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Calcium in PDB 2ran: Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes

Protein crystallography data

The structure of Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes, PDB code: 2ran was solved by N.O.Concha, J.F.Head, 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) 21.32 / 1.89
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 156.900, 156.900, 37.030, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes (pdb code 2ran). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes, PDB code: 2ran:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2ran

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Calcium binding site 1 out of 7 in the Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes


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 Crystal Structure: CA2+-Induced Conformational Changes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca320

b:34.4
occ:0.79
 O A:GLY30 2.4 37.7 1.0
O A:MET26 2.4 34.1 1.0
O A:GLY28 2.4 52.4 1.0
O A:HOH404 2.5 31.3 0.6
OE1 A:GLU70 2.5 40.3 1.0
OE2 A:GLU70 2.6 45.7 1.0
CD A:GLU70 2.9 42.3 1.0
C A:MET26 3.5 37.8 1.0
C A:GLY30 3.6 40.4 1.0
C A:GLY28 3.6 52.0 1.0
N A:GLY30 4.2 48.8 1.0
CA A:MET26 4.2 35.5 1.0
OG1 A:THR31 4.2 33.8 1.0
N A:GLY28 4.2 50.9 1.0
H A:GLY30 4.2 0.0 1.0
O A:LYS27 4.3 48.6 1.0
C A:LYS27 4.3 49.4 1.0
H A:GLY28 4.4 0.0 1.0
CG A:GLU70 4.4 40.3 1.0
C A:LEU29 4.5 52.5 1.0
CA A:GLY30 4.5 43.7 1.0
CA A:GLY28 4.5 52.0 1.0
N A:THR31 4.5 37.8 1.0
N A:LEU29 4.6 52.8 1.0
N A:LYS27 4.6 42.1 1.0
O A:HOH402 4.7 24.7 0.6
CA A:LEU29 4.7 53.2 1.0
O A:HOH405 4.7 12.7 0.7
CA A:THR31 4.7 34.9 1.0
HG1 A:THR31 4.8 0.0 1.0
CB A:MET26 4.8 35.4 1.0
CA A:LYS27 4.9 48.0 1.0
O A:LEU29 5.0 55.2 1.0
CB A:THR31 5.0 34.6 1.0

Calcium binding site 2 out of 7 in 2ran

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Calcium binding site 2 out of 7 in the Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes


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 Crystal Structure: CA2+-Induced Conformational Changes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca321

b:55.0
occ:0.70
 O A:LEU71 2.4 29.6 1.0
O A:LYS68 2.5 32.3 1.0
OE1 A:GLU76 2.6 50.7 1.0
O A:HOH499 2.6 26.2 0.6
OE2 A:GLU76 3.0 47.8 1.0
CD A:GLU76 3.1 44.6 1.0
C A:LEU71 3.6 31.1 1.0
C A:LYS68 3.6 33.3 1.0
CA A:THR72 4.0 34.0 1.0
N A:THR72 4.2 33.4 1.0
O A:SER69 4.3 37.4 1.0
CA A:LYS68 4.3 33.0 1.0
CG A:GLU76 4.3 39.8 1.0
CB A:THR72 4.5 35.5 1.0
OG1 A:THR72 4.5 38.1 1.0
N A:SER69 4.7 35.6 1.0
C A:SER69 4.7 34.5 1.0
CB A:LYS68 4.7 34.2 1.0
CA A:SER69 4.7 35.4 1.0
CA A:LEU71 4.8 31.6 1.0
H A:GLY73 4.8 0.0 1.0
H A:LEU71 4.8 0.0 1.0
N A:LEU71 4.8 33.2 1.0
CB A:GLU76 4.9 33.4 1.0

Calcium binding site 3 out of 7 in 2ran

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Calcium binding site 3 out of 7 in the Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes


