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Calcium in PDB 4ndd: X-Ray Structure of A Double Mutant of Calexcitin - A Neuronal Calcium- Signalling Protein

Protein crystallography data

The structure of X-Ray Structure of A Double Mutant of Calexcitin - A Neuronal Calcium- Signalling Protein, PDB code: 4ndd 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) 46.80 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.806, 69.387, 133.466, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 28.3

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 4ndd

Go back to Calcium Binding Sites List in 4ndd
Calcium binding site 1 out of 6 in the X-Ray Structure of A Double Mutant 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 Double Mutant of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:15.6
occ:1.00
 O A:VAL29 2.1 27.5 1.0
OD1 A:ASN25 2.3 39.3 1.0
O A:HOH501 2.3 25.0 1.0
OD1 A:ASP23 2.4 36.0 1.0
OD1 A:ASP27 2.4 38.7 1.0
OD2 A:ASP34 2.5 35.2 1.0
OD1 A:ASP34 2.6 35.1 1.0
CG A:ASP34 2.9 35.9 1.0
CG A:ASN25 3.0 41.0 1.0
ND2 A:ASN25 3.2 43.5 1.0
C A:VAL29 3.3 28.7 1.0
CG A:ASP27 3.4 39.8 1.0
CG A:ASP23 3.5 35.1 1.0
OD2 A:ASP27 3.8 40.8 1.0
N A:VAL29 4.0 31.5 1.0
N A:ASP27 4.2 38.5 1.0
CG2 A:VAL29 4.2 32.2 1.0
CA A:VAL29 4.2 30.2 1.0
OD2 A:ASP23 4.2 35.9 1.0
N A:ILE30 4.3 28.2 1.0
CA A:ASP23 4.3 36.5 1.0
CB A:ASP23 4.4 34.6 1.0
CB A:ASN25 4.4 40.2 1.0
CB A:ASP34 4.4 36.1 1.0
CA A:ILE30 4.4 27.9 1.0
N A:HIS26 4.5 39.3 1.0
N A:ASN25 4.5 41.0 1.0
CB A:ASP27 4.6 39.3 1.0
N A:GLY28 4.6 35.1 1.0
C A:ASP23 4.6 37.2 1.0
CA A:ASP27 4.7 37.9 1.0
CA A:ASN25 4.8 39.4 1.0
C A:ASN25 4.8 39.8 1.0
CB A:VAL29 4.8 31.7 1.0
N A:GLU31 4.8 30.0 1.0
O A:ASP23 4.9 36.9 1.0
C A:ASP27 4.9 36.6 1.0
C A:ILE30 5.0 29.7 1.0

Calcium binding site 2 out of 6 in 4ndd

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Calcium binding site 2 out of 6 in the X-Ray Structure of A Double Mutant 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 Double Mutant of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:14.3
occ:1.00
 O A:HOH502 2.2 25.9 1.0
O A:GLN80 2.3 37.4 1.0
OD1 A:ASP74 2.3 44.2 1.0
OD1 A:ASN76 2.4 44.7 1.0
OE1 A:GLU85 2.5 40.1 1.0
OD1 A:ASP78 2.7 50.8 1.0
OE2 A:GLU85 2.8 44.5 1.0
CD A:GLU85 3.0 42.0 1.0
CG A:ASN76 3.4 46.6 1.0
C A:GLN80 3.5 36.8 1.0
CG A:ASP74 3.5 45.1 1.0
CG A:ASP78 3.6 51.5 1.0
OD2 A:ASP78 3.9 53.5 1.0
ND2 A:ASN76 4.1 46.6 1.0
CA A:GLN80 4.3 37.8 1.0
CA A:ASP74 4.3 44.8 1.0
OD2 A:ASP74 4.3 45.5 1.0
CB A:GLN80 4.4 38.4 1.0
N A:GLN80 4.4 40.0 1.0
CG A:GLU85 4.4 41.8 1.0
CB A:ASP74 4.4 43.8 1.0
N A:VAL81 4.5 34.4 1.0
CB A:ASN76 4.5 48.4 1.0
CA A:VAL81 4.5 34.0 1.0
N A:ASN76 4.6 50.0 1.0
N A:ASP78 4.7 49.1 1.0
N A:THR82 4.8 35.8 1.0
CG A:GLN80 4.8 38.2 1.0
C A:ASP74 4.8 47.3 1.0
CA A:ASN76 4.9 49.6 1.0
N A:GLU77 4.9 49.0 1.0
CB A:ASP78 4.9 51.1 1.0

