Atomistry » Calcium » PDB 4n66-4nhf » 4ndb
Atomistry »
  Calcium »
    PDB 4n66-4nhf »
      4ndb »

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

Go back to Calcium Binding Sites List in 4ndb
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy