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Calcium in PDB 1g8i: Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1)

Protein crystallography data

The structure of Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1), PDB code: 1g8i was solved by Y.Bourne, J.Dannenberg, V.Pollmann, P.Marchot, O.Pongs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.75 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.811, 55.524, 77.705, 90.00, 94.25, 90.00
R / Rfree (%) 22 / 26.3

Other elements in 1g8i:

The structure of Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1) also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1) (pdb code 1g8i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1), PDB code: 1g8i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1g8i

Go back to Calcium Binding Sites List in 1g8i
Calcium binding site 1 out of 6 in the Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1)


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 Human Frequenin (Neuronal Calcium Sensor 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1597

b:23.5
occ:1.00
 OD1 A:ASN75 1.8 18.7 1.0
O A:ARG79 2.0 18.4 1.0
OD1 A:ASP73 2.2 25.3 1.0
O A:HOH733 2.3 30.1 1.0
OD1 A:ASP77 2.4 37.7 1.0
OE1 A:GLU84 2.5 18.1 1.0
OE2 A:GLU84 2.8 22.0 1.0
CG A:ASN75 2.9 32.0 1.0
CD A:GLU84 3.0 19.7 1.0
C A:ARG79 3.3 24.3 1.0
CG A:ASP77 3.3 38.9 1.0
CG A:ASP73 3.4 28.4 1.0
ND2 A:ASN75 3.4 34.5 1.0
OD2 A:ASP77 3.7 39.0 1.0
N A:ARG79 4.0 28.0 1.0
CA A:ILE80 4.1 21.0 1.0
CA A:ASP73 4.2 25.1 1.0
N A:ILE80 4.2 22.5 1.0
CA A:ARG79 4.2 26.6 1.0
OD2 A:ASP73 4.3 27.3 1.0
N A:ASP77 4.3 37.5 1.0
CB A:ASN75 4.3 31.2 1.0
CB A:ASP73 4.3 25.7 1.0
CB A:ASP77 4.4 38.0 1.0
N A:ASN75 4.4 33.1 1.0
N A:GLU81 4.4 19.6 1.0
CG A:GLU84 4.5 18.1 1.0
C A:ASP73 4.6 28.1 1.0
N A:LYS76 4.6 39.1 1.0
CA A:ASN75 4.7 35.6 1.0
N A:GLY78 4.7 32.3 1.0
CB A:ARG79 4.8 30.4 1.0
C A:ILE80 4.8 20.2 1.0
CA A:ASP77 4.8 36.0 1.0
C A:ASN75 4.8 37.5 1.0
N A:GLU74 4.8 29.3 1.0
CG A:GLU81 4.9 25.3 1.0
C A:ASP77 5.0 35.0 1.0

Calcium binding site 2 out of 6 in 1g8i

Go back to Calcium Binding Sites List in 1g8i
Calcium binding site 2 out of 6 in the Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1)


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 Human Frequenin (Neuronal Calcium Sensor 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1598

b:12.8
occ:1.00
 OD1 A:ASP113 2.2 17.3 1.0
OD1 A:ASP109 2.2 18.3 1.0
O A:HOH507 2.3 20.2 1.0
O A:TYR115 2.3 13.1 1.0
OD2 A:ASP111 2.4 19.6 1.0
OE1 A:GLU120 2.5 17.2 1.0
OE2 A:GLU120 2.6 19.0 1.0
CD A:GLU120 2.9 17.2 1.0
CG A:ASP113 3.2 19.9 1.0
CG A:ASP109 3.4 15.8 1.0
CG A:ASP111 3.4 23.2 1.0
C A:TYR115 3.5 15.8 1.0
OD2 A:ASP113 3.8 17.3 1.0
OD1 A:ASP111 3.9 23.9 1.0
OD2 A:ASP109 4.1 17.1 1.0
N A:TYR115 4.1 15.2 1.0
N A:ASP113 4.1 17.6 1.0
N A:ASP111 4.2 18.7 1.0
CA A:ASP109 4.2 15.2 1.0
CB A:ASP113 4.3 18.2 1.0
CB A:ASP109 4.3 15.0 1.0
CA A:TYR115 4.4 13.8 1.0
C A:ASP109 4.4 15.1 1.0
CG A:GLU120 4.4 15.1 1.0
N A:ILE116 4.5 12.3 1.0
CA A:ILE116 4.5 11.7 1.0
N A:LEU110 4.5 14.6 1.0
N A:ASN112 4.6 19.8 1.0
CB A:ASP111 4.6 21.0 1.0
CA A:ASP113 4.7 17.0 1.0
CB A:TYR115 4.7 14.2 1.0
CA A:ASP111 4.7 20.4 1.0
N A:THR117 4.7 11.8 1.0
N A:GLY114 4.8 14.4 1.0
C A:ASP111 4.8 21.2 1.0
O A:HOH608 4.8 30.6 1.0
O A:HOH523 4.8 15.6 1.0
O A:ASP109 4.9 15.3 1.0
CG2 A:THR117 5.0 16.1 1.0
C A:ASP113 5.0 18.0 1.0

