Calcium in PDB 1pk8: Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp

The structure of Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp, PDB code: 1pk8 was solved by C.A.Brautigam, Y.Chelliah, J.Deisenhofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.600, 78.400, 135.000, 80.60, 76.90, 71.80
R / Rfree (%)	22.2 / 25.9

The binding sites of Calcium atom in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp (pdb code 1pk8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp, PDB code: 1pk8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp


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 Rat Synapsin I C Domain Complexed to Ca.Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca817 b:29.1 occ:1.00 O3G A:ATP800 2.4 22.8 0.8 O2A A:ATP800 2.4 18.0 0.8 O3B A:ATP800 2.4 23.5 0.2 OE1 A:GLU373 2.5 23.1 1.0 O1B A:ATP800 2.5 14.2 0.8 O1G A:ATP800 2.5 23.2 0.2 OE2 A:GLU373 2.5 23.8 1.0 O2A A:ATP800 2.6 26.6 0.2 OE2 A:GLU386 2.6 28.6 1.0 CD A:GLU373 2.9 23.2 1.0 PG A:ATP800 2.9 23.1 0.2 O2B A:ATP800 3.1 24.2 0.2 PB A:ATP800 3.2 24.3 0.2 O3G A:ATP800 3.4 24.4 0.2 O3A A:ATP800 3.4 25.5 0.2 PA A:ATP800 3.5 26.7 0.2 PA A:ATP800 3.5 19.4 0.8 PB A:ATP800 3.5 16.2 0.8 PG A:ATP800 3.6 21.7 0.8 O3B A:ATP800 3.6 16.8 0.8 CD A:GLU386 3.6 26.4 1.0 O A:HOH903 3.7 30.4 1.0 O3A A:ATP800 3.9 17.4 0.8 O1A A:ATP800 4.1 19.1 0.8 O2G A:ATP800 4.2 15.8 0.8 OE1 A:GLU386 4.3 29.2 1.0 O2G A:ATP800 4.3 21.9 0.2 O1A A:ATP800 4.3 26.6 0.2 CG A:GLU373 4.4 19.4 1.0 O A:HOH922 4.4 35.5 1.0 O A:HOH831 4.4 23.2 1.0 O1B A:ATP800 4.6 24.4 0.2 NZ A:LYS225 4.6 30.7 1.0 CG A:GLU386 4.6 23.1 1.0 CB A:GLU386 4.6 16.8 1.0 O1G A:ATP800 4.7 21.9 0.8 CG1 A:VAL388 4.7 22.4 1.0 O5' A:ATP800 4.8 27.8 0.2 O5' A:ATP800 4.8 19.0 0.8 O2B A:ATP800 4.9 15.6 0.8 O A:HOH917 5.0 38.8 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp


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 Rat Synapsin I C Domain Complexed to Ca.Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca817 b:28.5 occ:1.00 OE2 B:GLU386 2.3 24.4 1.0 O2A B:ATP801 2.3 32.3 0.2 O3G B:ATP801 2.4 18.9 0.8 O2A B:ATP801 2.5 21.3 0.8 O1B B:ATP801 2.5 15.3 0.8 OE2 B:GLU373 2.6 29.6 1.0 OE1 B:GLU373 2.7 27.6 1.0 O3B B:ATP801 2.7 31.5 0.2 O1G B:ATP801 2.8 31.8 0.2 CD B:GLU373 3.0 26.9 1.0 PA B:ATP801 3.1 32.1 0.2 O3A B:ATP801 3.2 31.7 0.2 PB B:ATP801 3.4 31.6 0.2 PG B:ATP801 3.4 31.4 0.2 O2B B:ATP801 3.4 32.0 0.2 CD B:GLU386 3.4 26.2 1.0 PB B:ATP801 3.5 19.2 0.8 O3B B:ATP801 3.5 19.8 0.8 PG B:ATP801 3.5 23.1 0.8 PA B:ATP801 3.6 20.5 0.8 O1A B:ATP801 3.7 32.0 0.2 O3A B:ATP801 3.9 18.3 0.8 OE1 B:GLU386 4.2 25.8 1.0 O2G B:ATP801 4.2 21.7 0.8 O1A B:ATP801 4.3 17.6 0.8 O2G B:ATP801 4.4 31.2 0.2 CG B:GLU373 4.5 24.8 1.0 CG B:GLU386 4.5 22.9 1.0 O3G B:ATP801 4.5 31.8 0.2 CB B:GLU386 4.5 20.9 1.0 O5' B:ATP801 4.5 32.1 0.2 CG1 B:VAL388 4.7 19.1 1.0 NZ B:LYS225 4.7 35.4 1.0 O1G B:ATP801 4.7 18.5 0.8 O1B B:ATP801 4.8 31.3 0.2 O B:HOH890 4.8 24.4 1.0 O2B B:ATP801 4.9 15.7 0.8 O5' B:ATP801 4.9 21.9 0.8

