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Calcium in PDB 1a25: C2 Domain From Protein Kinase C (Beta)

Protein crystallography data

The structure of C2 Domain From Protein Kinase C (Beta), PDB code: 1a25 was solved by R.B.Sutton, S.R.Sprang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.798, 77.798, 140.826, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 25.4

Calcium Binding Sites:

The binding sites of Calcium atom in the C2 Domain From Protein Kinase C (Beta) (pdb code 1a25). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the C2 Domain From Protein Kinase C (Beta), PDB code: 1a25:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1a25

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Calcium binding site 1 out of 6 in the C2 Domain From Protein Kinase C (Beta)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C2 Domain From Protein Kinase C (Beta) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca290

b:22.5
occ:1.00
OD2 A:ASP193 2.3 14.5 1.0
OD1 A:ASP248 2.3 25.9 1.0
O A:TRP247 2.4 27.4 1.0
OD2 A:ASP187 2.5 20.3 1.0
OD1 A:ASP187 2.6 16.2 1.0
OD1 A:ASP246 2.6 29.6 1.0
CG A:ASP187 2.9 21.3 1.0
OD2 A:ASP246 3.2 27.2 1.0
CG A:ASP246 3.3 27.2 1.0
CG A:ASP193 3.4 26.6 1.0
CG A:ASP248 3.5 24.3 1.0
C A:TRP247 3.5 25.0 1.0
CA A:CA291 3.8 24.5 1.0
CA A:ASP248 3.9 30.1 1.0
CB A:ASP193 4.1 23.3 1.0
N A:ASP248 4.1 25.4 1.0
O A:HOH16 4.2 25.8 1.0
N A:ASP193 4.2 18.3 1.0
CB A:ASP248 4.3 22.9 1.0
OD2 A:ASP248 4.3 24.3 1.0
CB A:ASP187 4.3 19.1 1.0
OD1 A:ASP193 4.4 25.0 1.0
N A:TRP247 4.5 24.9 1.0
CA A:TRP247 4.6 26.6 1.0
C A:ASP246 4.7 23.3 1.0
CB A:ASP246 4.7 19.7 1.0
CA A:SER192 4.8 26.9 1.0
C A:SER192 4.8 23.8 1.0
CA A:ASP193 4.8 25.8 1.0
O A:ASP246 4.9 27.0 1.0
CE3 A:TRP247 4.9 54.1 1.0

Calcium binding site 2 out of 6 in 1a25

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Calcium binding site 2 out of 6 in the C2 Domain From Protein Kinase C (Beta)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C2 Domain From Protein Kinase C (Beta) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca291

b:24.5
occ:1.00
OD2 A:ASP246 2.4 27.2 1.0
OD1 A:ASP187 2.4 16.2 1.0
OD2 A:ASP254 2.5 33.9 1.0
OD2 A:ASP248 2.5 24.3 1.0
O A:MET186 2.6 27.5 1.0
OD1 A:ASP248 2.6 25.9 1.0
OE1 B:GLU281 2.6 38.7 1.0
CG A:ASP248 2.9 24.3 1.0
OE2 B:GLU281 2.9 38.5 1.0
CD B:GLU281 3.0 37.2 1.0
C A:MET186 3.5 26.4 1.0
CG A:ASP246 3.6 27.2 1.0
CG A:ASP187 3.6 21.3 1.0
CG A:ASP254 3.6 37.6 1.0
CA A:CA290 3.8 22.5 1.0
CB A:MET186 4.0 23.5 1.0
CA A:ASP187 4.1 23.3 1.0
N A:ASP187 4.2 19.9 1.0
OD1 A:ASP246 4.2 29.6 1.0
CA A:CA292 4.3 45.7 1.0
OD1 A:ASP254 4.4 47.6 1.0
CG B:GLU281 4.4 38.9 1.0
CA A:MET186 4.4 24.4 1.0
OD2 A:ASP187 4.4 20.3 1.0
CB A:ASP248 4.4 22.9 1.0
CB A:ASP187 4.4 19.1 1.0
CB A:ASP254 4.5 33.1 1.0
CB A:ASP246 4.6 19.7 1.0
CB B:GLU281 4.7 39.5 1.0

