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Calcium in PDB 2r2i: Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound

Protein crystallography data

The structure of Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound, PDB code: 2r2i was solved by R.Stephen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.333, 73.333, 73.229, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound (pdb code 2r2i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound, PDB code: 2r2i:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2r2i

Go back to Calcium Binding Sites List in 2r2i
Calcium binding site 1 out of 3 in the Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:16.6
occ:1.00
 O A:TYR69 2.2 15.5 1.0
OD2 A:ASP63 2.4 16.0 1.0
O A:HOH505 2.4 18.1 1.0
OD2 A:ASP67 2.4 16.1 1.0
OD1 A:ASN65 2.4 16.6 1.0
OE1 A:GLU74 2.4 17.3 1.0
OE2 A:GLU74 2.5 13.1 1.0
CD A:GLU74 2.8 16.2 1.0
CG A:ASP67 3.3 18.9 1.0
CG A:ASN65 3.4 19.0 1.0
C A:TYR69 3.4 17.1 1.0
CG A:ASP63 3.5 16.9 1.0
OD1 A:ASP67 3.6 17.3 1.0
ND2 A:ASN65 3.8 18.9 1.0
N A:ASP67 4.1 17.3 1.0
N A:TYR69 4.2 14.1 1.0
OD1 A:ASP63 4.2 16.1 1.0
CA A:ASP63 4.2 17.4 1.0
N A:ASN65 4.2 22.4 1.0
N A:ILE70 4.3 16.7 1.0
CA A:TYR69 4.3 14.6 1.0
CA A:ILE70 4.3 17.2 1.0
CG A:GLU74 4.3 16.1 1.0
CB A:ASP63 4.4 15.8 1.0
C A:ASP63 4.4 17.6 1.0
CB A:ASP67 4.5 18.4 1.0
N A:ASP71 4.5 15.7 1.0
N A:LYS66 4.5 20.6 1.0
CB A:ASN65 4.5 21.1 1.0
N A:PHE64 4.6 20.0 1.0
OD1 A:ASP71 4.6 17.2 1.0
CB A:TYR69 4.7 15.6 1.0
O A:HOH559 4.7 17.2 1.0
CA A:ASN65 4.7 20.9 1.0
C A:ASN65 4.7 21.9 1.0
CA A:ASP67 4.8 18.5 1.0
N A:GLY68 4.9 14.4 1.0
CG A:ASP71 4.9 18.0 1.0
C A:ILE70 4.9 15.9 1.0
O A:ASP63 4.9 17.2 1.0

Calcium binding site 2 out of 3 in 2r2i

Go back to Calcium Binding Sites List in 2r2i
Calcium binding site 2 out of 3 in the Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:16.6
occ:1.00
 O A:CYS105 2.2 19.2 1.0
OD1 A:ASP99 2.2 14.9 1.0
OD1 A:ASP101 2.3 19.0 1.0
OE1 A:GLU110 2.4 18.1 1.0
OD1 A:ASN103 2.4 16.9 1.0
O A:HOH567 2.5 15.7 1.0
OE2 A:GLU110 2.5 14.2 1.0
CD A:GLU110 2.8 14.8 1.0
CG A:ASN103 3.4 16.2 1.0
CG A:ASP101 3.4 19.5 1.0
CG A:ASP99 3.4 16.6 1.0
C A:CYS105 3.4 17.4 1.0
OD2 A:ASP101 4.0 20.3 1.0
ND2 A:ASN103 4.1 16.7 1.0
N A:ASN103 4.1 18.1 1.0
N A:CYS105 4.1 16.4 1.0
CA A:ASP99 4.2 17.0 1.0
N A:ASP101 4.2 20.4 1.0
OD2 A:ASP99 4.2 17.3 1.0
CA A:CYS105 4.3 18.7 1.0
CB A:ASP99 4.3 14.8 1.0
CB A:ASN103 4.3 17.2 1.0
CG A:GLU110 4.3 16.6 1.0
OD2 A:ASP107 4.4 20.9 1.0
N A:ILE106 4.4 16.1 1.0
C A:ASP99 4.4 17.7 1.0
N A:GLY102 4.4 18.0 1.0
CA A:ILE106 4.5 16.7 1.0
CB A:ASP101 4.5 20.3 1.0
N A:VAL100 4.5 18.0 1.0
N A:ASP107 4.6 17.9 1.0
CB A:CYS105 4.6 18.1 1.0
CA A:ASN103 4.7 18.3 1.0
CA A:ASP101 4.7 18.8 1.0
C A:ASP101 4.8 19.6 1.0
N A:GLY104 4.9 18.7 1.0
O A:HOH529 4.9 22.7 1.0
O A:ASP99 4.9 17.8 1.0
C A:ASN103 5.0 19.0 1.0
C A:ILE106 5.0 16.4 1.0

Calcium binding site 3 out of 3 in 2r2i

Go back to Calcium Binding Sites List in 2r2i
Calcium binding site 3 out of 3 in the Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:19.1
occ:1.00
 O A:GLU148 2.3 17.5 1.0
OD1 A:ASP142 2.3 18.6 1.0
OD1 A:ASP146 2.4 18.1 1.0
O A:HOH512 2.4 16.9 1.0
OD1 A:ASN144 2.4 17.9 1.0
OE1 A:GLU153 2.5 20.1 1.0
OE2 A:GLU153 2.6 22.3 1.0
CD A:GLU153 2.9 21.7 1.0
CG A:ASP146 3.3 17.2 1.0
C A:GLU148 3.5 18.7 1.0
CG A:ASP142 3.5 20.0 1.0
CG A:ASN144 3.6 20.7 1.0
OD2 A:ASP146 3.6 17.4 1.0
ND2 A:ASN144 4.1 19.8 1.0
N A:GLU148 4.2 17.6 1.0
OD2 A:ASP142 4.3 20.0 1.0
N A:ASP146 4.3 17.4 1.0
CA A:GLU148 4.4 18.8 1.0
N A:LEU149 4.4 17.7 1.0
CA A:ASP142 4.4 20.0 1.0
CG A:GLU153 4.4 21.9 1.0
CA A:LEU149 4.4 18.0 1.0
CB A:ASP142 4.5 19.4 1.0
CB A:ASP146 4.5 15.9 1.0
N A:ASN144 4.5 21.4 1.0
C A:ASP142 4.6 22.1 1.0
CB A:GLU148 4.7 22.4 1.0
N A:SER150 4.7 17.4 1.0
N A:GLY145 4.8 19.1 1.0
O A:HOH546 4.8 23.4 1.0
CB A:ASN144 4.8 20.5 1.0
N A:ILE143 4.9 22.4 1.0
CA A:ASP146 4.9 17.4 1.0
O A:ASP142 5.0 23.2 1.0
C A:ASN144 5.0 20.1 1.0
N A:GLY147 5.0 17.6 1.0
CA A:ASN144 5.0 20.1 1.0

Reference:

R.Stephen, G.Bereta, M.Golczak, K.Palczewski, M.C.Sousa. Stabilizing Function For Myristoyl Group Revealed By the Crystal Structure of A Neuronal Calcium Sensor, Guanylate Cyclase-Activating Protein 1. Structure V. 15 1392 2007.
ISSN: ISSN 0969-2126
PubMed: 17997965
DOI: 10.1016/J.STR.2007.09.013
Page generated: Fri Jul 12 15:44:54 2024

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