Calcium binding site 3 out of 8 in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp


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 Rat Synapsin I C Domain Complexed to Ca.Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca817 b:44.5 occ:1.00 O2A C:ATP802 2.3 34.2 0.5 O3G C:ATP802 2.4 37.9 0.6 OE2 C:GLU386 2.4 34.6 1.0 O2A C:ATP802 2.5 29.6 0.6 O1G C:ATP802 2.6 31.7 0.5 OE2 C:GLU373 2.7 40.7 1.0 O2B C:ATP802 2.9 35.0 0.5 OE1 C:GLU373 2.9 42.9 1.0 O1B C:ATP802 2.9 36.4 0.6 O3B C:ATP802 2.9 36.6 0.6 O3B C:ATP802 3.0 33.7 0.5 CD C:GLU373 3.2 40.6 1.0 PG C:ATP802 3.3 38.0 0.6 PB C:ATP802 3.4 34.6 0.5 PB C:ATP802 3.4 35.5 0.6 PG C:ATP802 3.4 33.6 0.5 PA C:ATP802 3.5 35.9 0.5 CD C:GLU386 3.5 34.8 1.0 O3A C:ATP802 3.6 35.2 0.5 PA C:ATP802 3.6 32.4 0.6 O3A C:ATP802 3.8 33.2 0.6 OE1 C:GLU386 4.0 36.1 1.0 O2G C:ATP802 4.1 36.6 0.6 O3G C:ATP802 4.3 31.0 0.5 O1G C:ATP802 4.3 36.9 0.6 C5' C:ATP802 4.5 35.3 0.5 O5' C:ATP802 4.5 36.0 0.5 O1A C:ATP802 4.5 35.5 0.5 O1A C:ATP802 4.6 31.0 0.6 CG C:GLU386 4.6 31.5 1.0 CG C:GLU373 4.7 36.5 1.0 O3' C:ATP802 4.7 37.4 0.5 O2G C:ATP802 4.7 32.0 0.5 O2B C:ATP802 4.8 35.6 0.6 O5' C:ATP802 4.8 30.7 0.6 O1B C:ATP802 4.8 34.5 0.5

Calcium binding site 4 out of 8 in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp


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 Rat Synapsin I C Domain Complexed to Ca.Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca817 b:39.5 occ:1.00 OE2 D:GLU386 2.2 36.8 1.0 O3G D:ATP803 2.3 23.1 0.8 O2A D:ATP803 2.4 31.5 0.2 O2A D:ATP803 2.5 27.5 0.8 O1B D:ATP803 2.5 26.7 0.8 O1G D:ATP803 2.6 33.0 0.2 OE2 D:GLU373 2.6 34.9 1.0 OE1 D:GLU373 2.7 35.9 1.0 O3B D:ATP803 2.9 32.9 0.2 O3A D:ATP803 3.0 32.0 0.2 CD D:GLU373 3.0 34.5 1.0 PA D:ATP803 3.0 31.5 0.2 CD D:GLU386 3.1 35.0 1.0 O2B D:ATP803 3.2 33.7 0.2 PB D:ATP803 3.3 32.5 0.2 PG D:ATP803 3.4 33.3 0.2 OE1 D:GLU386 3.5 33.7 1.0 PG D:ATP803 3.5 28.7 0.8 PB D:ATP803 3.6 26.9 0.8 PA D:ATP803 3.6 28.5 0.8 O3B D:ATP803 3.7 28.3 0.8 O1A D:ATP803 3.7 31.5 0.2 O3A D:ATP803 3.9 27.0 0.8 O2G D:ATP803 4.0 27.4 0.8 O1A D:ATP803 4.2 27.8 0.8 CG D:GLU386 4.3 35.0 1.0 NZ D:LYS225 4.3 39.8 1.0 O2G D:ATP803 4.4 32.0 0.2 O5' D:ATP803 4.5 31.2 0.2 CG D:GLU373 4.5 33.8 1.0 CB D:GLU386 4.5 32.0 1.0 O3G D:ATP803 4.5 33.6 0.2 O1B D:ATP803 4.7 33.2 0.2 O1G D:ATP803 4.7 25.7 0.8 O D:HOH877 4.8 32.5 1.0 CG1 D:VAL388 4.9 32.6 1.0 O5' D:ATP803 4.9 29.6 0.8 C5' D:ATP803 4.9 30.3 0.2 O2B D:ATP803 5.0 30.0 0.8

