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Calcium in PDB 1ad5: Src Family Kinase Hck-Amp-Pnp Complex

Enzymatic activity of Src Family Kinase Hck-Amp-Pnp Complex

All present enzymatic activity of Src Family Kinase Hck-Amp-Pnp Complex:
2.7.1.112;

Protein crystallography data

The structure of Src Family Kinase Hck-Amp-Pnp Complex, PDB code: 1ad5 was solved by F.Sicheri, I.Moarefi, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.767, 92.360, 178.290, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 30.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Src Family Kinase Hck-Amp-Pnp Complex (pdb code 1ad5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Src Family Kinase Hck-Amp-Pnp Complex, PDB code: 1ad5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1ad5

Go back to Calcium Binding Sites List in 1ad5
Calcium binding site 1 out of 4 in the Src Family Kinase Hck-Amp-Pnp Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Src Family Kinase Hck-Amp-Pnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:41.9
occ:1.00
OE1 B:GLU490 2.7 27.4 1.0
O A:PTR527 2.7 34.8 1.0
OE2 B:GLU490 2.8 25.8 1.0
O A:GLU524 2.8 25.8 1.0
CD B:GLU490 3.2 25.2 1.0
OE2 A:GLU524 3.9 29.4 1.0
C A:PTR527 3.9 32.7 1.0
H A:PTR527 3.9 0.0 1.0
C A:GLU524 4.0 24.5 1.0
CD A:GLU524 4.0 28.9 1.0
OE1 A:GLN529 4.0 64.8 1.0
CG A:GLN529 4.0 61.5 1.0
CD A:GLN529 4.1 64.0 1.0
N A:GLN529 4.2 49.8 1.0
H B:GLU489 4.2 0.0 1.0
H A:GLN529 4.2 0.0 1.0
CB B:PRO488 4.2 36.4 1.0
OE1 A:GLU524 4.3 31.2 1.0
C A:GLN528 4.4 45.9 1.0
H B:GLU490 4.5 0.0 1.0
CA A:GLN529 4.6 53.2 1.0
CG A:GLU524 4.6 25.8 1.0
N A:PTR527 4.7 24.1 1.0
NE2 A:GLN529 4.7 63.5 1.0
CG B:GLU490 4.7 22.2 1.0
CA A:PTR527 4.7 28.0 1.0
CA A:GLN528 4.8 42.8 1.0
N A:GLN528 4.8 38.0 1.0
CB A:GLN529 4.8 55.8 1.0
CA A:GLU524 4.8 23.7 1.0
O A:GLN528 4.9 45.8 1.0
CB A:PTR527 4.9 26.4 1.0
N B:GLU489 4.9 35.8 1.0
CA B:PRO488 4.9 36.1 1.0
CA A:SER525 4.9 22.9 1.0
N A:SER525 4.9 23.0 1.0

Calcium binding site 2 out of 4 in 1ad5

Go back to Calcium Binding Sites List in 1ad5
Calcium binding site 2 out of 4 in the Src Family Kinase Hck-Amp-Pnp Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Src Family Kinase Hck-Amp-Pnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:33.8
occ:1.00
O B:GLU524 2.6 25.0 1.0
OE1 A:GLU490 2.6 21.2 1.0
OE2 A:GLU490 2.7 21.0 1.0
O B:PTR527 2.7 29.5 1.0
CD A:GLU490 3.0 19.7 1.0
OE2 B:GLU524 3.5 35.0 1.0
C B:GLU524 3.8 23.3 1.0
CD B:GLU524 3.8 34.5 1.0
H B:PTR527 3.8 0.0 1.0
C B:PTR527 3.9 30.8 1.0
CD B:GLN529 4.2 45.8 1.0
CG B:GLN529 4.2 44.4 1.0
OE1 B:GLN529 4.2 44.0 1.0
H A:GLU489 4.2 0.0 1.0
CB A:PRO488 4.3 22.6 1.0
CG B:GLU524 4.3 30.2 1.0
N B:GLN529 4.3 37.8 1.0
OE1 B:GLU524 4.4 36.6 1.0
H A:GLU490 4.4 0.0 1.0
H B:GLN529 4.4 0.0 1.0
CA B:GLU524 4.5 23.4 1.0
CG A:GLU490 4.6 16.5 1.0
C B:GLN528 4.6 35.7 1.0
N B:PTR527 4.6 24.3 1.0
N B:SER525 4.7 23.0 1.0
CA B:GLN529 4.7 41.0 1.0
CA B:SER525 4.8 25.5 1.0
NE2 B:GLN529 4.8 43.5 1.0
CA B:PTR527 4.8 28.2 1.0
H B:GLN526 4.8 0.0 1.0
N B:GLN528 4.9 33.1 1.0
CB B:GLU524 4.9 24.5 1.0
N A:GLU489 4.9 22.0 1.0
CA A:PRO488 4.9 22.4 1.0
CA B:GLN528 5.0 34.1 1.0
CB B:PTR527 5.0 30.8 1.0
CB B:GLN529 5.0 40.5 1.0