Calcium binding site 3 out of 6 in 1a25

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Calcium binding site 3 out of 6 in the C2 Domain From Protein Kinase C (Beta)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C2 Domain From Protein Kinase C (Beta) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca292

b:45.7
occ:1.00
OE2 B:GLU281 2.5 38.5 1.0
O A:ARG252 2.5 56.7 1.0
OD2 A:ASP248 2.6 24.3 1.0
OD1 A:ASP254 2.6 47.6 1.0
OG A:SER251 2.6 49.3 1.0
CB A:SER251 3.3 44.0 1.0
CG A:ASP254 3.3 37.6 1.0
OD2 A:ASP254 3.4 33.9 1.0
CG A:ASP248 3.5 24.3 1.0
CD B:GLU281 3.6 37.2 1.0
C A:ARG252 3.7 54.5 1.0
CB A:ASP248 3.8 22.9 1.0
C A:SER251 3.9 48.4 1.0
N A:ARG252 4.0 56.4 1.0
O A:SER251 4.1 50.2 1.0
CA A:SER251 4.2 47.9 1.0
CA A:CA291 4.3 24.5 1.0
OE1 B:GLU281 4.4 38.7 1.0
CA A:ARG252 4.5 57.8 1.0
OD1 A:ASP248 4.5 25.9 1.0
C A:ASN253 4.5 37.9 1.0
N A:ASP254 4.5 33.6 1.0
CG B:GLU281 4.6 38.9 1.0
N A:ASN253 4.6 47.4 1.0
CA A:ASN253 4.7 41.0 1.0
CB A:ASP254 4.7 33.1 1.0
O A:ASN253 4.9 36.9 1.0
CB A:ARG252 5.0 62.4 1.0

Calcium binding site 4 out of 6 in 1a25

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Calcium binding site 4 out of 6 in the C2 Domain From Protein Kinase C (Beta)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of C2 Domain From Protein Kinase C (Beta) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca290

b:22.7
occ:1.00
OD2 B:ASP193 2.3 24.8 1.0
O B:TRP247 2.3 20.4 1.0
OD1 B:ASP248 2.4 23.1 1.0
OD1 B:ASP246 2.5 28.6 1.0
OD2 B:ASP187 2.5 29.0 1.0
O B:HOH299 2.5 25.3 1.0
OD1 B:ASP187 2.6 19.3 1.0
CG B:ASP187 2.9 23.0 1.0
OD2 B:ASP246 3.0 22.8 1.0
CG B:ASP246 3.1 25.3 1.0
C B:TRP247 3.4 24.2 1.0
CG B:ASP248 3.4 31.8 1.0
CG B:ASP193 3.4 29.8 1.0
CA B:CA291 3.8 19.8 1.0
CA B:ASP248 3.9 32.7 1.0
CB B:ASP193 4.0 26.2 1.0
N B:ASP248 4.1 26.0 1.0
N B:ASP193 4.1 21.6 1.0
OD2 B:ASP248 4.2 34.0 1.0
CB B:ASP248 4.3 32.7 1.0
CB B:ASP187 4.3 24.6 1.0
N B:TRP247 4.4 21.4 1.0
OD1 B:ASP193 4.4 21.5 1.0
C B:ASP246 4.5 20.0 1.0
CA B:TRP247 4.5 25.9 1.0
CB B:ASP246 4.5 11.9 1.0
O B:HOH303 4.6 20.4 1.0
CA B:SER192 4.7 26.6 1.0
C B:SER192 4.7 23.5 1.0
O B:ASP246 4.7 24.6 1.0
CA B:ASP193 4.8 22.4 1.0
CE3 B:TRP247 5.0 57.0 1.0

