CD A:GLU70 2.9 35.5 1.0
C A:MET26 3.5 28.3 1.0
C A:GLY30 3.6 34.0 1.0
C A:GLY28 3.6 34.8 1.0
N A:GLY28 4.1 29.9 1.0
N A:GLY30 4.1 42.8 1.0
CA A:MET26 4.2 25.3 1.0
C A:LYS27 4.2 43.1 1.0
O A:LYS27 4.3 47.0 1.0
C A:LEU29 4.3 54.4 1.0
O A:HOH663 4.4 30.0 1.0
OG1 A:THR31 4.4 21.8 1.0
CA A:GLY28 4.4 33.6 1.0
CG A:GLU70 4.4 36.7 1.0
CA A:GLY30 4.5 37.3 1.0
N A:LYS27 4.5 37.2 1.0
N A:LEU29 4.6 56.4 1.0
N A:THR31 4.6 31.2 1.0
CA A:LEU29 4.6 54.7 1.0
CB A:MET26 4.7 29.2 1.0
CA A:LYS27 4.7 42.4 1.0
O A:LEU29 4.8 63.5 1.0
O A:HOH572 4.8 30.1 1.0
CA A:THR31 4.9 27.9 1.0

Calcium binding site 2 out of 10 in 1a8a

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Calcium binding site 2 out of 10 in the Rat Annexin V Complexed with Glycerophosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rat Annexin V Complexed with Glycerophosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:21.0
occ:0.83
 O A:LYS68 2.4 23.1 1.0
O A:LEU71 2.4 28.5 1.0
O A:HOH591 2.5 32.9 1.0
OE1 A:GLU76 2.5 51.4 1.0
OE2 A:GLU76 2.5 47.0 1.0
CD A:GLU76 2.9 42.7 1.0
C A:LYS68 3.6 21.8 1.0
C A:LEU71 3.6 25.7 1.0
CA A:THR72 4.2 30.6 1.0
CG A:GLU76 4.2 35.7 1.0
OG1 A:THR72 4.3 34.1 1.0
CA A:LYS68 4.4 18.9 1.0
N A:THR72 4.4 31.1 1.0
CB A:THR72 4.5 31.4 1.0
N A:SER69 4.6 27.7 1.0
O A:SER69 4.6 37.1 1.0
CA A:LEU71 4.7 25.9 1.0
N A:LEU71 4.7 30.9 1.0
C A:SER69 4.8 29.5 1.0
CA A:SER69 4.8 30.1 1.0
CB A:GLU76 4.9 31.2 1.0
CB A:LYS68 5.0 23.1 1.0

Calcium binding site 3 out of 10 in 1a8a

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Calcium binding site 3 out of 10 in the Rat Annexin V Complexed with Glycerophosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rat Annexin V Complexed with Glycerophosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:21.3
occ:0.88
 O A:THR31 2.5 29.0 1.0
O A:HOH637 2.5 40.5 1.0
OE1 A:GLU33 2.5 33.6 1.0
O A:HOH630 2.5 51.6 1.0
O A:HOH638 2.6 52.6 1.0
OE2 A:GLU33 2.7 33.0 1.0
CD A:GLU33 3.0 30.2 1.0
C A:THR31 3.7 27.6 1.0
N A:THR31 4.3 31.2 1.0
O A:HOH631 4.3 37.0 1.0
CA A:THR31 4.5 27.9 1.0
CG A:GLU33 4.5 28.2 1.0
N A:GLU33 4.6 24.3 1.0
CB A:THR31 4.6 25.9 1.0
O A:HOH623 4.7 47.2 1.0
N A:ASP32 4.7 21.9 1.0
CA A:ASP32 4.8 22.3 1.0

Calcium binding site 4 out of 10 in 1a8a

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Calcium binding site 4 out of 10 in the Rat Annexin V Complexed with Glycerophosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rat Annexin V Complexed with Glycerophosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:12.0
occ:0.49
 O A:GLY102 2.3 36.3 1.0
O A:LEU98 2.5 37.3 1.0
OD2 A:ASP142 2.5 46.8 1.0
O A:ALA101 2.5 92.1 1.0
OD1 A:ASP142 2.6 47.1 1.0
O A:GLY100 2.8 54.3 1.0
CG A:ASP142 3.0 47.6 1.0
C A:ALA101 3.5 90.4 1.0
C A:GLY102 3.5 58.7 1.0
O A:LYS99 3.6 79.4 1.0
C A:LEU98 3.6 37.8 1.0
C A:GLY100 3.9 79.6 1.0
C A:LYS99 4.1 72.0 1.0
OG1 A:THR103 4.1 46.1 1.0
N A:GLY102 4.2 67.8 1.0
CA A:GLY102 4.3 63.1 1.0
CA A:ALA101 4.4 91.1 1.0
CB A:ASP142 4.5 44.4 1.0
CA A:LEU98 4.5 32.7 1.0
N A:LYS99 4.5 62.5 1.0
N A:ALA101 4.5 90.7 1.0
N A:THR103 4.6 33.7 1.0
CA A:LYS99 4.7 69.6 1.0
N A:GLY100 4.7 74.7 1.0
CA A:THR103 4.8 30.6 1.0
CA A:GLY100 4.9 78.1 1.0
CB A:THR103 4.9 45.8 1.0

