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Calcium in PDB 2ccm: X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A

Protein crystallography data

The structure of X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A, PDB code: 2ccm was solved by P.T.Erskine, G.D.E.Beaven, S.P.Wood, G.Fox, J.Vernon, K.P.Giese, J.B.Cooper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.3 / 1.8
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.635, 69.222, 134.787, 90.00, 90.00, 90.00
R / Rfree (%) 19.06 / 24.88

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A (pdb code 2ccm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A, PDB code: 2ccm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2ccm

Go back to Calcium Binding Sites List in 2ccm
Calcium binding site 1 out of 6 in the X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1192

b:20.1
occ:1.00
 OD1 A:ASP27 2.3 22.0 1.0
O A:VAL29 2.3 18.3 1.0
OD2 A:ASP34 2.3 21.5 1.0
OD1 A:ASN25 2.3 24.0 1.0
OD1 A:ASP23 2.3 20.1 1.0
OD1 A:ASP34 2.3 21.7 1.0
O A:HOH2084 2.3 16.8 1.0
CG A:ASP34 2.7 22.1 1.0
CG A:ASN25 3.2 26.2 1.0
CG A:ASP27 3.2 27.2 1.0
CG A:ASP23 3.4 20.6 1.0
C A:VAL29 3.5 16.0 1.0
ND2 A:ASN25 3.5 23.7 1.0
OD2 A:ASP27 3.7 25.5 1.0
CB A:ASP34 4.1 21.4 1.0
OD2 A:ASP23 4.2 20.8 1.0
N A:VAL29 4.2 16.1 1.0
CA A:ASP23 4.3 21.5 1.0
N A:ASP27 4.3 27.2 1.0
N A:ASN25 4.3 27.0 1.0
CB A:ASP23 4.3 21.5 1.0
CG2 A:VAL29 4.3 19.2 1.0
CA A:ILE30 4.4 18.1 1.0
N A:ILE30 4.4 17.7 1.0
CB A:ASP27 4.4 27.1 1.0
CA A:VAL29 4.4 16.2 1.0
C A:ASP23 4.5 22.6 1.0
CB A:ASN25 4.5 25.8 1.0
N A:HIS26 4.6 29.3 1.0
N A:GLU31 4.7 18.1 1.0
N A:CYS24 4.7 23.3 1.0
N A:GLY28 4.7 22.5 1.0
CA A:ASN25 4.8 27.7 1.0
C A:ASN25 4.8 28.2 1.0
CA A:ASP27 4.8 26.5 1.0
C A:ILE30 4.9 19.5 1.0
O A:ASP23 5.0 20.5 1.0

Calcium binding site 2 out of 6 in 2ccm

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Calcium binding site 2 out of 6 in the X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1193

b:24.2
occ:1.00
 OE2 A:GLU85 2.3 28.1 1.0
O A:HOH2181 2.3 31.6 1.0
O A:GLN80 2.3 22.8 1.0
OE1 A:GLU85 2.3 29.9 1.0
OD1 A:ASP74 2.3 27.5 1.0
OD1 A:ASP78 2.3 34.4 1.0
OD1 A:ASN76 2.3 25.6 1.0
CD A:GLU85 2.6 29.6 1.0
CG A:ASP78 3.2 34.2 1.0
CG A:ASP74 3.4 27.5 1.0
CG A:ASN76 3.4 30.3 1.0
C A:GLN80 3.5 23.9 1.0
OD2 A:ASP78 3.6 33.2 1.0
CG A:GLU85 4.1 26.2 1.0
ND2 A:ASN76 4.1 25.1 1.0
N A:ASP78 4.1 33.7 1.0
OD2 A:ASP74 4.1 27.3 1.0
CA A:ASP74 4.1 28.7 1.0
CB A:ASP74 4.2 27.5 1.0
N A:ASN76 4.2 35.7 1.0
N A:GLN80 4.3 24.1 1.0
CA A:GLN80 4.3 25.1 1.0
O A:HOH2190 4.4 47.8 1.0
N A:VAL81 4.5 21.5 1.0
C A:ASP74 4.5 31.4 1.0
CA A:VAL81 4.5 20.3 1.0
CB A:ASP78 4.5 33.4 1.0
CB A:GLN80 4.5 24.7 1.0
N A:GLU77 4.5 35.0 1.0
CB A:ASN76 4.6 30.3 1.0
N A:GLU75 4.7 34.6 1.0
CA A:ASN76 4.7 33.6 1.0
C A:ASN76 4.7 34.3 1.0
CA A:ASP78 4.8 32.5 1.0
N A:THR82 4.9 23.1 1.0
N A:GLU79 5.0 30.1 1.0

Calcium binding site 3 out of 6 in 2ccm

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Calcium binding site 3 out of 6 in the X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1194

b:15.9
occ:1.00
 O A:ILE125 2.3 16.9 1.0
OD1 A:ASP119 2.3 15.8 1.0
OG A:SER121 2.3 23.0 1.0
OD1 A:ASP123 2.3 21.5 1.0
OE1 A:GLU130 2.3 19.8 1.0
O A:HOH2226 2.3 26.1 1.0
OE2 A:GLU130 2.3 18.3 1.0
CD A:GLU130 2.7 18.4 1.0
CG A:ASP123 3.4 22.3 1.0
CG A:ASP119 3.4 17.8 1.0
C A:ILE125 3.5 17.9 1.0
CB A:SER121 3.6 22.6 1.0
OD2 A:ASP123 3.8 22.9 1.0
N A:SER121 4.1 22.1 1.0
CA A:ASP119 4.2 15.3 1.0
CG A:GLU130 4.2 16.0 1.0
CB A:ASP119 4.2 17.0 1.0
N A:ILE125 4.2 16.0 1.0
CA A:SER121 4.3 22.8 1.0
N A:ASP123 4.3 20.6 1.0
CA A:ILE125 4.3 16.8 1.0
OD2 A:ASP119 4.3 16.1 1.0
CA A:ILE126 4.4 15.9 1.0
N A:ASP127 4.4 15.2 1.0
N A:ILE126 4.4 16.3 1.0
N A:GLY122 4.5 23.4 1.0
OD2 A:ASP127 4.5 21.2 1.0
C A:ASP119 4.6 18.0 1.0
O A:HOH2220 4.6 39.5 1.0
CB A:ASP123 4.6 20.1 1.0
C A:SER121 4.7 23.6 1.0
O A:HOH2223 4.7 39.4 1.0
CB A:ILE125 4.7 19.1 1.0
N A:THR120 4.8 18.3 1.0
C A:ILE126 4.8 14.8 1.0
CG A:ASP127 4.9 21.2 1.0
CA A:ASP123 4.9 20.1 1.0

Calcium binding site 4 out of 6 in 2ccm

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Calcium binding site 4 out of 6 in the X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1192

b:15.8
occ:1.00
 OD1 B:ASP23 2.3 17.7 1.0
OD1 B:ASN25 2.3 17.7 1.0
O B:VAL29 2.3 15.1 1.0
O B:HOH2131 2.3 13.9 1.0
OD1 B:ASP27 2.3 15.0 1.0
OD2 B:ASP34 2.3 15.4 1.0
OD1 B:ASP34 2.4 16.5 1.0
CG B:ASP34 2.7 13.7 1.0
CG B:ASN25 3.2 19.4 1.0
CG B:ASP27 3.2 18.4 1.0
CG B:ASP23 3.5 17.6 1.0
OD2 B:ASP27 3.5 18.1 1.0
ND2 B:ASN25 3.5 17.7 1.0
C B:VAL29 3.5 13.2 1.0
N B:ASP27 4.2 19.3 1.0
OD2 B:ASP23 4.2 16.2 1.0
CB B:ASP34 4.2 12.8 1.0
N B:VAL29 4.3 12.3 1.0
N B:ASN25 4.3 16.3 1.0
CA B:ILE30 4.4 14.4 1.0
CA B:ASP23 4.4 17.2 1.0
CB B:ASP23 4.4 17.0 1.0
N B:ILE30 4.4 11.9 1.0
CB B:ASP27 4.4 18.1 1.0
CA B:VAL29 4.5 13.4 1.0
CB B:ASN25 4.5 18.1 1.0
N B:HIS26 4.6 18.8 1.0
N B:GLU31 4.6 13.8 1.0
CG2 B:VAL29 4.6 15.3 1.0
C B:ASP23 4.6 16.7 1.0
CA B:ASN25 4.8 17.8 1.0
CA B:ASP27 4.8 18.8 1.0
C B:ASN25 4.8 18.9 1.0
N B:GLY28 4.8 17.9 1.0
N B:CYS24 4.9 16.3 1.0
C B:ILE30 4.9 15.0 1.0