Calcium binding site 5 out of 8 in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp


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 Rat Synapsin I C Domain Complexed to Ca.Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca817 b:56.2 occ:1.00 O3G E:ATP804 2.2 39.6 0.6 O2A E:ATP804 2.4 35.8 0.4 O2A E:ATP804 2.4 34.7 0.6 OE2 E:GLU386 2.4 33.4 1.0 OE1 E:GLU373 2.5 50.3 1.0 O1G E:ATP804 2.5 37.1 0.4 OE2 E:GLU373 2.6 49.7 1.0 CD E:GLU373 2.9 47.8 1.0 O3B E:ATP804 3.0 35.8 0.4 O3B E:ATP804 3.0 36.9 0.6 O1B E:ATP804 3.0 37.0 0.6 PG E:ATP804 3.1 37.6 0.6 O2B E:ATP804 3.2 35.3 0.4 PG E:ATP804 3.4 37.2 0.4 CD E:GLU386 3.5 37.9 1.0 PB E:ATP804 3.5 35.3 0.6 PB E:ATP804 3.6 34.8 0.4 PA E:ATP804 3.6 34.9 0.4 PA E:ATP804 3.7 33.6 0.6 O3A E:ATP804 3.8 35.4 0.4 O3A E:ATP804 3.9 35.3 0.6 O1G E:ATP804 4.0 36.4 0.6 O2G E:ATP804 4.1 37.9 0.6 CG E:GLU386 4.3 35.5 1.0 O3G E:ATP804 4.3 33.8 0.4 OE1 E:GLU386 4.4 36.6 1.0 CG E:GLU373 4.4 43.3 1.0 O2G E:ATP804 4.6 34.6 0.4 C5' E:ATP804 4.6 37.2 0.4 O5' E:ATP804 4.6 36.4 0.4 O1A E:ATP804 4.7 33.3 0.6 O1A E:ATP804 4.7 34.9 0.4 O5' E:ATP804 4.7 34.1 0.6 O3' E:ATP804 4.7 40.1 0.4 C5' E:ATP804 4.8 33.9 0.6 O2B E:ATP804 4.9 37.5 0.6 O1B E:ATP804 5.0 36.3 0.4

Calcium binding site 6 out of 8 in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp


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 Rat Synapsin I C Domain Complexed to Ca.Atp within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca817 b:48.5 occ:1.00 OE2 F:GLU386 2.3 39.1 1.0 O2A F:ATP805 2.4 35.2 0.3 OE2 F:GLU373 2.4 39.6 1.0 O3G F:ATP805 2.5 30.6 0.7 O2A F:ATP805 2.5 31.9 0.7 O1B F:ATP805 2.6 26.4 0.7 O3B F:ATP805 2.6 35.4 0.3 O1G F:ATP805 2.8 34.8 0.3 O2B F:ATP805 3.0 36.9 0.3 OE1 F:GLU373 3.0 41.5 1.0 CD F:GLU373 3.0 39.9 1.0 PG F:ATP805 3.2 35.0 0.3 PB F:ATP805 3.2 34.9 0.3 PA F:ATP805 3.4 35.7 0.3 O3A F:ATP805 3.4 36.1 0.3 CD F:GLU386 3.5 39.5 1.0 PB F:ATP805 3.6 29.4 0.7 PA F:ATP805 3.6 33.6 0.7 PG F:ATP805 3.6 30.0 0.7 O3B F:ATP805 3.7 29.7 0.7 O3G F:ATP805 3.8 34.1 0.3 O2G F:ATP805 3.9 29.8 0.7 O3A F:ATP805 3.9 31.8 0.7 OE1 F:GLU386 4.1 40.1 1.0 O1A F:ATP805 4.2 31.1 0.7 O1A F:ATP805 4.3 33.8 0.3 CG1 F:VAL388 4.5 35.2 1.0 CG F:GLU373 4.5 38.7 1.0 O2G F:ATP805 4.6 35.0 0.3 O5' F:ATP805 4.6 35.4 0.3 CG F:GLU386 4.6 36.6 1.0 O1B F:ATP805 4.6 37.6 0.3 CB F:GLU386 4.7 33.5 1.0 NZ F:LYS225 4.7 38.5 1.0 C5' F:ATP805 4.8 35.9 0.3 O1G F:ATP805 4.9 30.3 0.7 O5' F:ATP805 4.9 34.1 0.7 O2B F:ATP805 5.0 31.0 0.7

