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Calcium in PDB 4ndb: X-Ray Structure of A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein

Protein crystallography data

The structure of X-Ray Structure of A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein, PDB code: 4ndb was solved by P.T.Erskine, A.Fokas, C.Muriithi, E.Razzall, A.Bowyer, I.S.Findlow, J.M.Werner, B.A.Wallace, S.P.Wood, J.B.Cooper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.90 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.165, 69.194, 135.431, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 21.2

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein (pdb code 4ndb). 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 A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein, PDB code: 4ndb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4ndb

Go back to Calcium Binding Sites List in 4ndb
Calcium binding site 1 out of 6 in the X-Ray Structure of A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein


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 A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:10.2
occ:1.00
 O A:VAL29 2.3 17.5 1.0
OD1 A:ASP23 2.3 16.5 1.0
OD1 A:ASP27 2.4 20.6 1.0
O A:HOH501 2.4 15.7 1.0
OD1 A:ASN25 2.4 19.0 1.0
OD1 A:ASP34 2.5 15.8 1.0
OD2 A:ASP34 2.5 16.2 1.0
CG A:ASP34 2.8 15.8 1.0
CG A:ASP27 3.3 22.7 1.0
CG A:ASN25 3.3 21.7 1.0
CG A:ASP23 3.4 18.7 1.0
C A:VAL29 3.5 16.1 1.0
OD2 A:ASP27 3.6 21.8 1.0
ND2 A:ASN25 3.7 23.0 1.0
N A:VAL29 4.2 16.9 1.0
CB A:ASP23 4.2 18.9 1.0
OD2 A:ASP23 4.2 18.8 1.0
CA A:ASP23 4.3 19.6 1.0
N A:ASP27 4.3 25.0 1.0
CB A:ASP34 4.3 16.0 1.0
N A:ASN25 4.3 18.9 1.0
CG2 A:VAL29 4.3 17.1 1.0
N A:ILE30 4.4 15.6 1.0
CA A:VAL29 4.4 16.5 1.0
CA A:ILE30 4.4 15.2 1.0
N A:HIS26 4.5 23.4 1.0
C A:ASP23 4.6 19.8 1.0
CB A:ASP27 4.6 24.3 1.0
N A:GLU31 4.6 15.4 1.0
CB A:ASN25 4.6 19.9 1.0
C A:ASN25 4.7 21.8 1.0
CA A:ASN25 4.7 20.8 1.0
N A:GLY28 4.8 20.4 1.0
CA A:ASP27 4.9 24.1 1.0
N A:CYS24 4.9 20.3 1.0
C A:ILE30 4.9 15.5 1.0
OE1 A:GLU31 5.0 18.9 1.0

Calcium binding site 2 out of 6 in 4ndb

Go back to Calcium Binding Sites List in 4ndb
Calcium binding site 2 out of 6 in the X-Ray Structure of A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein


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 A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:10.9
occ:1.00
 O A:HOH502 2.3 19.7 1.0
O A:GLN80 2.3 21.7 1.0
OD1 A:ASP74 2.3 22.3 1.0
OE2 A:GLU85 2.4 25.2 1.0
OD1 A:ASN76 2.4 24.7 1.0
OD1 A:ASP78 2.5 22.3 1.0
OE1 A:GLU85 2.6 25.1 1.0
CD A:GLU85 2.8 24.8 1.0
CG A:ASP78 3.4 25.5 1.0
CG A:ASP74 3.4 22.8 1.0
C A:GLN80 3.5 19.7 1.0
CG A:ASN76 3.6 24.9 1.0
OD2 A:ASP78 3.8 23.0 1.0
OD2 A:ASP74 4.2 23.7 1.0
CA A:ASP74 4.2 22.8 1.0
N A:GLN80 4.2 20.2 1.0
ND2 A:ASN76 4.3 23.8 1.0
N A:ASN76 4.3 25.7 1.0
CB A:ASP74 4.3 23.0 1.0
CG A:GLU85 4.3 23.2 1.0
O A:HOH597 4.4 30.2 1.0
CA A:GLN80 4.4 20.1 1.0
N A:ASP78 4.4 24.7 1.0
CB A:GLN80 4.4 19.6 1.0
N A:VAL81 4.4 17.7 1.0
C A:ASP74 4.5 24.4 1.0
CA A:VAL81 4.5 17.1 1.0
CB A:ASP78 4.6 24.8 1.0
N A:GLU75 4.6 25.8 1.0
N A:GLU77 4.7 25.0 1.0
CB A:ASN76 4.7 24.6 1.0
CA A:ASN76 4.8 25.6 1.0
C A:ASN76 4.9 25.6 1.0
N A:THR82 4.9 18.2 1.0
CA A:ASP78 4.9 24.8 1.0
N A:GLU79 5.0 23.4 1.0