Calcium binding site 5 out of 6 in 2ccm

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Calcium binding site 5 out of 6 in the X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1193

b:17.7
occ:1.00
 O B:HOH2254 2.3 24.5 1.0
OD1 B:ASP74 2.3 25.1 1.0
OD1 B:ASN76 2.3 31.9 1.0
O B:GLN80 2.3 20.4 1.0
OE2 B:GLU85 2.3 23.8 1.0
OE1 B:GLU85 2.3 20.2 1.0
OD1 B:ASP78 2.3 21.2 1.0
CD B:GLU85 2.7 23.1 1.0
CG B:ASP78 3.3 24.0 1.0
CG B:ASN76 3.5 33.0 1.0
C B:GLN80 3.5 19.1 1.0
CG B:ASP74 3.5 23.7 1.0
OD2 B:ASP78 3.7 23.1 1.0
ND2 B:ASN76 4.1 32.3 1.0
CA B:ASP74 4.2 26.6 1.0
CG B:GLU85 4.2 22.5 1.0
N B:GLN80 4.3 18.6 1.0
N B:ASP78 4.3 29.1 1.0
OD2 B:ASP74 4.3 24.5 1.0
N B:ASN76 4.4 33.4 1.0
CA B:GLN80 4.4 19.5 1.0
CB B:ASP74 4.4 24.0 1.0
C B:ASP74 4.5 29.8 1.0
N B:VAL81 4.5 17.9 1.0
CA B:VAL81 4.5 14.9 1.0
N B:GLU75 4.6 32.0 1.0
CB B:ASP78 4.6 25.3 1.0
N B:GLU77 4.6 34.3 1.0
CB B:ASN76 4.6 32.5 1.0
CG2 B:THR82 4.7 16.1 1.0
CB B:GLN80 4.7 21.4 1.0
N B:THR82 4.8 14.7 1.0
O B:HOH2264 4.8 29.4 1.0
C B:ASN76 4.8 33.8 1.0
O B:HOH2258 4.8 34.3 1.0
CA B:ASN76 4.8 33.5 1.0
CA B:ASP78 4.9 26.3 1.0

Calcium binding site 6 out of 6 in 2ccm

Go back to Calcium Binding Sites List in 2ccm
Calcium binding site 6 out of 6 in the X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of Calexcitin From Loligo Pealeii at 1.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1194

b:23.9
occ:1.00
 OD1 B:ASP119 2.3 30.8 1.0
O B:HOH2305 2.3 38.6 1.0
OG B:SER121 2.3 36.7 1.0
OD1 B:ASP123 2.3 39.9 1.0
OE1 B:GLU130 2.3 24.6 1.0
O B:ILE125 2.3 25.4 1.0
OE2 B:GLU130 2.3 24.0 1.0
CD B:GLU130 2.7 24.9 1.0
CG B:ASP119 3.3 31.6 1.0
CG B:ASP123 3.3 40.8 1.0
CB B:SER121 3.4 36.6 1.0
C B:ILE125 3.5 25.9 1.0
OD2 B:ASP123 3.9 41.3 1.0
CA B:ASP119 4.1 31.8 1.0
OD2 B:ASP119 4.1 32.3 1.0
N B:SER121 4.1 36.3 1.0
CG B:GLU130 4.2 23.4 1.0
CB B:ASP119 4.2 31.1 1.0
O B:HOH2302 4.2 37.6 1.0
CA B:SER121 4.3 36.9 1.0
N B:ILE125 4.4 29.4 1.0
N B:ASP127 4.4 20.1 1.0
CA B:ILE125 4.4 27.4 1.0
N B:ASP123 4.4 38.7 1.0
C B:ASP119 4.5 32.7 1.0
CA B:ILE126 4.5 22.2 1.0
N B:ILE126 4.5 23.0 1.0
CB B:ASP123 4.5 39.0 1.0
OD1 B:ASP127 4.5 34.5 1.0
N B:GLY122 4.6 38.5 1.0
N B:THR120 4.7 33.5 1.0
CB B:ILE125 4.7 29.9 1.0
C B:SER121 4.7 37.9 1.0
CG2 B:ILE125 4.8 31.1 1.0
O B:HOH2314 4.8 42.2 1.0
CG B:ASP127 4.9 31.4 1.0
C B:ILE126 4.9 22.5 1.0
CA B:ASP123 4.9 37.5 1.0

Reference:

P.T.Erskine, G.D.E.Beaven, R.Hagan, I.S.Findlow, J.M.Werner, S.P.Wood, J.Vernon, K.P.Giese, G.Fox, J.B.Cooper. Structure of the Neuronal Protein Calexcitin Suggests A Mode of Interaction in Signalling Pathways of Learning and Memory. J.Mol.Biol. V. 357 1536 2006.
ISSN: ISSN 0022-2836
PubMed: 16497326
DOI: 10.1016/J.JMB.2006.01.083
Page generated: Tue Jul 8 04:47:52 2025

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