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Calcium in PDB 3w57: Structure of A C2 Domain

Protein crystallography data

The structure of Structure of A C2 Domain, PDB code: 3w57 was solved by D.A.K.Traore, J.C.Whisstock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.01 / 1.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.803, 52.751, 49.055, 90.00, 107.15, 90.00
R / Rfree (%) 15.9 / 18.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A C2 Domain (pdb code 3w57). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of A C2 Domain, PDB code: 3w57:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3w57

Go back to Calcium Binding Sites List in 3w57
Calcium binding site 1 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A C2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:6.3
occ:1.00
 OD2 A:ASP35 2.3 9.1 1.0
O A:GLU89 2.4 9.0 1.0
OD1 A:ASP90 2.4 10.4 1.0
OD2 A:ASP41 2.5 6.2 1.0
OD1 A:ASP88 2.5 5.8 1.0
O A:HOH325 2.6 11.3 1.0
OD2 A:ASP88 2.6 9.2 1.0
CG A:ASP88 2.9 8.7 1.0
CG A:ASP90 3.3 11.9 1.0
CG A:ASP35 3.3 9.8 1.0
C A:GLU89 3.5 8.1 1.0
CG A:ASP41 3.5 6.7 1.0
OD1 A:ASP35 3.8 9.2 1.0
CB A:ASP41 3.9 7.3 1.0
O A:HOH303 3.9 9.2 1.0
OD2 A:ASP90 4.0 12.6 1.0
CA A:ASP90 4.1 7.8 1.0
N A:ASP90 4.2 8.1 1.0
O A:HOH349 4.3 18.5 1.0
N A:ASP41 4.3 5.1 1.0
CB A:ASP90 4.3 9.9 1.0
CA A:CA202 4.4 8.3 1.0
N A:GLU89 4.4 5.5 1.0
CB A:ASP88 4.4 5.9 1.0
O A:HOH346 4.4 13.8 1.0
CA A:GLU89 4.5 6.2 1.0
O A:HOH376 4.5 17.4 1.0
CB A:ASP35 4.6 8.7 1.0
CA A:CA203 4.6 8.0 1.0
C A:ASP88 4.6 7.7 1.0
OD1 A:ASP41 4.6 7.5 1.0
O A:HOH327 4.8 12.6 1.0
CA A:ASP41 4.8 4.7 1.0
O A:HOH367 4.8 20.4 1.0
O A:ASP88 5.0 7.0 1.0
CA A:ASP88 5.0 6.0 1.0

Calcium binding site 2 out of 6 in 3w57

Go back to Calcium Binding Sites List in 3w57
Calcium binding site 2 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A C2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:8.3
occ:1.00
 OD2 A:ASP90 2.4 12.6 1.0
OD2 A:ASP95 2.4 12.3 1.0
OD1 A:ASP35 2.4 9.2 1.0
O A:HOH305 2.5 9.3 1.0
O A:HOH329 2.5 11.5 1.0
OD2 A:ASP88 2.5 9.2 1.0
O A:HOH312 2.6 12.3 1.0
CG A:ASP90 3.3 11.9 1.0
CG A:ASP95 3.5 13.1 1.0
CG A:ASP35 3.5 9.8 1.0
CG A:ASP88 3.6 8.7 1.0
OD1 A:ASP90 3.6 10.4 1.0
OD2 A:ASP35 4.0 9.1 1.0
CB A:ASP95 4.1 8.0 1.0
CB A:ASP88 4.2 5.9 1.0
CA A:CA201 4.4 6.3 1.0
N A:LEU36 4.5 10.8 1.0
O A:HOH339 4.5 10.7 1.0
OD1 A:ASP95 4.6 14.5 1.0
O A:HOH372 4.6 25.4 1.0
O A:HOH338 4.6 12.5 1.0
OD1 A:ASP88 4.6 5.8 1.0
CB A:ASP90 4.6 9.9 1.0
O A:HOH346 4.7 13.8 1.0
CB A:ASP35 4.7 8.7 1.0
CA A:ASP35 4.8 9.7 1.0
O A:HOH358 4.9 19.5 1.0
CB A:LEU36 5.0 10.9 1.0