Calcium binding site 3 out of 6 in 4ndb

Go back to Calcium Binding Sites List in 4ndb
Calcium binding site 3 out of 6 in the X-Ray Structure of A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein


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 A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:10.6
occ:1.00
 O A:ILE125 2.2 17.0 1.0
OD1 A:ASP123 2.3 19.7 1.0
OD1 A:ASP119 2.4 17.2 1.0
OE2 A:GLU130 2.4 15.8 1.0
O A:HOH503 2.4 18.8 1.0
OE1 A:GLU130 2.5 17.8 1.0
OG A:SER121 2.5 20.9 1.0
CD A:GLU130 2.8 16.3 1.0
C A:ILE125 3.5 17.0 1.0
CG A:ASP123 3.5 20.8 1.0
CG A:ASP119 3.5 18.0 1.0
CB A:SER121 3.7 20.7 1.0
OD2 A:ASP123 4.0 21.4 1.0
N A:SER121 4.1 18.7 1.0
N A:ILE125 4.2 16.7 1.0
O A:HOH619 4.2 28.0 1.0
CA A:ASP119 4.2 17.1 1.0
N A:ASP123 4.3 20.3 1.0
CA A:SER121 4.3 19.9 1.0
CG A:GLU130 4.3 16.1 1.0
OD2 A:ASP119 4.3 19.1 1.0
CA A:ILE125 4.3 16.8 1.0
O A:HOH621 4.4 31.9 1.0
CB A:ASP119 4.4 17.1 1.0
OD2 A:ASP127 4.4 20.1 1.0
N A:ILE126 4.4 15.9 1.0
CA A:ILE126 4.4 15.5 1.0
N A:ASP127 4.4 16.1 1.0
N A:GLY122 4.5 19.6 1.0
C A:ASP119 4.6 17.0 1.0
CB A:ASP123 4.6 20.8 1.0
C A:SER121 4.7 20.8 1.0
CB A:ILE125 4.7 18.1 1.0
C A:ILE126 4.9 16.5 1.0
CA A:ASP123 4.9 20.6 1.0
CG A:ASP127 4.9 18.8 1.0
O A:HOH617 4.9 36.3 1.0
N A:THR120 4.9 17.2 1.0

Calcium binding site 4 out of 6 in 4ndb

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Calcium binding site 4 out of 6 in the X-Ray Structure of A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein


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 A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:8.6
occ:1.00
 OD1 B:ASP23 2.3 16.3 1.0
O B:VAL29 2.3 15.0 1.0
OD1 B:ASP27 2.4 16.2 1.0
OD1 B:ASN25 2.5 16.6 1.0
OD2 B:ASP34 2.5 14.9 1.0
O B:HOH501 2.5 12.2 1.0
OD1 B:ASP34 2.6 15.2 1.0
CG B:ASP34 2.9 15.2 1.0
CG B:ASP27 3.3 16.1 1.0
CG B:ASN25 3.4 17.1 1.0
CG B:ASP23 3.4 16.3 1.0
C B:VAL29 3.5 15.4 1.0
OD2 B:ASP27 3.6 15.7 1.0
ND2 B:ASN25 3.7 16.8 1.0
N B:ASP27 4.1 16.3 1.0
N B:VAL29 4.2 16.6 1.0
OD2 B:ASP23 4.2 15.7 1.0
CA B:ASP23 4.3 15.6 1.0
CB B:ASP23 4.4 15.3 1.0
CB B:ASP34 4.4 14.6 1.0
CA B:ILE30 4.4 14.8 1.0
N B:ASN25 4.4 16.8 1.0
CA B:VAL29 4.4 16.9 1.0
CG2 B:VAL29 4.5 16.8 1.0
N B:ILE30 4.5 15.2 1.0
CB B:ASP27 4.5 16.4 1.0
N B:GLU31 4.5 15.0 1.0
N B:HIS26 4.6 18.7 1.0
N B:GLY28 4.6 16.7 1.0
CB B:ASN25 4.6 16.5 1.0
C B:ASP23 4.6 15.6 1.0
CA B:ASP27 4.7 16.9 1.0
CA B:ASN25 4.8 17.6 1.0
C B:ASN25 4.8 17.8 1.0
C B:ILE30 4.9 15.3 1.0
C B:ASP27 4.9 17.2 1.0

Calcium binding site 5 out of 6 in 4ndb

Go back to Calcium Binding Sites List in 4ndb
Calcium binding site 5 out of 6 in the X-Ray Structure of A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein


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 A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:11.7
occ:1.00
 OD1 B:ASP74 2.3 24.7 1.0
O B:GLN80 2.4 20.2 1.0
O B:HOH502 2.4 22.5 1.0
OD1 B:ASN76 2.4 31.3 1.0
OE2 B:GLU85 2.4 26.4 1.0
OD1 B:ASP78 2.5 27.3 1.0
OE1 B:GLU85 2.6 23.9 1.0
CD B:GLU85 2.8 25.6 1.0
CG B:ASP78 3.3 27.5 1.0
CG B:ASP74 3.5 26.1 1.0
CG B:ASN76 3.6 33.5 1.0
C B:GLN80 3.6 19.9 1.0
OD2 B:ASP78 3.6 27.8 1.0
ND2 B:ASN76 4.2 32.3 1.0
CA B:ASP74 4.2 28.5 1.0
N B:GLN80 4.3 20.9 1.0
N B:ASP78 4.3 32.5 1.0
CB B:ASP74 4.3 27.3 1.0
N B:ASN76 4.3 34.6 1.0
OD2 B:ASP74 4.3 25.9 1.0
CG B:GLU85 4.3 26.5 1.0
CA B:GLN80 4.4 20.6 1.0
N B:VAL81 4.5 18.9 1.0
C B:ASP74 4.5 32.1 1.0
CA B:VAL81 4.5 18.5 1.0
CB B:GLN80 4.6 20.8 1.0
N B:GLU75 4.6 33.4 1.0
CB B:ASP78 4.6 27.4 1.0
N B:GLU77 4.7 36.2 1.0
O B:HOH622 4.7 30.2 1.0
CB B:ASN76 4.7 34.5 1.0
N B:THR82 4.8 19.0 1.0
CG2 B:THR82 4.8 20.4 1.0
CA B:ASP78 4.9 28.7 1.0
N B:GLU79 4.9 25.6 1.0
CA B:ASN76 4.9 35.3 1.0
C B:ASN76 4.9 35.3 1.0

Calcium binding site 6 out of 6 in 4ndb

Go back to Calcium Binding Sites List in 4ndb
Calcium binding site 6 out of 6 in the X-Ray Structure of A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein


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 A Mutant (T61D) of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:15.0
occ:1.00
 OD1 B:ASP119 2.2 26.4 1.0
O B:ILE125 2.2 24.0 1.0
O B:HOH503 2.3 33.2 1.0
OE2 B:GLU130 2.5 22.4 1.0
OE1 B:GLU130 2.5 26.4 1.0
OD1 B:ASP123 2.5 32.9 1.0
OG B:SER121 2.5 33.9 1.0
CD B:GLU130 2.8 24.8 1.0
CG B:ASP119 3.2 29.8 1.0
C B:ILE125 3.4 24.9 1.0
CG B:ASP123 3.6 36.6 1.0
CB B:SER121 3.6 36.5 1.0
CB B:ASP119 4.0 28.0 1.0
N B:SER121 4.0 34.4 1.0
CA B:ASP119 4.1 27.7 1.0
OD2 B:ASP123 4.2 36.0 1.0
OD2 B:ASP119 4.2 33.4 1.0
CA B:ILE125 4.2 25.9 1.0
N B:ILE125 4.2 27.9 1.0
CA B:SER121 4.3 36.0 1.0
N B:ASP123 4.3 38.3 1.0
N B:GLY122 4.3 37.0 1.0
OD1 B:ASP127 4.3 31.2 1.0
CG B:GLU130 4.4 24.4 1.0
CB B:ILE125 4.4 26.0 1.0
C B:ASP119 4.4 29.2 1.0
N B:ILE126 4.4 22.8 1.0
O B:HOH644 4.4 39.7 1.0
CA B:ILE126 4.5 22.0 1.0
N B:ASP127 4.5 20.7 1.0
O B:HOH649 4.5 41.5 1.0
C B:SER121 4.6 38.0 1.0
N B:THR120 4.7 28.3 1.0
CB B:ASP123 4.7 36.6 1.0
CG B:ASP127 4.8 28.7 1.0
O B:ASP119 4.9 32.5 1.0
CA B:ASP123 4.9 37.4 1.0
C B:ILE126 4.9 21.1 1.0

Reference:

P.T.Erskine, A.Fokas, C.Muriithi, E.Razzall, A.Bowyer, I.S.Findlow, J.M.Werner, B.A.Wallace, S.P.Wood, J.B.Cooper. X-Ray and uc(Nmr) Structure-Function Studies of Calexcitin - A Neuronal Calcium-Signalling Protein To Be Published.
Page generated: Sun Jul 14 11:00:41 2024

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