Calcium binding site 3 out of 6 in 4ndd

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Calcium binding site 3 out of 6 in the X-Ray Structure of A Double Mutant 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 Double Mutant of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:27.0
occ:1.00
 O A:HOH503 2.3 55.1 1.0
O A:ILE125 2.5 35.0 1.0
OE2 A:GLU130 2.5 40.4 1.0
OG A:SER121 2.6 46.3 1.0
OD1 A:ASP123 2.6 48.2 1.0
OD1 A:ASP119 2.7 39.0 1.0
OE1 A:GLU130 2.8 42.0 1.0
CD A:GLU130 2.9 40.0 1.0
CG A:ASP123 3.4 49.8 1.0
OD2 A:ASP123 3.5 51.3 1.0
C A:ILE125 3.7 35.4 1.0
CB A:SER121 3.9 45.7 1.0
CG A:ASP119 4.0 38.6 1.0
N A:SER121 4.2 41.8 1.0
CG A:GLU130 4.3 38.5 1.0
N A:GLY122 4.4 45.6 1.0
N A:ASP123 4.4 45.8 1.0
N A:ILE125 4.4 38.6 1.0
CA A:ASP119 4.4 35.3 1.0
CA A:ILE125 4.5 37.2 1.0
CA A:SER121 4.5 44.7 1.0
OD1 A:ASP127 4.5 41.0 1.0
N A:ILE126 4.7 33.5 1.0
N A:ASP127 4.7 34.3 1.0
C A:SER121 4.7 46.1 1.0
C A:ASP119 4.7 36.4 1.0
CB A:ASP119 4.7 36.3 1.0
CA A:ILE126 4.7 32.4 1.0
CB A:ILE125 4.7 38.8 1.0
CB A:ASP123 4.8 49.3 1.0
OD2 A:ASP119 4.9 38.9 1.0
N A:THR120 4.9 36.8 1.0

Calcium binding site 4 out of 6 in 4ndd

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Calcium binding site 4 out of 6 in the X-Ray Structure of A Double Mutant 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 Double Mutant of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:19.8
occ:1.00
 ND2 B:ASN25 2.2 41.2 1.0
OD1 B:ASP27 2.2 36.0 1.0
OD1 B:ASP23 2.3 35.5 1.0
O B:VAL29 2.3 30.6 1.0
O B:HOH501 2.4 30.0 1.0
OD1 B:ASP34 2.5 32.0 1.0
OD2 B:ASP34 2.6 32.3 1.0
CG B:ASP34 2.9 31.3 1.0
CG B:ASN25 3.4 43.5 1.0
CG B:ASP27 3.4 35.4 1.0
C B:VAL29 3.4 31.3 1.0
CG B:ASP23 3.5 37.1 1.0
OD1 B:ASN25 3.8 46.9 1.0
OD2 B:ASP27 3.8 35.3 1.0
N B:VAL29 4.0 33.6 1.0
CA B:VAL29 4.2 32.7 1.0
OD2 B:ASP23 4.3 38.8 1.0
N B:ASP27 4.3 35.8 1.0
CA B:ASP23 4.3 37.3 1.0
N B:ASN25 4.4 38.7 1.0
CB B:ASP34 4.4 29.7 1.0
N B:HIS26 4.4 39.2 1.0
N B:ILE30 4.4 30.9 1.0
C B:ASP23 4.5 37.9 1.0
CB B:ASP23 4.5 35.5 1.0
CA B:ILE30 4.5 30.1 1.0
CG1 B:VAL29 4.5 33.8 1.0
N B:CYS24 4.6 37.5 1.0
CB B:ASN25 4.6 41.7 1.0
CB B:VAL29 4.6 33.9 1.0
CB B:ASP27 4.7 35.3 1.0
C B:ASN25 4.7 40.7 1.0
CA B:ASN25 4.8 40.3 1.0
N B:GLY28 4.8 34.1 1.0
N B:GLU31 4.9 30.4 1.0
CA B:ASP27 4.9 35.1 1.0
O B:ASP23 4.9 37.0 1.0

