Calcium in PDB 2hqw: Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide

The structure of Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide, PDB code: 2hqw was solved by Z.Akyol, L.Gakhar, B.R.Sorensen, J.H.Hell, M.A.Shea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.57 / 1.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	40.371, 40.371, 175.765, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 24.8

The binding sites of Calcium atom in the Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide (pdb code 2hqw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide, PDB code: 2hqw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:31.9 occ:1.00 OD1 A:ASP20 2.3 34.2 1.0 O A:THR26 2.4 32.8 1.0 OD1 A:ASP22 2.4 36.5 1.0 OD1 A:ASP24 2.4 38.9 1.0 O A:HOH1027 2.4 35.8 1.0 OE1 A:GLU31 2.5 33.9 1.0 OE2 A:GLU31 2.6 35.5 1.0 CD A:GLU31 2.9 32.2 1.0 CG A:ASP24 3.2 36.5 1.0 CG A:ASP22 3.3 35.1 1.0 CG A:ASP20 3.4 32.8 1.0 C A:THR26 3.5 32.6 1.0 OD2 A:ASP24 3.6 41.1 1.0 OD2 A:ASP22 3.7 34.2 1.0 N A:THR26 4.1 32.8 1.0 N A:ASP24 4.1 34.9 1.0 OD2 A:ASP20 4.2 32.4 1.0 CA A:ASP20 4.2 32.1 1.0 CB A:ASP24 4.2 35.5 1.0 N A:ASP22 4.3 36.2 1.0 CB A:ASP20 4.3 33.0 1.0 OG1 A:THR26 4.3 38.6 1.0 CA A:THR26 4.4 33.6 1.0 CG A:GLU31 4.4 33.0 1.0 C A:ASP20 4.5 33.4 1.0 N A:ILE27 4.5 31.0 1.0 N A:LYS21 4.6 35.2 1.0 CB A:ASP22 4.6 35.5 1.0 CA A:ASP24 4.6 34.7 1.0 CA A:ILE27 4.6 29.1 1.0 N A:GLY25 4.6 34.0 1.0 N A:GLY23 4.7 36.3 1.0 CA A:ASP22 4.7 36.1 1.0 C A:ASP24 4.8 34.6 1.0 O A:HOH1009 4.8 30.0 1.0 O A:HOH1041 4.8 38.6 1.0 C A:ASP22 4.9 36.4 1.0 CG2 A:THR28 4.9 30.7 1.0 N A:THR28 4.9 29.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:31.3 occ:1.00 OD1 A:ASP56 2.3 33.6 1.0 O A:THR62 2.3 29.0 1.0 OD1 A:ASN60 2.3 35.6 1.0 OE1 A:GLU67 2.3 27.6 1.0 OE2 A:GLU67 2.4 22.0 1.0 O A:HOH1050 2.5 44.9 1.0 OD1 A:ASP58 2.5 39.0 1.0 CD A:GLU67 2.7 25.4 1.0 CG A:ASN60 3.3 35.0 1.0 CG A:ASP56 3.4 35.2 1.0 CG A:ASP58 3.4 36.6 1.0 C A:THR62 3.5 29.4 1.0 ND2 A:ASN60 3.7 37.6 1.0 OD2 A:ASP58 3.7 36.5 1.0 O A:HOH1056 3.9 55.9 1.0 OD2 A:ASP56 4.1 32.4 1.0 CG A:GLU67 4.2 26.2 1.0 N A:ASN60 4.3 35.2 1.0 CA A:ILE63 4.3 29.2 1.0 N A:ILE63 4.3 28.7 1.0 CA A:ASP56 4.4 36.4 1.0 CB A:ASP56 4.4 36.9 1.0 CB A:ASN60 4.4 35.1 1.0 N A:ASP64 4.4 28.4 1.0 N A:THR62 4.4 31.2 1.0 N A:ASP58 4.4 35.4 1.0 CA A:THR62 4.6 29.9 1.0 OG1 A:THR62 4.6 28.6 1.0 CB A:ASP58 4.6 35.5 1.0 N A:ALA57 4.7 35.6 1.0 N A:GLY59 4.7 35.3 1.0 CG A:ASP64 4.8 30.0 1.0 C A:ASP56 4.8 36.5 1.0 C A:ILE63 4.8 28.6 1.0 CA A:ASN60 4.8 35.1 1.0 OD1 A:ASP64 4.8 32.2 1.0 CA A:ASP58 4.8 35.5 1.0 OD2 A:ASP64 4.9 29.