Calcium binding site 3 out of 6 in 1g8i

Go back to Calcium Binding Sites List in 1g8i
Calcium binding site 3 out of 6 in the Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1)


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 Human Frequenin (Neuronal Calcium Sensor 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1599

b:15.8
occ:1.00
 OD1 A:ASP157 2.2 15.4 1.0
O A:LYS163 2.3 15.4 1.0
OE1 A:GLU168 2.3 16.4 1.0
OD1 A:ASN159 2.4 24.9 1.0
O A:HOH565 2.4 21.6 1.0
OD1 A:ASP161 2.4 23.5 1.0
OE2 A:GLU168 2.5 18.7 1.0
CD A:GLU168 2.8 16.4 1.0
CG A:ASP161 3.4 25.8 1.0
CG A:ASP157 3.4 15.1 1.0
CG A:ASN159 3.4 28.9 1.0
C A:LYS163 3.5 15.3 1.0
OD2 A:ASP161 3.8 22.9 1.0
ND2 A:ASN159 4.0 26.8 1.0
OD2 A:ASP157 4.1 13.4 1.0
N A:ASP161 4.2 27.4 1.0
N A:LYS163 4.2 17.4 1.0
CG A:GLU168 4.3 14.8 1.0
CA A:LEU164 4.4 12.9 1.0
N A:ASN159 4.4 30.5 1.0
CA A:ASP157 4.4 17.5 1.0
N A:LEU164 4.4 13.5 1.0
CA A:LYS163 4.4 17.9 1.0
CB A:ASP157 4.4 17.6 1.0
CB A:ASP161 4.6 25.6 1.0
N A:LYS158 4.6 25.6 1.0
CB A:ASN159 4.6 29.4 1.0
N A:ALA160 4.7 30.8 1.0
O A:HOH731 4.7 28.6 1.0
C A:ASP157 4.7 22.6 1.0
N A:THR165 4.8 12.5 1.0
CB A:LYS163 4.8 19.9 1.0
CA A:ASP161 4.8 24.5 1.0
O A:HOH637 4.9 27.3 1.0
CA A:ASN159 4.9 31.2 1.0
CD2 A:LEU164 4.9 9.2 1.0
C A:ASN159 4.9 30.5 1.0
N A:GLY162 4.9 22.8 1.0

Calcium binding site 4 out of 6 in 1g8i

Go back to Calcium Binding Sites List in 1g8i
Calcium binding site 4 out of 6 in the Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1)


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 Human Frequenin (Neuronal Calcium Sensor 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1600

b:24.6
occ:1.00
 O B:ARG79 2.1 23.0 1.0
OD1 B:ASN75 2.2 34.8 1.0
OD1 B:ASP73 2.2 23.0 1.0
OD2 B:ASP77 2.5 31.0 1.0
O B:HOH696 2.5 28.9 1.0
OE2 B:GLU84 2.5 20.6 1.0
OE1 B:GLU84 2.6 19.8 1.0
CD B:GLU84 2.9 21.5 1.0
CG B:ASN75 3.2 35.5 1.0
CG B:ASP77 3.2 32.6 1.0
C B:ARG79 3.3 23.8 1.0
CG B:ASP73 3.4 26.5 1.0
OD1 B:ASP77 3.6 33.7 1.0
ND2 B:ASN75 3.7 34.1 1.0
N B:ARG79 4.1 27.0 1.0
N B:ASP77 4.2 36.6 1.0
OD2 B:ASP73 4.2 26.4 1.0
N B:ILE80 4.2 22.0 1.0
CB B:ASP77 4.3 34.8 1.0
CA B:ASP73 4.3 26.7 1.0
CA B:ARG79 4.3 25.9 1.0
CA B:ILE80 4.3 22.7 1.0
CB B:ASP73 4.4 25.5 1.0
N B:ASN75 4.4 36.0 1.0
CG B:GLU84 4.5 22.1 1.0
N B:GLU81 4.5 24.6 1.0
CB B:ASN75 4.5 35.9 1.0
C B:ASP73 4.6 29.9 1.0
CA B:ASP77 4.7 34.7 1.0
N B:LYS76 4.7 37.4 1.0
CA B:ASN75 4.8 36.2 1.0
C B:ASN75 4.8 37.0 1.0
N B:GLY78 4.8 32.0 1.0
N B:GLU74 4.8 32.5 1.0
C B:ILE80 4.9 22.6 1.0
CB B:ARG79 4.9 29.4 1.0
C B:ASP77 4.9 34.0 1.0