Calcium binding site 3 out of 6 in 3w57

Go back to Calcium Binding Sites List in 3w57
Calcium binding site 3 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A C2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:8.0
occ:1.00
 OD1 A:ASN61 2.4 10.6 1.0
O A:ILE39 2.4 7.8 1.0
O A:HOH303 2.4 9.2 1.0
OD1 A:ASP41 2.5 7.5 1.0
O A:HOH327 2.5 12.6 1.0
O A:HOH317 2.5 12.2 1.0
OD2 A:ASP41 2.6 6.2 1.0
CG A:ASP41 2.9 6.7 1.0
CG A:ASN61 3.5 11.1 1.0
C A:ILE39 3.6 7.1 1.0
O A:HOH325 4.1 11.3 1.0
N A:ILE39 4.2 7.7 1.0
OD2 A:ASP35 4.2 9.1 1.0
ND2 A:ASN61 4.3 13.7 1.0
CA A:ASN61 4.3 6.5 1.0
N A:ASN61 4.3 5.6 1.0
CB A:ASP41 4.4 7.3 1.0
O A:HOH314 4.4 14.2 1.0
CA A:ILE39 4.4 7.4 1.0
O A:MET37 4.4 17.0 1.0
O A:HOH323 4.4 14.7 1.0
CB A:ASN61 4.5 8.6 1.0
C A:THR40 4.5 6.7 1.0
O A:HOH451 4.5 28.7 1.0
N A:THR40 4.5 5.7 1.0
CA A:CA201 4.6 6.3 1.0
N A:ASP41 4.6 5.1 1.0
CA A:THR40 4.7 5.3 1.0
O A:HOH426 4.7 25.3 1.0
O A:THR40 4.7 6.8 1.0
O A:HOH424 4.7 25.0 1.0
C A:GLY38 4.8 7.4 1.0
O A:HOH367 4.9 20.4 1.0
CB A:ILE39 5.0 9.9 1.0
CA A:ASP41 5.0 4.7 1.0

Calcium binding site 4 out of 6 in 3w57

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Calcium binding site 4 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A C2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:9.5
occ:1.00
 OD1 B:ASP35 2.3 13.2 1.0
O B:GLU89 2.4 8.9 1.0
OD1 B:ASP90 2.4 10.2 1.0
O B:HOH317 2.5 14.0 1.0
OD2 B:ASP41 2.5 9.2 1.0
OD1 B:ASP88 2.5 8.3 1.0
OD2 B:ASP88 2.6 10.9 1.0
CG B:ASP88 2.9 10.8 1.0
CG B:ASP35 3.4 13.1 1.0
C B:GLU89 3.4 10.4 1.0
CG B:ASP90 3.5 11.2 1.0
CG B:ASP41 3.6 9.8 1.0
OD2 B:ASP35 3.9 12.6 1.0
O B:HOH312 3.9 13.0 1.0
CB B:ASP41 4.0 10.6 1.0
O B:HOH370 4.1 19.2 1.0
CA B:ASP90 4.1 9.8 1.0
N B:ASP90 4.1 8.2 1.0
CA B:CA203 4.1 11.1 1.0
OD2 B:ASP90 4.3 14.1 1.0
N B:ASP41 4.3 9.1 1.0
N B:GLU89 4.3 8.1 1.0
CB B:ASP88 4.4 7.7 1.0
CB B:ASP90 4.4 11.4 1.0
CB B:ASP35 4.5 11.8 1.0
CA B:GLU89 4.5 7.9 1.0
O B:HOH411 4.5 28.0 1.0
CA B:CA202 4.5 11.2 1.0
O B:HOH377 4.5 19.0 1.0
C B:ASP88 4.5 10.6 1.0
OD1 B:ASP41 4.7 10.8 1.0
CA B:ASP41 4.8 7.5 1.0
O B:ILE39 4.9 12.7 1.0
O B:ASP88 4.9 10.3 1.0
CA B:ASP88 5.0 7.0 1.0