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 Crystal Structure: CA2+-Induced Conformational Changes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca322

b:57.7
occ:0.82
 O A:LEU98 2.4 48.7 1.0
O A:ALA101 2.5 74.6 1.0
O A:GLY100 2.5 77.5 1.0
O A:GLY102 2.5 65.5 1.0
OD1 A:ASP142 2.6 38.7 1.0
O A:HOH408 2.7 50.4 0.6
OD2 A:ASP142 2.7 43.6 1.0
CG A:ASP142 2.9 38.2 1.0
OG1 A:THR103 3.0 58.3 1.0
HG1 A:THR103 3.3 0.0 1.0
C A:ALA101 3.5 74.8 1.0
C A:GLY102 3.5 65.8 1.0
C A:LEU98 3.5 49.0 1.0
HZ2 A:LYS99 3.6 0.0 1.0
C A:GLY100 3.7 76.6 1.0
CB A:ASP142 4.0 36.0 1.0
CE A:LYS99 4.1 82.1 1.0
CA A:LYS99 4.1 66.3 1.0
N A:THR103 4.2 61.0 1.0
N A:GLY100 4.2 74.0 1.0
N A:GLY102 4.2 72.5 1.0
CB A:THR103 4.2 56.3 1.0
C A:LYS99 4.2 70.3 1.0
H A:GLY100 4.3 0.0 1.0
NZ A:LYS99 4.3 83.7 1.0
CA A:ALA101 4.3 76.0 1.0
N A:LYS99 4.3 57.6 1.0
CA A:THR103 4.4 56.9 1.0
N A:ALA101 4.4 76.6 1.0
CA A:GLY102 4.5 69.0 1.0
CA A:LEU98 4.5 42.3 1.0
O A:LYS99 4.6 70.1 1.0
HZ1 A:LYS99 4.6 0.0 1.0
CA A:GLY100 4.7 75.9 1.0
H A:THR103 4.9 0.0 1.0
CG2 A:THR103 4.9 56.3 1.0
H A:GLY102 5.0 0.0 1.0

Calcium binding site 4 out of 7 in 2ran

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Calcium binding site 4 out of 7 in the Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes


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 Crystal Structure: CA2+-Induced Conformational Changes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca323

b:68.0
occ:0.43
 O A:VAL140 2.4 25.6 1.0
O A:THR143 2.4 31.8 1.0
O A:HOH410 2.5 47.0 0.6
O A:HOH409 2.5 41.0 0.5
OE1 A:GLN148 2.6 25.6 1.0
O A:HOH411 2.6 27.2 0.6
C A:VAL140 3.6 25.9 1.0
C A:THR143 3.7 30.6 1.0
CD A:GLN148 3.8 22.5 1.0
H A:THR143 4.0 0.0 1.0
O A:GLY141 4.1 28.8 1.0
C A:GLY141 4.3 28.7 1.0
N A:THR143 4.3 31.0 1.0
CA A:GLY141 4.4 26.8 1.0
N A:GLY141 4.4 29.2 1.0
CA A:SER144 4.5 33.2 1.0
N A:SER144 4.5 31.6 1.0
HE21 A:GLN148 4.5 0.0 1.0
CA A:VAL140 4.5 24.2 1.0
CG1 A:VAL140 4.6 26.6 1.0
CA A:THR143 4.6 28.5 1.0
NE2 A:GLN148 4.7 26.4 1.0
CG A:GLN148 4.9 24.3 1.0
N A:ASP142 4.9 29.7 1.0
CB A:SER144 4.9 32.1 1.0

Calcium binding site 5 out of 7 in 2ran

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Calcium binding site 5 out of 7 in the Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes


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 Crystal Structure: CA2+-Induced Conformational Changes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca324

b:21.1
occ:0.95
 O A:GLY181 2.3 13.5 1.0
O A:GLY186 2.4 13.8 1.0
O A:HOH412 2.5 2.0 0.6
O A:LYS184 2.5 17.9 1.0
O A:HOH414 2.6 17.1 0.6
OE2 A:GLU226 2.6 19.8 1.0
OE1 A:GLU226 2.6 25.3 1.0
CD A:GLU226 3.0 24.1 1.0
C A:GLY181 3.4 12.7 1.0
H A:GLY186 3.4 0.0 1.0
C A:GLY186 3.5 15.7 1.0
C A:LYS184 3.6 15.7 1.0
H A:LYS184 3.8 0.0 1.0
N A:GLY186 3.8 17.2 1.0
O A:HOH415 4.0 17.4 0.6
CA A:GLY181 4.2 10.8 1.0
CA A:GLY186 4.2 17.4 1.0
CA A:LYS184 4.2 15.5 1.0
CB A:LYS184 4.3 12.8 1.0
N A:GLU182 4.3 13.4 1.0
N A:LYS184 4.3 15.3 1.0
O A:GLU182 4.4 14.4 1.0
CA A:GLU182 4.4 13.4 1.0
OG1 A:THR187 4.5 17.2 1.0
CG A:GLU226 4.5 18.4 1.0
C A:GLU182 4.5 13.8 1.0
N A:TRP185 4.6 15.1 1.0
N A:THR187 4.6 15.3 1.0
C A:TRP185 4.6 18.5 1.0
CA A:TRP185 4.7 15.2 1.0
CA A:THR187 4.7 15.0 1.0