Calcium binding site 5 out of 10 in 1a8a

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Calcium binding site 5 out of 10 in the Rat Annexin V Complexed with Glycerophosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Rat Annexin V Complexed with Glycerophosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:25.0
occ:0.38
 O A:THR143 2.4 31.2 1.0
O A:HOH640 2.4 47.3 1.0
O A:VAL140 2.5 29.1 1.0
O A:HOH607 2.6 53.4 1.0
O A:GLY141 3.3 35.0 1.0
OE1 A:GLN148 3.5 25.5 1.0
C A:THR143 3.6 30.2 1.0
C A:VAL140 3.7 21.9 1.0
C A:GLY141 3.8 19.4 1.0
N A:THR143 3.9 28.0 1.0
CA A:GLY141 4.2 17.9 1.0
CA A:THR143 4.3 27.0 1.0
N A:GLY141 4.4 19.4 1.0
C A:ASP142 4.4 28.4 1.0
N A:ASP142 4.4 24.3 1.0
N A:SER144 4.6 30.9 1.0
CD A:GLN148 4.7 20.8 1.0
CA A:ASP142 4.8 28.9 1.0
CA A:VAL140 4.8 23.7 1.0
CA A:SER144 4.8 29.8 1.0
CG1 A:VAL140 5.0 31.9 1.0
CB A:SER144 5.0 38.2 1.0
O A:HOH613 5.0 60.1 1.0
O A:ASP142 5.0 37.4 1.0

Calcium binding site 6 out of 10 in 1a8a

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Calcium binding site 6 out of 10 in the Rat Annexin V Complexed with Glycerophosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Rat Annexin V Complexed with Glycerophosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:21.0
occ:0.48
 O A:THR103 2.4 44.7 1.0
OE1 A:GLU105 2.4 31.6 1.0
OE2 A:GLU105 2.5 32.7 1.0
O A:HOH639 2.5 48.2 1.0
CD A:GLU105 2.9 32.7 1.0
C A:THR103 3.7 27.9 1.0
N A:THR103 4.2 33.7 1.0
CG A:GLU105 4.4 30.9 1.0
CA A:THR103 4.5 30.6 1.0
N A:GLU105 4.6 31.1 1.0
N A:ASP104 4.6 24.6 1.0
CB A:THR103 4.7 45.8 1.0
CA A:ASP104 4.8 21.3 1.0

Calcium binding site 7 out of 10 in 1a8a

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Calcium binding site 7 out of 10 in the Rat Annexin V Complexed with Glycerophosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Rat Annexin V Complexed with Glycerophosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:10.0
occ:1.01
 O A:GLY181 2.3 9.3 1.0
O14 A:GSE997 2.4 14.9 0.8
O A:GLY186 2.4 17.0 1.0
O A:LYS184 2.4 22.8 1.0
OE2 A:GLU226 2.5 24.3 1.0
O A:HOH512 2.5 15.2 1.0
OE1 A:GLU226 2.5 20.3 1.0
CD A:GLU226 2.9 25.4 1.0
C A:GLY181 3.4 14.4 1.0
C A:GLY186 3.5 10.8 1.0
C A:LYS184 3.6 10.7 1.0
P A:GSE997 3.7 14.9 0.8
N A:GLY186 3.9 11.5 1.0
N A:LYS184 4.1 13.0 1.0
O12 A:GSE997 4.1 14.9 0.8
O13 A:GSE997 4.2 14.9 0.8
CA A:LYS184 4.2 11.2 1.0
CA A:GLY181 4.2 8.5 1.0
CA A:GLY186 4.2 11.8 1.0
N A:GLU182 4.3 16.7 1.0
CB A:LYS184 4.4 22.7 1.0
CA A:GLU182 4.4 16.2 1.0
CG A:GLU226 4.4 19.3 1.0
C A:GLU182 4.4 17.2 1.0
OG1 A:THR187 4.4 11.5 1.0
O A:GLU182 4.5 12.5 1.0
O A:HOH511 4.5 16.5 1.0
N A:TRP185 4.5 9.6 1.0
C A:TRP185 4.5 11.2 1.0
N A:THR187 4.5 15.1 1.0
CA A:TRP185 4.6 8.2 1.0
CA A:THR187 4.8 15.6 1.0
O11 A:GSE997 4.8 14.9 0.8
CG A:LYS184 5.0 26.9 1.0