Calcium binding site 5 out of 6 in 1a25

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Calcium binding site 5 out of 6 in the C2 Domain From Protein Kinase C (Beta)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of C2 Domain From Protein Kinase C (Beta) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca291

b:19.8
occ:1.00
OD1 B:ASP187 2.4 19.3 1.0
OD2 B:ASP246 2.4 22.8 1.0
OE1 A:GLU281 2.4 42.8 1.0
OD2 B:ASP254 2.4 28.6 1.0
OD2 B:ASP248 2.5 34.0 1.0
OD1 B:ASP248 2.6 23.1 1.0
O B:MET186 2.6 32.2 1.0
OE2 A:GLU281 2.8 39.2 1.0
CD A:GLU281 2.8 41.5 1.0
CG B:ASP248 2.9 31.8 1.0
C B:MET186 3.5 28.8 1.0
CG B:ASP254 3.6 28.7 1.0
CG B:ASP187 3.6 23.0 1.0
CG B:ASP246 3.7 25.3 1.0
CA B:CA290 3.8 22.7 1.0
O B:HOH296 3.9 23.8 1.0
CB B:MET186 4.1 22.9 1.0
CA B:ASP187 4.1 23.3 1.0
N B:ASP187 4.2 23.9 1.0
CA B:CA292 4.2 35.4 1.0
CG A:GLU281 4.2 41.2 1.0
OD1 B:ASP254 4.3 33.0 1.0
OD1 B:ASP246 4.3 28.6 1.0
CB B:ASP248 4.4 32.7 1.0
CB B:ASP187 4.4 24.6 1.0
CA B:MET186 4.4 25.5 1.0
OD2 B:ASP187 4.4 29.0 1.0
CB B:ASP254 4.5 32.9 1.0
CB A:GLU281 4.6 36.1 1.0
O B:HOH299 4.7 25.3 1.0
CB B:ASP246 4.7 11.9 1.0

Calcium binding site 6 out of 6 in 1a25

Go back to Calcium Binding Sites List in 1a25
Calcium binding site 6 out of 6 in the C2 Domain From Protein Kinase C (Beta)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of C2 Domain From Protein Kinase C (Beta) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca292

b:35.4
occ:1.00
OE2 A:GLU281 2.4 39.2 1.0
OD2 B:ASP248 2.5 34.0 1.0
O B:ARG252 2.5 48.5 1.0
OD1 B:ASP254 2.5 33.0 1.0
OG B:SER251 2.7 42.6 1.0
CG B:ASP254 3.3 28.7 1.0
CB B:SER251 3.4 36.4 1.0
OD2 B:ASP254 3.4 28.6 1.0
CG B:ASP248 3.4 31.8 1.0
CD A:GLU281 3.6 41.5 1.0
C B:ARG252 3.7 49.5 1.0
CB B:ASP248 3.8 32.7 1.0
C B:SER251 3.9 49.0 1.0
N B:ARG252 4.1 51.3 1.0
CA B:CA291 4.2 19.8 1.0
O B:SER251 4.2 51.4 1.0
CA B:SER251 4.3 45.1 1.0
OE1 A:GLU281 4.4 42.8 1.0
OD1 B:ASP248 4.5 23.1 1.0
N B:ASP254 4.5 29.0 1.0
C B:ASN253 4.5 34.6 1.0
CA B:ARG252 4.5 52.9 1.0
CG A:GLU281 4.5 41.2 1.0
N B:ASN253 4.6 43.3 1.0
CA B:ASN253 4.6 36.9 1.0
CB B:ASP254 4.7 32.9 1.0
O B:ASN253 4.9 34.9 1.0

Reference:

R.B.Sutton, S.R.Sprang. Structure of the Protein Kinase Cbeta Phospholipid-Binding C2 Domain Complexed with CA2+. Structure V. 6 1395 1998.
ISSN: ISSN 0969-2126
PubMed: 9817842
DOI: 10.1016/S0969-2126(98)00139-7
Page generated: Sat Dec 12 02:47:43 2020

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