Calcium binding site 5 out of 6 in 3w57

Go back to Calcium Binding Sites List in 3w57
Calcium binding site 5 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of A C2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:11.2
occ:1.00
 O B:HOH312 2.4 13.0 1.0
O B:ILE39 2.4 12.7 1.0
OD1 B:ASN61 2.4 11.4 1.0
OD1 B:ASP41 2.5 10.8 1.0
O B:HOH363 2.5 21.5 1.0
O B:HOH319 2.6 13.7 1.0
OD2 B:ASP41 2.7 9.2 1.0
CG B:ASP41 2.9 9.8 1.0
C B:ILE39 3.6 11.3 1.0
CG B:ASN61 3.6 12.7 1.0
N B:ILE39 4.0 16.0 1.0
OD1 B:ASP35 4.2 13.2 1.0
O B:HOH317 4.3 14.0 1.0
CA B:ILE39 4.3 13.3 1.0
O B:HOH351 4.3 19.7 1.0
ND2 B:ASN61 4.4 16.4 1.0
CA B:ASN61 4.4 8.8 1.0
N B:ASN61 4.4 9.4 1.0
CB B:ASP41 4.4 10.6 1.0
O B:HOH347 4.4 16.7 1.0
C B:THR40 4.5 9.2 1.0
CA B:CA201 4.5 9.5 1.0
CB B:ASN61 4.6 10.0 1.0
O B:HOH416 4.6 25.2 1.0
N B:THR40 4.6 8.3 1.0
N B:ASP41 4.6 9.1 1.0
CB B:ILE39 4.6 12.2 1.0
O B:HOH348 4.7 18.6 1.0
O B:THR40 4.7 10.0 1.0
O B:HOH485 4.8 34.5 1.0
CA B:THR40 4.8 10.4 1.0
C B:GLY38 5.0 17.0 1.0

Calcium binding site 6 out of 6 in 3w57

Go back to Calcium Binding Sites List in 3w57
Calcium binding site 6 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of A C2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:11.1
occ:1.00
 OD2 B:ASP35 2.4 12.6 1.0
OD2 B:ASP88 2.4 10.9 1.0
O B:HOH305 2.4 11.6 1.0
OD2 B:ASP95 2.4 17.4 1.0
OD2 B:ASP90 2.5 14.1 1.0
O B:HOH383 2.6 22.5 1.0
O B:HOH385 2.6 23.5 1.0
OD1 B:ASP90 3.2 10.2 1.0
CG B:ASP90 3.2 11.2 1.0
CG B:ASP35 3.4 13.1 1.0
CG B:ASP88 3.6 10.8 1.0
CG B:ASP95 3.6 17.4 1.0
OD1 B:ASP35 3.8 13.2 1.0
CA B:CA201 4.1 9.5 1.0
CB B:ASP95 4.1 14.1 1.0
CB B:ASP88 4.2 7.7 1.0
O B:HOH362 4.3 22.1 1.0
O B:HOH411 4.4 28.0 1.0
OD1 B:ASP88 4.5 8.3 1.0
OD1 B:ASP95 4.6 18.3 1.0
O B:HOH314 4.6 12.2 1.0
CB B:ASP90 4.6 11.4 1.0
CB B:ASP35 4.6 11.8 1.0
O B:HOH337 4.7 16.7 1.0
O B:HOH449 4.9 30.7 1.0
CA B:ASP35 4.9 15.0 1.0

Reference:

D.A.Traore, A.J.Brennan, R.H.Law, C.Dogovski, M.A.Perugini, N.Lukoyanova, E.W.Leung, R.S.Norton, J.A.Lopez, K.A.Browne, H.Yagita, G.J.Lloyd, A.Ciccone, S.Verschoor, J.A.Trapani, J.C.Whisstock, I.Voskoboinik. Defining the Interaction of Perforin with Calcium and the Phospholipid Membrane. Biochem.J. V. 456 323 2013.
ISSN: ISSN 0264-6021
PubMed: 24070258
DOI: 10.1042/BJ20130999
Page generated: Tue Jul 8 17:44:36 2025

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