Calcium binding site 8 out of 10 in 1a8a

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Calcium binding site 8 out of 10 in the Rat Annexin V Complexed with Glycerophosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Rat Annexin V Complexed with Glycerophosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:19.0
occ:0.68
 O A:THR227 2.4 21.1 1.0
OE2 A:GLU232 2.5 35.7 1.0
O A:ASP224 2.5 26.0 1.0
OE1 A:GLU232 2.8 27.7 1.0
OD1 A:ASP224 3.0 30.8 1.0
CD A:GLU232 3.1 22.8 1.0
C A:ASP224 3.6 21.5 1.0
C A:THR227 3.6 16.4 1.0
CA A:ASP224 3.9 20.9 1.0
CA A:SER228 3.9 28.1 1.0
CG A:ASP224 3.9 30.0 1.0
N A:SER228 4.1 27.1 1.0
CB A:SER228 4.3 23.0 1.0
CG A:GLU232 4.4 15.4 1.0
CB A:ASP224 4.5 26.2 1.0
O A:ILE223 4.7 12.4 1.0
OD2 A:ASP224 4.7 38.0 1.0
N A:THR227 4.8 17.1 1.0
N A:ARG225 4.8 22.8 1.0
CA A:THR227 4.8 15.9 1.0
CB A:GLU232 4.9 14.8 1.0

Calcium binding site 9 out of 10 in 1a8a

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Calcium binding site 9 out of 10 in the Rat Annexin V Complexed with Glycerophosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Rat Annexin V Complexed with Glycerophosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:20.0
occ:0.96
 O A:THR187 2.4 9.8 1.0
O A:HOH642 2.5 27.7 1.0
O A:HOH626 2.5 36.6 1.0
O16 A:GSE997 2.6 18.2 0.8
OE1 A:GLU189 2.6 22.3 1.0
OE2 A:GLU189 2.7 27.9 1.0
O A:HOH644 2.7 49.7 1.0
CD A:GLU189 3.1 21.4 1.0
C A:THR187 3.6 16.6 1.0
C13 A:GSE997 3.7 18.2 0.8
N A:THR187 3.9 15.1 1.0
O15 A:GSE997 4.0 18.2 0.8
CA A:THR187 4.2 15.6 1.0
CB A:THR187 4.4 10.1 1.0
O A:HOH577 4.4 31.8 1.0
N A:ASP188 4.6 16.8 1.0
CG A:GLU189 4.6 16.9 1.0
N A:GLU189 4.8 15.3 1.0
CA A:ASP188 4.9 18.2 1.0
C12 A:GSE997 5.0 18.2 0.8

Calcium binding site 10 out of 10 in 1a8a

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Calcium binding site 10 out of 10 in the Rat Annexin V Complexed with Glycerophosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Rat Annexin V Complexed with Glycerophosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca410

b:25.0
occ:0.62
 O A:GLY261 2.4 54.7 1.0
O A:MET257 2.4 41.4 1.0
O A:ALA260 2.5 61.6 1.0
OD1 A:ASP301 2.5 38.6 1.0
O A:GLY259 2.5 82.1 1.0
OD2 A:ASP301 2.5 35.0 1.0
CG A:ASP301 2.9 36.1 1.0
C A:ALA260 3.4 62.0 1.0
C A:MET257 3.5 53.1 1.0
C A:GLY261 3.5 70.9 1.0
C A:GLY259 3.7 79.9 1.0
N A:GLY261 4.1 78.1 1.0
CA A:ALA260 4.2 63.5 1.0
CA A:MET257 4.2 50.7 1.0
CA A:GLY261 4.2 75.3 1.0
C A:LYS258 4.3 42.7 1.0
O A:LYS258 4.4 89.9 1.0
N A:ALA260 4.4 64.7 1.0
CB A:ASP301 4.5 34.8 1.0
N A:LYS258 4.5 34.7 1.0
N A:GLY259 4.5 74.8 1.0
N A:THR262 4.5 39.7 1.0
OG1 A:THR262 4.6 38.9 1.0
CA A:LYS258 4.7 42.0 1.0
CA A:GLY259 4.7 78.8 1.0
CA A:THR262 4.7 37.3 1.0
CB A:MET257 4.8 36.2 1.0

Reference:

M.A.Swairjo, N.O.Concha, M.A.Kaetzel, J.R.Dedman, B.A.Seaton. Ca(2+)-Bridging Mechanism and Phospholipid Head Group Recognition in the Membrane-Binding Protein Annexin V. Nat.Struct.Biol. V. 2 968 1995.
ISSN: ISSN 1072-8368
PubMed: 7583670
DOI: 10.1038/NSB1195-968
Page generated: Thu Jul 11 05:46:12 2024

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