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:31.0 occ:1.00 O A:TYR99 2.2 30.3 1.0 OD1 A:ASP93 2.3 31.8 1.0 O A:HOH1010 2.3 29.8 1.0 OD1 A:ASP95 2.4 33.0 1.0 OD1 A:ASN97 2.4 32.2 1.0 OE1 A:GLU104 2.5 31.1 1.0 OE2 A:GLU104 2.6 33.6 1.0 CD A:GLU104 2.9 32.7 1.0 CG A:ASP95 3.3 33.2 1.0 CG A:ASN97 3.4 29.1 1.0 C A:TYR99 3.4 30.2 1.0 CG A:ASP93 3.5 32.5 1.0 OD2 A:ASP95 3.7 31.5 1.0 ND2 A:ASN97 4.1 28.2 1.0 N A:TYR99 4.2 30.4 1.0 N A:ASN97 4.2 31.2 1.0 OD2 A:ASP93 4.2 31.0 1.0 O A:HOH1013 4.3 26.5 1.0 CA A:ASP93 4.3 33.1 1.0 CA A:TYR99 4.3 29.4 1.0 N A:ASP95 4.4 35.1 1.0 CG A:GLU104 4.4 32.2 1.0 CB A:ASP93 4.4 33.3 1.0 N A:ILE100 4.4 30.9 1.0 C A:ASP93 4.4 34.1 1.0 CB A:ASN97 4.4 29.9 1.0 CA A:ILE100 4.5 29.5 1.0 CB A:ASP95 4.5 33.4 1.0 N A:LYS94 4.6 36.0 1.0 N A:GLY96 4.7 33.2 1.0 N A:SER101 4.7 29.3 1.0 CA A:ASN97 4.7 29.0 1.0 CB A:TYR99 4.8 31.1 1.0 N A:GLY98 4.8 29.6 1.0 CA A:ASP95 4.8 33.9 1.0 O A:HOH1029 4.8 44.0 1.0 O A:ASP93 4.9 33.4 1.0 C A:ASP95 4.9 33.6 1.0 O A:HOH1023 4.9 35.0 1.0 C A:ASN97 5.0 29.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of CA2+/Calmodulin Bound to Nmda Receptor NR1C1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:31.3 occ:1.00 O A:GLN135 2.3 30.8 1.0 OD1 A:ASP129 2.3 30.5 1.0 OD2 A:ASP133 2.4 33.6 1.0 OD2 A:ASP131 2.4 31.3 1.0 OE1 A:GLU140 2.5 29.2 1.0 O A:HOH1012 2.5 24.1 1.0 OE2 A:GLU140 2.5 27.8 1.0 CD A:GLU140 2.9 30.9 1.0 CG A:ASP131 3.3 29.9 1.0 CG A:ASP133 3.3 28.9 1.0 CG A:ASP129 3.4 27.7 1.0 C A:GLN135 3.4 31.3 1.0 OD1 A:ASP131 3.6 32.3 1.0 OD1 A:ASP133 3.8 30.5 1.0 OD2 A:ASP129 4.1 29.4 1.0 N A:GLN135 4.1 30.4 1.0 CB A:ASP129 4.2 29.5 1.0 N A:ASP133 4.3 27.7 1.0 N A:ASP131 4.3 28.3 1.0 CA A:ASP129 4.3 29.0 1.0 N A:VAL136 4.3 31.0 1.0 CA A:VAL136 4.4 30.6 1.0 N A:ILE130 4.4 26.6 1.0 CG A:GLU140 4.4 30.1 1.0 CA A:GLN135 4.4 30.5 1.0 N A:GLY132 4.4 28.6 1.0 CB A:ASP133 4.5 27.6 1.0 N A:ASN137 4.5 30.3 1.0 CB A:ASP131 4.6 28.8 1.0 N A:GLY134 4.6 27.0 1.0 CA A:ASP133 4.7 27.2 1.0 CA A:ASP131 4.8 28.8 1.0 C A:ASP129 4.9 28.2 1.0 C A:VAL136 4.9 30.6 1.0 C A:ASP133 4.9 27.8 1.0 C A:ASP131 4.9 28.9 1.0 CB A:GLN135 5.0 31.9 1.0

Z.A.Ataman, L.Gakhar, B.R.Sorensen, J.W.Hell, M.A.Shea. The Nmda Receptor NR1 C1 Region Bound to Calmodulin: Structural Insights Into Functional Differences Between Homologous Domains. Structure V. 15 1603 2007.
ISSN: ISSN 0969-2126
PubMed: 18073110
DOI: 10.1016/J.STR.2007.10.012