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Calcium in PDB 7p1v: Apo Structure of Kdnase From Trichophyton Rubrum

Protein crystallography data

The structure of Apo Structure of Kdnase From Trichophyton Rubrum, PDB code: 7p1v was solved by T.M.Gloster, S.A.Mcmahon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.36 / 1.47
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.03, 180.85, 98.34, 90, 103.77, 90
R / Rfree (%) 17.4 / 22.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Apo Structure of Kdnase From Trichophyton Rubrum (pdb code 7p1v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Apo Structure of Kdnase From Trichophyton Rubrum, PDB code: 7p1v:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7p1v

Go back to Calcium Binding Sites List in 7p1v
Calcium binding site 1 out of 4 in the Apo Structure of Kdnase From Trichophyton Rubrum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Apo Structure of Kdnase From Trichophyton Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:23.1
occ:1.00
OD1 A:ASP90 2.6 22.9 1.0
OD1 A:ASN92 2.7 22.4 1.0
O A:HIS123 2.7 18.1 1.0
O A:GLY121 2.9 21.2 1.0
O A:GLY119 3.0 26.7 1.0
O A:ILE91 3.4 15.8 1.0
C A:GLY119 3.6 20.1 1.0
N A:HIS123 3.7 20.2 1.0
O A:THR120 3.7 21.1 1.0
CG A:ASP90 3.7 20.9 1.0
N A:ILE91 3.7 15.4 1.0
C A:HIS123 3.8 17.1 1.0
O A:HOH689 3.8 27.2 1.0
CD1 A:TRP125 3.8 20.2 1.0
C A:GLY121 3.9 21.6 1.0
CG A:ASN92 3.9 18.8 1.0
C A:ILE91 3.9 16.3 1.0
C A:PRO122 4.1 21.4 1.0
O A:HOH638 4.1 79.1 1.0
CA A:GLY119 4.1 16.9 1.0
NE1 A:TRP125 4.2 18.8 1.0
CA A:ASP90 4.2 16.3 1.0
C A:THR120 4.2 22.4 1.0
C A:ASP90 4.2 17.2 1.0
CA A:HIS123 4.3 19.6 1.0
CA A:PRO122 4.4 22.9 1.0
N A:THR120 4.5 21.3 1.0
CA A:ILE91 4.5 15.1 1.0
OD2 A:ASP90 4.5 26.0 1.0
N A:PRO122 4.5 20.9 1.0
N A:ASN92 4.6 16.3 1.0
CB A:ASP90 4.6 18.9 1.0
ND2 A:ASN92 4.6 24.9 1.0
O A:PRO122 4.7 20.6 1.0
N A:GLY121 4.7 22.9 1.0
CA A:ASN92 4.8 15.7 1.0
CA A:GLY121 4.9 22.8 1.0
CB A:HIS123 4.9 17.8 1.0
N A:THR124 4.9 16.5 1.0
CA A:THR120 5.0 25.2 1.0
CB A:ASN92 5.0 18.8 1.0

Calcium binding site 2 out of 4 in 7p1v

Go back to Calcium Binding Sites List in 7p1v
Calcium binding site 2 out of 4 in the Apo Structure of Kdnase From Trichophyton Rubrum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Apo Structure of Kdnase From Trichophyton Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:20.3
occ:1.00
OD1 B:ASP90 2.6 20.5 1.0
OD1 B:ASN92 2.6 20.3 1.0
O B:HIS123 2.7 16.4 1.0
O B:GLY121 2.9 19.1 1.0
O B:GLY119 3.0 22.8 1.0
O B:ILE91 3.3 15.6 1.0
N B:ILE91 3.7 14.6 1.0
C B:GLY119 3.7 17.2 1.0
O B:HOH703 3.7 35.2 1.0
O B:THR120 3.7 19.4 0.5
CG B:ASP90 3.7 18.7 1.0
N B:HIS123 3.7 18.5 1.0
O B:THR120 3.8 20.5 0.5
C B:HIS123 3.8 15.0 1.0
C B:ILE91 3.8 15.7 1.0
CG B:ASN92 3.9 19.0 1.0
C B:GLY121 3.9 19.2 1.0
CD1 B:TRP125 3.9 16.7 1.0
C B:PRO122 4.1 19.1 1.0
CA B:GLY119 4.2 16.4 1.0
C B:ASP90 4.2 14.9 1.0
CA B:ASP90 4.2 14.2 1.0
C B:THR120 4.2 18.8 0.5
C B:THR120 4.3 19.8 0.5
NE1 B:TRP125 4.3 16.0 1.0
CA B:HIS123 4.3 16.3 1.0
O B:HOH770 4.4 44.8 1.0
CA B:PRO122 4.4 17.7 1.0
CA B:ILE91 4.4 14.8 1.0
N B:ASN92 4.5 14.1 1.0
N B:THR120 4.5 19.3 0.5
N B:PRO122 4.5 18.9 1.0
N B:THR120 4.5 18.5 0.5
CB B:ASP90 4.6 16.7 1.0
OD2 B:ASP90 4.6 23.5 1.0
ND2 B:ASN92 4.6 24.4 1.0
N B:GLY121 4.7 18.6 1.0
O B:PRO122 4.7 18.4 1.0
CA B:ASN92 4.7 15.0 1.0
CA B:GLY121 4.8 18.7 1.0
CB B:ASN92 4.9 17.4 1.0
N B:THR124 4.9 15.4 1.0
CB B:HIS123 5.0 14.8 1.0
CA B:THR120 5.0 18.3 0.5
CA B:THR120 5.0 19.9 0.5

