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Calcium in PDB 1atn: Atomic Structure of the Actin:Dnase I Complex

Protein crystallography data

The structure of Atomic Structure of the Actin:Dnase I Complex, PDB code: 1atn was solved by W.Kabsch, H.G.Mannherz, D.Suck, E.Pai, K.C.Holmes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 132.900, 56.300, 109.700, 90.00, 90.00, 90.00
R / Rfree (%) 21 / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Atomic Structure of the Actin:Dnase I Complex (pdb code 1atn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Atomic Structure of the Actin:Dnase I Complex, PDB code: 1atn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1atn

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Calcium binding site 1 out of 4 in the Atomic Structure of the Actin:Dnase I Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Atomic Structure of the Actin:Dnase I Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca373

b:32.6
occ:1.00
 O2G A:ATP375 2.5 18.2 1.0
O1B A:ATP375 2.6 17.8 1.0
OE1 A:GLN137 3.0 23.8 1.0
PG A:ATP375 3.8 17.7 1.0
PB A:ATP375 3.9 17.6 1.0
CD A:GLN137 4.0 20.3 1.0
O3B A:ATP375 4.2 17.1 1.0
O3G A:ATP375 4.3 13.0 1.0
OD1 A:ASP11 4.4 20.3 1.0
O3A A:ATP375 4.5 14.9 1.0
O1A A:ATP375 4.6 17.8 1.0
OD2 A:ASP11 4.7 20.2 1.0
OD2 A:ASP154 4.7 30.7 1.0
NE2 A:GLN137 4.7 18.6 1.0
CG A:GLN137 4.8 20.7 1.0
CA A:GLY13 4.9 19.3 1.0
CG2 A:VAL339 4.9 12.9 1.0
OD1 A:ASP154 4.9 30.4 1.0
PA A:ATP375 5.0 14.6 1.0
O1G A:ATP375 5.0 17.2 1.0

Calcium binding site 2 out of 4 in 1atn

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Calcium binding site 2 out of 4 in the Atomic Structure of the Actin:Dnase I Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Atomic Structure of the Actin:Dnase I Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca264

b:7.0
occ:1.00
 OD2 D:ASP201 2.3 19.7 1.0
OD1 D:ASP201 2.5 18.4 1.0
O D:THR205 2.5 24.8 1.0
O D:THR203 2.7 17.4 1.0
O D:THR207 2.7 19.3 1.0
OG1 D:THR203 2.8 17.0 1.0
CG D:ASP201 2.8 15.7 1.0
C D:THR203 3.6 15.0 1.0
C D:THR205 3.7 22.7 1.0
C D:THR207 3.9 18.1 1.0
CB D:THR203 4.0 13.7 1.0
CA D:THR203 4.2 13.4 1.0
CB D:ASP201 4.3 13.8 1.0
N D:THR203 4.3 10.9 1.0
C D:SER206 4.4 24.2 1.0
N D:THR205 4.4 20.9 1.0
C D:ALA204 4.4 20.7 1.0
N D:THR207 4.5 22.1 1.0
O D:SER206 4.5 22.5 1.0
N D:ALA204 4.6 15.7 1.0
N D:SER206 4.6 23.2 1.0
OH D:TYR253 4.7 18.4 1.0
CA D:SER206 4.7 24.4 1.0
O D:ALA204 4.7 22.5 1.0
CA D:THR205 4.7 20.4 1.0
CA D:ASN208 4.7 19.5 1.0
CA D:ALA204 4.8 17.5 1.0
N D:ASN208 4.8 18.0 1.0
CA D:THR207 4.8 17.7 1.0
OG1 D:THR207 4.9 15.2 1.0
CE2 D:TYR253 5.0 15.4 1.0

Calcium binding site 3 out of 4 in 1atn

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Calcium binding site 3 out of 4 in the Atomic Structure of the Actin:Dnase I Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Atomic Structure of the Actin:Dnase I Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca265

b:19.2
occ:1.00
 OE2 D:GLU112 2.4 24.6 1.0
OD2 D:ASP107 2.5 43.0 1.0
OD2 D:ASP99 2.5 36.7 1.0
O D:CYS101 2.5 51.4 1.0
O D:PHE109 2.6 16.3 1.0
OD1 D:ASP99 3.0 35.9 1.0
CG D:ASP99 3.1 35.8 1.0
CG D:ASP107 3.3 42.1 1.0
CD D:GLU112 3.4 20.4 1.0
CB D:ASP107 3.6 40.0 1.0
C D:CYS101 3.6 51.4 1.0
C D:PHE109 3.8 18.7 1.0
OE1 D:GLU112 4.0 20.4 1.0
O D:SER110 4.0 22.9 1.0
CG D:GLU112 4.2 17.2 1.0
OD1 D:ASP107 4.5 40.7 1.0
CB D:CYS101 4.5 55.3 1.0
N D:PHE109 4.5 20.8 1.0
C D:SER110 4.6 21.7 1.0
CB D:ASP99 4.6 34.3 1.0
CA D:CYS101 4.6 51.5 1.0
CA D:PHE109 4.6 18.8 1.0
CA D:ASP107 4.8 39.5 1.0
N D:SER110 4.8 20.7 1.0
CA D:SER110 4.9 21.8 1.0
C D:ASP107 4.9 36.3 1.0
N D:CYS101 5.0 48.6 1.0
NH1 D:ARG73 5.0 33.1 1.0

Calcium binding site 4 out of 4 in 1atn

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Calcium binding site 4 out of 4 in the Atomic Structure of the Actin:Dnase I Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Atomic Structure of the Actin:Dnase I Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca266

b:46.6
occ:1.00
 OD2 D:ASP172 2.4 27.8 1.0
O D:ASP198 2.4 22.5 1.0
OD1 D:ASN208 3.3 24.6 1.0
CG D:ASP172 3.4 25.7 1.0
OD1 D:ASP172 3.5 29.1 1.0
O D:SER199 3.6 26.8 1.0
C D:ASP198 3.7 21.7 1.0
O D:ASN208 3.8 20.4 1.0
C D:SER199 4.2 25.2 1.0
O D:ALA200 4.3 21.9 1.0
CA D:CYS209 4.4 17.3 1.0
N D:ALA210 4.4 15.6 1.0
CA D:SER199 4.4 24.1 1.0
CG D:ASN208 4.5 22.5 1.0
N D:SER199 4.5 22.7 1.0
C D:ASN208 4.6 20.5 1.0
CA D:ASP198 4.8 21.1 1.0
C D:CYS209 4.8 15.1 1.0
CB D:ASP172 4.8 19.6 1.0
CB D:ALA210 4.8 12.6 1.0
N D:CYS209 4.8 19.6 1.0

Reference:

W.Kabsch, H.G.Mannherz, D.Suck, E.F.Pai, K.C.Holmes. Atomic Structure of the Actin:Dnase I Complex. Nature V. 347 37 1990.
ISSN: ISSN 0028-0836
PubMed: 2395459
DOI: 10.1038/347037A0
Page generated: Thu Jul 11 06:04:16 2024

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