Calcium binding site 5 out of 6 in 1g8i

Go back to Calcium Binding Sites List in 1g8i
Calcium binding site 5 out of 6 in the Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1601

b:27.9
occ:1.00
 OD1 B:ASP113 2.0 28.7 1.0
OE2 B:GLU120 2.4 27.9 1.0
O B:TYR115 2.4 26.0 1.0
O B:HOH583 2.4 25.6 1.0
OD1 B:ASP111 2.4 34.6 1.0
OD1 B:ASP109 2.5 26.0 1.0
OE1 B:GLU120 2.5 27.3 1.0
CD B:GLU120 2.7 27.1 1.0
CG B:ASP113 3.1 35.4 1.0
CG B:ASP111 3.4 36.4 1.0
CG B:ASP109 3.6 26.6 1.0
C B:TYR115 3.6 26.7 1.0
OD2 B:ASP113 3.8 34.9 1.0
OD2 B:ASP111 3.9 36.8 1.0
CB B:ASP113 4.1 34.5 1.0
CA B:ASP109 4.2 25.1 1.0
N B:ASP111 4.2 32.7 1.0
CG B:GLU120 4.2 25.3 1.0
C B:ASP109 4.3 26.4 1.0
N B:ASP113 4.3 35.5 1.0
N B:TYR115 4.3 30.1 1.0
OD2 B:ASP109 4.4 24.3 1.0
CB B:ASP109 4.4 24.1 1.0
CA B:ILE116 4.4 23.7 1.0
N B:ILE116 4.5 23.5 1.0
CA B:TYR115 4.5 28.4 1.0
N B:LEU110 4.5 28.4 1.0
N B:THR117 4.6 24.0 1.0
CG2 B:THR117 4.6 21.6 1.0
CB B:ASP111 4.6 34.4 1.0
N B:ASN112 4.7 36.0 1.0
CA B:ASP111 4.7 34.7 1.0
CA B:ASP113 4.8 34.7 1.0
O B:ASP109 4.8 26.4 1.0
C B:ASP111 4.9 34.9 1.0
CB B:TYR115 4.9 32.4 1.0
C B:ILE116 5.0 24.2 1.0

Calcium binding site 6 out of 6 in 1g8i

Go back to Calcium Binding Sites List in 1g8i
Calcium binding site 6 out of 6 in the Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1602

b:29.7
occ:1.00
 O B:LYS163 2.3 26.3 1.0
OD1 B:ASN159 2.3 41.0 1.0
OD1 B:ASP157 2.3 22.2 1.0
OD1 B:ASP161 2.4 35.2 1.0
OE1 B:GLU168 2.4 25.7 1.0
O B:HOH701 2.5 31.9 1.0
OE2 B:GLU168 2.6 27.1 1.0
CD B:GLU168 2.9 26.0 1.0
CG B:ASP161 3.3 37.6 1.0
CG B:ASP157 3.4 26.0 1.0
CG B:ASN159 3.5 41.3 1.0
C B:LYS163 3.5 27.2 1.0
OD2 B:ASP161 3.6 38.0 1.0
ND2 B:ASN159 4.0 42.7 1.0
OD2 B:ASP157 4.1 27.7 1.0
N B:LYS163 4.3 27.8 1.0
CA B:LEU164 4.3 23.0 1.0
N B:LEU164 4.4 24.0 1.0
N B:ASP161 4.4 36.4 1.0
N B:ASN159 4.4 36.5 1.0
CA B:ASP157 4.4 26.6 1.0
CG B:GLU168 4.4 26.2 1.0
CA B:LYS163 4.4 28.1 1.0
CB B:ASP157 4.4 24.6 1.0
CB B:ASP161 4.6 36.2 1.0
N B:LYS158 4.6 31.7 1.0
CB B:ASN159 4.7 39.3 1.0
CB B:LYS163 4.7 29.9 1.0
N B:THR165 4.8 22.4 1.0
C B:ASP157 4.8 29.1 1.0
O B:HOH643 4.8 32.1 1.0
N B:ALA160 4.8 38.2 1.0
CD2 B:LEU164 4.8 21.4 1.0
CA B:ASN159 4.9 37.9 1.0
CA B:ASP161 4.9 35.4 1.0
C B:ASN159 5.0 37.7 1.0

Reference:

Y.Bourne, J.Dannenberg, V.Pollmann, P.Marchot, O.Pongs. Immunocytochemical Localization and Crystal Structure of Human Frequenin (Neuronal Calcium Sensor 1). J.Biol.Chem. V. 276 11949 2001.
ISSN: ISSN 0021-9258
PubMed: 11092894
DOI: 10.1074/JBC.M009373200
Page generated: Thu Jul 11 08:35:36 2024

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