Calcium binding site 7 out of 8 in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca817 b:39.1 occ:1.00 O3G G:ATP806 2.2 30.9 0.7 O2A G:ATP806 2.4 26.3 0.3 OE2 G:GLU386 2.4 45.1 1.0 O2A G:ATP806 2.5 28.3 0.7 O1B G:ATP806 2.6 30.0 0.7 O1G G:ATP806 2.6 25.1 0.3 OE1 G:GLU373 2.6 42.2 1.0 O3B G:ATP806 2.7 25.1 0.3 OE2 G:GLU373 2.7 43.0 1.0 CD G:GLU373 3.0 41.1 1.0 O3B G:ATP806 3.0 30.8 0.7 O2B G:ATP806 3.1 25.7 0.3 PG G:ATP806 3.2 26.5 0.3 PG G:ATP806 3.2 31.2 0.7 PB G:ATP806 3.3 25.8 0.3 PB G:ATP806 3.3 30.3 0.7 O3A G:ATP806 3.3 25.8 0.3 PA G:ATP806 3.4 26.4 0.3 CD G:GLU386 3.4 43.0 1.0 PA G:ATP806 3.6 29.1 0.7 O3A G:ATP806 3.8 29.1 0.7 OE1 G:GLU386 3.9 44.0 1.0 O2G G:ATP806 4.0 29.6 0.7 O3G G:ATP806 4.0 25.3 0.3 O1A G:ATP806 4.3 24.7 0.3 O1A G:ATP806 4.3 26.7 0.7 O1G G:ATP806 4.4 30.6 0.7 O2G G:ATP806 4.5 25.4 0.3 CG G:GLU373 4.6 38.0 1.0 O G:HOH878 4.6 35.9 1.0 O5' G:ATP806 4.6 27.5 0.3 CG G:GLU386 4.7 39.3 1.0 NZ G:LYS225 4.7 44.1 1.0 O1B G:ATP806 4.7 25.4 0.3 O2B G:ATP806 4.7 30.0 0.7 CG1 G:VAL388 4.7 26.0 1.0 C5' G:ATP806 4.7 27.7 0.3 CB G:GLU386 4.9 32.1 1.0 O5' G:ATP806 4.9 28.9 0.7

Calcium binding site 8 out of 8 in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca817 b:39.0 occ:1.00 O3G H:ATP807 2.3 43.1 0.5 O H:HOH842 2.3 36.0 1.0 OE2 H:GLU386 2.3 32.3 1.0 O2A H:ATP807 2.3 28.8 0.5 O2A H:ATP807 2.6 33.6 0.5 O3B H:ATP807 2.6 41.2 0.5 OE1 H:GLU373 2.7 41.0 1.0 O1B H:ATP807 2.7 40.8 0.5 O1G H:ATP807 2.8 32.2 0.5 O2B H:ATP807 2.8 32.6 0.5 O3B H:ATP807 2.9 33.5 0.5 OE2 H:GLU373 2.9 39.4 1.0 PG H:ATP807 3.0 43.4 0.5 CD H:GLU373 3.1 39.1 1.0 PB H:ATP807 3.2 38.8 0.5 PB H:ATP807 3.3 31.8 0.5 PG H:ATP807 3.3 33.1 0.5 CD H:GLU386 3.5 35.1 1.0 PA H:ATP807 3.5 30.9 0.5 O3A H:ATP807 3.7 30.7 0.5 PA H:ATP807 3.7 34.7 0.5 O3A H:ATP807 3.7 36.6 0.5 O2G H:ATP807 3.8 43.1 0.5 O3G H:ATP807 3.9 30.2 0.5 O1G H:ATP807 4.1 42.3 0.5 OE1 H:GLU386 4.2 36.6 1.0 CG H:GLU386 4.5 32.4 1.0 O2B H:ATP807 4.6 40.1 0.5 C5' H:ATP807 4.6 32.7 0.5 O5' H:ATP807 4.6 31.0 0.5 O1A H:ATP807 4.6 28.9 0.5 O1A H:ATP807 4.6 33.6 0.5 CG H:GLU373 4.7 32.7 1.0 O2G H:ATP807 4.7 32.4 0.5 O1B H:ATP807 4.7 32.9 0.5 O3' H:ATP807 4.8 34.0 0.5 O H:HOH855 4.8 46.3 1.0 O5' H:ATP807 4.8 34.2 0.5

C.A.Brautigam, Y.Chelliah, J.Deisenhofer. Tetramerization and Atp Binding By A Protein Comprising the A, B, and C Domains of Rat Synapsin I. J.Biol.Chem. V. 279 11948 2004.
ISSN: ISSN 0021-9258
PubMed: 14688264
DOI: 10.1074/JBC.M312015200