Calcium binding site 3 out of 4 in 1ad5

Go back to Calcium Binding Sites List in 1ad5
Calcium binding site 3 out of 4 in the Src Family Kinase Hck-Amp-Pnp Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Src Family Kinase Hck-Amp-Pnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:22.4
occ:1.00
HD21 A:ASN391 1.9 0.0 1.0
O1B A:ANP1 2.5 68.4 1.0
OD2 A:ASP404 2.5 23.3 1.0
ND2 A:ASN391 2.5 15.5 1.0
HD22 A:ASN391 2.5 0.0 1.0
O2A A:ANP1 2.7 51.7 1.0
PB A:ANP1 3.4 69.9 1.0
O3A A:ANP1 3.5 60.8 1.0
HZ3 A:LYS295 3.5 0.0 1.0
PA A:ANP1 3.6 50.7 1.0
CG A:ASP404 3.7 23.3 1.0
CG A:ASN391 3.7 15.8 1.0
O2B A:ANP1 4.0 71.0 1.0
OD1 A:ASN391 4.1 19.8 1.0
CE A:LYS295 4.3 33.6 1.0
NZ A:LYS295 4.4 34.9 1.0
O1A A:ANP1 4.4 50.8 1.0
CB A:ASP404 4.5 24.1 1.0
OD1 A:ASP404 4.5 26.9 1.0
O A:ALA390 4.7 25.8 1.0
O5' A:ANP1 4.8 43.0 1.0
HH21 A:ARG388 4.8 0.0 1.0
N3B A:ANP1 4.8 77.6 1.0
CB A:ASN391 4.9 15.5 1.0
HZ1 A:LYS295 4.9 0.0 1.0
C5' A:ANP1 5.0 35.6 1.0
CA A:ASN391 5.0 17.0 1.0

Calcium binding site 4 out of 4 in 1ad5

Go back to Calcium Binding Sites List in 1ad5
Calcium binding site 4 out of 4 in the Src Family Kinase Hck-Amp-Pnp Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Src Family Kinase Hck-Amp-Pnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:30.2
occ:1.00
HD21 B:ASN391 1.8 0.0 1.0
ND2 B:ASN391 2.4 29.6 1.0
OD2 B:ASP404 2.4 25.1 1.0
O1B B:ANP532 2.4 72.7 1.0
HD22 B:ASN391 2.5 0.0 1.0
O2A B:ANP532 2.8 62.1 1.0
PB B:ANP532 3.4 72.5 1.0
CG B:ASN391 3.5 28.0 1.0
HZ3 B:LYS295 3.5 0.0 1.0
O3A B:ANP532 3.6 66.9 1.0
CG B:ASP404 3.6 29.1 1.0
PA B:ANP532 3.7 59.9 1.0
OD1 B:ASN391 3.9 31.2 1.0
O2B B:ANP532 4.0 73.4 1.0
CE B:LYS295 4.2 29.6 1.0
CB B:ASP404 4.3 28.8 1.0
NZ B:LYS295 4.3 34.2 1.0
OD1 B:ASP404 4.5 30.4 1.0
O1A B:ANP532 4.5 58.1 1.0
O B:ALA390 4.6 29.8 1.0
CB B:ASN391 4.7 24.8 1.0
N3B B:ANP532 4.8 78.8 1.0
CA B:ASN391 4.8 21.2 1.0
HH21 B:ARG388 4.8 0.0 1.0
HZ1 B:LYS295 4.9 0.0 1.0
O5' B:ANP532 4.9 54.6 1.0
O3G B:ANP532 4.9 84.2 1.0

Reference:

F.Sicheri, I.Moarefi, J.Kuriyan. Crystal Structure of the Src Family Tyrosine Kinase Hck. Nature V. 385 602 1997.
ISSN: ISSN 0028-0836
PubMed: 9024658
DOI: 10.1038/385602A0
Page generated: Sat Dec 12 02:47:57 2020

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