Calcium binding site 6 out of 7 in 2ran

Go back to Calcium Binding Sites List in 2ran
Calcium binding site 6 out of 7 in the Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes


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 Crystal Structure: CA2+-Induced Conformational Changes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca325

b:44.4
occ:0.68
 O A:THR227 2.5 24.8 1.0
O A:ASP224 2.6 26.3 1.0
OE1 A:GLU232 2.6 24.8 1.0
O A:HOH503 2.7 33.8 0.6
O A:HOH418 2.8 45.7 0.4
CD A:GLU232 3.0 24.6 1.0
OD1 A:ASP224 3.2 33.0 1.0
OE2 A:GLU232 3.2 31.3 1.0
C A:ASP224 3.6 24.4 1.0
C A:THR227 3.7 22.8 1.0
CA A:ASP224 3.9 20.9 1.0
CG A:GLU232 3.9 18.8 1.0
CG A:ASP224 4.0 30.3 1.0
CA A:SER228 4.1 27.8 1.0
N A:SER228 4.3 24.3 1.0
H A:THR227 4.4 0.0 1.0
O A:ILE223 4.5 12.3 1.0
CB A:ASP224 4.6 26.5 1.0
CB A:GLU232 4.7 15.2 1.0
CB A:SER228 4.7 25.1 1.0
N A:THR227 4.8 21.9 1.0
H A:GLY229 4.8 0.0 1.0
N A:ARG225 4.8 25.2 1.0
CA A:THR227 4.8 20.9 1.0
OD2 A:ASP224 4.9 39.5 1.0

Calcium binding site 7 out of 7 in 2ran

Go back to Calcium Binding Sites List in 2ran
Calcium binding site 7 out of 7 in the Rat Annexin V Crystal Structure: CA2+-Induced Conformational Changes


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 Crystal Structure: CA2+-Induced Conformational Changes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca326

b:25.4
occ:0.45
 O A:GLY261 2.4 62.7 1.0
O A:ALA260 2.4 74.3 1.0
O A:MET257 2.4 57.8 1.0
OD2 A:ASP301 2.5 53.3 1.0
O A:HOH419 2.5 44.2 0.4
OD1 A:ASP301 2.6 54.2 1.0
O A:LYS258 2.8 75.5 1.0
CG A:ASP301 2.9 54.5 1.0
C A:ALA260 3.3 73.3 1.0
C A:MET257 3.4 57.0 1.0
C A:GLY261 3.5 61.7 1.0
C A:LYS258 3.9 72.8 1.0
CA A:MET257 4.0 52.6 1.0
N A:GLY261 4.1 70.4 1.0
CA A:ALA260 4.1 74.9 1.0
OG1 A:THR262 4.1 54.0 1.0
CA A:GLY261 4.2 66.0 1.0
N A:ALA260 4.2 77.2 1.0
N A:LYS258 4.3 63.3 1.0
CA A:LYS258 4.4 69.7 1.0
N A:THR262 4.4 56.8 1.0
CB A:ASP301 4.5 52.5 1.0
C A:GLY259 4.5 78.0 1.0
CB A:MET257 4.6 49.4 1.0
H A:ALA260 4.6 0.0 1.0
CA A:THR262 4.6 52.9 1.0
HG1 A:THR262 4.7 0.0 1.0
O A:GLY259 4.7 79.5 1.0
N A:GLY259 4.8 74.8 1.0
CB A:THR262 4.9 52.0 1.0
H A:GLY261 4.9 0.0 1.0

Reference:

N.O.Concha, J.F.Head, M.A.Kaetzel, J.R.Dedman, B.A.Seaton. Rat Annexin V Crystal Structure: Ca(2+)-Induced Conformational Changes. Science V. 261 1321 1993.
ISSN: ISSN 0036-8075
PubMed: 8362244
Page generated: Fri Jul 12 15:49:37 2024

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