Calcium binding site 3 out of 4 in 7p1v

Go back to Calcium Binding Sites List in 7p1v
Calcium binding site 3 out of 4 in the Apo Structure of Kdnase From Trichophyton Rubrum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Apo Structure of Kdnase From Trichophyton Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:22.5
occ:1.00
OD1 C:ASP90 2.6 21.1 1.0
OD1 C:ASN92 2.7 20.9 1.0
O C:HIS123 2.7 17.8 1.0
O C:GLY121 2.8 21.8 1.0
O C:GLY119 2.9 24.9 1.0
O C:ILE91 3.4 16.3 1.0
C C:GLY119 3.6 22.4 1.0
N C:HIS123 3.6 20.1 1.0
CG C:ASP90 3.7 21.0 1.0
O C:THR120 3.7 22.2 1.0
C C:HIS123 3.8 16.5 1.0
N C:ILE91 3.8 15.2 1.0
C C:GLY121 3.8 21.7 1.0
O C:HOH680 3.8 26.8 1.0
CD1 C:TRP125 3.9 18.1 1.0
CG C:ASN92 3.9 15.7 1.0
C C:ILE91 4.0 15.3 1.0
C C:PRO122 4.0 20.4 1.0
CA C:GLY119 4.2 20.8 1.0
O C:HOH629 4.2 50.4 1.0
C C:THR120 4.2 21.6 1.0
CA C:ASP90 4.2 17.5 1.0
NE1 C:TRP125 4.2 20.3 1.0
CA C:HIS123 4.2 16.8 1.0
C C:ASP90 4.3 15.8 1.0
CA C:PRO122 4.3 19.5 1.0
N C:PRO122 4.5 20.1 1.0
N C:THR120 4.5 21.4 1.0
OD2 C:ASP90 4.5 23.6 1.0
CB C:ASP90 4.6 17.4 1.0
CA C:ILE91 4.6 14.4 1.0
ND2 C:ASN92 4.6 23.8 1.0
O C:PRO122 4.6 21.3 1.0
N C:GLY121 4.7 23.2 1.0
N C:ASN92 4.7 15.8 1.0
CA C:GLY121 4.8 22.9 1.0
O C:HOH626 4.9 35.4 1.0
CB C:HIS123 4.9 16.2 1.0
CA C:ASN92 4.9 15.4 1.0
N C:THR124 4.9 15.6 1.0
CA C:THR120 4.9 23.1 1.0

Calcium binding site 4 out of 4 in 7p1v

Go back to Calcium Binding Sites List in 7p1v
Calcium binding site 4 out of 4 in the Apo Structure of Kdnase From Trichophyton Rubrum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Apo Structure of Kdnase From Trichophyton Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:22.1
occ:1.00
OD1 D:ASP90 2.6 19.6 1.0
OD1 D:ASN92 2.7 20.2 1.0
O D:HIS123 2.7 16.8 1.0
O D:GLY121 2.8 21.2 1.0
O D:GLY119 3.0 24.4 1.0
O D:ILE91 3.3 16.2 1.0
N D:ILE91 3.7 16.0 1.0
C D:GLY119 3.7 21.3 1.0
N D:HIS123 3.7 19.0 1.0
O D:THR120 3.7 21.9 0.5
CG D:ASP90 3.7 20.5 1.0
C D:HIS123 3.8 17.3 1.0
O D:THR120 3.8 21.7 0.5
C D:GLY121 3.8 18.8 1.0
C D:ILE91 3.9 15.8 1.0
CG D:ASN92 3.9 15.8 1.0
CD1 D:TRP125 3.9 16.7 1.0
C D:PRO122 4.1 18.9 1.0
CA D:ASP90 4.2 17.5 1.0
C D:ASP90 4.2 17.4 1.0
CA D:GLY119 4.2 21.3 1.0
C D:THR120 4.2 21.4 0.5
C D:THR120 4.2 21.9 0.5
CA D:HIS123 4.3 17.1 1.0
NE1 D:TRP125 4.3 17.8 1.0
CA D:PRO122 4.4 20.8 1.0
CA D:ILE91 4.5 15.2 1.0
N D:PRO122 4.5 20.9 1.0
N D:THR120 4.5 20.2 0.5
N D:THR120 4.5 20.3 0.5
N D:ASN92 4.5 14.8 1.0
CB D:ASP90 4.6 18.2 1.0
OD2 D:ASP90 4.6 25.9 1.0
ND2 D:ASN92 4.6 23.1 1.0
N D:GLY121 4.6 21.4 1.0
O D:PRO122 4.7 18.9 1.0
CA D:GLY121 4.8 20.2 1.0
CA D:ASN92 4.8 13.5 1.0
CB D:HIS123 4.9 19.0 1.0
N D:THR124 4.9 16.0 1.0
CA D:THR120 5.0 22.6 0.5
CB D:ASN92 5.0 14.8 1.0
CA D:THR120 5.0 23.0 0.5

Reference:

T.M.Gloster, S.A.Mcmahon. Apo Structure of Kdnase From Trichophyton Rubrum To Be Published.
Page generated: Fri Jul 19 02:41:43 2024

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