Calcium binding site 5 out of 6 in 4ndd

Go back to Calcium Binding Sites List in 4ndd
Calcium binding site 5 out of 6 in the X-Ray Structure of A Double Mutant 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 Double Mutant of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:27.9
occ:1.00
 O B:HOH502 2.2 38.6 1.0
OD1 B:ASP74 2.3 52.7 1.0
O B:GLN80 2.5 36.6 1.0
OE1 B:GLU85 2.5 45.8 1.0
OE2 B:GLU85 2.6 49.0 1.0
OD1 B:ASP78 2.7 53.5 1.0
CD B:GLU85 2.9 48.8 1.0
OD1 B:ASN76 3.1 68.3 1.0
CG B:ASP74 3.3 52.4 1.0
CG B:ASP78 3.6 54.1 1.0
C B:GLN80 3.7 35.1 1.0
OD2 B:ASP78 3.8 54.5 1.0
CB B:ASP74 3.9 52.8 1.0
CA B:ASP74 3.9 55.5 1.0
OD2 B:ASP74 4.2 51.7 1.0
CG B:ASN76 4.3 70.3 1.0
C B:ASP74 4.4 60.8 1.0
N B:GLU75 4.4 66.7 1.0
N B:ASN76 4.4 71.3 1.0
CA B:VAL81 4.4 33.4 1.0
CG B:GLU85 4.4 49.7 1.0
N B:GLN80 4.5 36.9 1.0
N B:VAL81 4.5 33.2 1.0
CG2 B:THR82 4.6 37.0 1.0
CG B:GLN80 4.6 36.1 1.0
CA B:GLN80 4.6 34.9 1.0
N B:ASP78 4.7 57.9 1.0
N B:THR82 4.8 35.1 1.0
N B:GLU77 4.8 68.5 1.0
CB B:ASP78 5.0 53.2 1.0
C B:ASN76 5.0 69.2 1.0

Calcium binding site 6 out of 6 in 4ndd

Go back to Calcium Binding Sites List in 4ndd
Calcium binding site 6 out of 6 in the X-Ray Structure of A Double Mutant 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 Double Mutant of Calexcitin - A Neuronal Calcium- Signalling Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:37.0
occ:1.00
 O B:ILE125 2.3 49.8 1.0
OD1 B:ASP123 2.5 66.6 1.0
OE2 B:GLU130 2.6 47.9 1.0
O B:HOH503 2.7 50.8 1.0
OD1 B:ASP119 2.7 53.5 1.0
OE1 B:GLU130 2.8 51.8 1.0
CD B:GLU130 3.0 49.0 1.0
OG B:SER121 3.3 63.9 1.0
C B:ILE125 3.5 49.0 1.0
CG B:ASP123 3.6 69.0 1.0
CG B:ASP119 3.9 53.4 1.0
OD2 B:ASP123 4.0 70.5 1.0
CA B:ILE125 4.3 51.6 1.0
CB B:SER121 4.4 65.7 1.0
OD1 B:ASP127 4.4 56.1 1.0
CG B:GLU130 4.5 46.8 1.0
N B:ASP123 4.5 66.5 1.0
N B:ILE125 4.5 55.9 1.0
CB B:ILE125 4.5 51.8 1.0
CG B:ASP127 4.5 54.2 1.0
N B:ILE126 4.5 45.4 1.0
N B:ASP127 4.6 46.4 1.0
OD2 B:ASP127 4.6 53.4 1.0
CG2 B:ILE125 4.6 51.3 1.0
N B:GLY122 4.6 60.4 1.0
OD2 B:ASP119 4.6 53.6 1.0
CA B:ILE126 4.7 44.1 1.0
CA B:ASP119 4.8 50.9 1.0
N B:SER121 4.8 60.7 1.0
C B:SER121 4.8 63.4 1.0
CA B:SER121 4.9 63.6 1.0
CB B:ASP119 4.9 50.7 1.0
CB B:ASP123 4.9 69.3 1.0
C B:ILE126 5.0 45.3 1.0
C B:ASP119 5.0 53.5 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 11:00:50 2024

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