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Sodium in PDB 1x27: Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS

Enzymatic activity of Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS

All present enzymatic activity of Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS:
2.7.1.112;

Protein crystallography data

The structure of Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS, PDB code: 1x27 was solved by F.Nasertorabi, K.Tars, K.Becherer, R.Kodandapani, L.Liljas, K.Vuori, K.R.Ely, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.415, 107.289, 166.389, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 31.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS (pdb code 1x27). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS, PDB code: 1x27:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 1x27

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Sodium binding site 1 out of 6 in the Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na227

b:51.9
occ:1.00
 O A:GLU123 2.5 60.1 1.0
O A:GLU125 2.7 52.8 1.0
O A:PHE128 2.8 63.0 1.0
C A:GLU123 3.7 61.4 1.0
C A:PHE128 3.7 60.9 1.0
C A:GLU125 3.8 53.3 1.0
N A:PHE128 4.3 54.0 1.0
CA A:GLU123 4.4 63.1 1.0
CA A:PHE128 4.4 58.0 1.0
N A:GLU125 4.5 56.4 1.0
C A:PRO124 4.5 57.5 1.0
CE1 A:PHE129 4.6 64.5 1.0
CD1 A:PHE129 4.6 64.3 1.0
N A:PHE129 4.6 62.1 1.0
CB A:PHE128 4.7 58.2 1.0
C A:PRO126 4.7 52.5 1.0
N A:PRO126 4.7 53.4 1.0
CA A:PRO126 4.7 52.2 1.0
CA A:GLU125 4.7 55.3 1.0
N A:PRO124 4.8 59.5 1.0
O A:PRO124 4.8 58.8 1.0
CA A:PHE129 4.9 63.4 1.0
O A:PRO126 4.9 52.9 1.0
CZ A:PHE129 4.9 63.5 1.0
CG A:PHE129 4.9 63.4 1.0
CA A:PRO124 4.9 57.2 1.0
O A:LEU122 5.0 64.0 1.0

Sodium binding site 2 out of 6 in 1x27

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Sodium binding site 2 out of 6 in the Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na6

b:39.8
occ:1.00
 O B:PHE128 2.7 45.6 1.0
O B:GLU125 2.8 53.7 1.0
O B:GLU123 2.8 60.5 1.0
C B:PHE128 3.9 46.1 1.0
C B:GLU125 3.9 53.4 1.0
C B:GLU123 4.0 60.0 1.0
N B:GLU125 4.4 56.3 1.0
N B:PHE128 4.4 44.0 1.0
C B:PRO124 4.4 58.3 1.0
CA B:PHE128 4.5 46.0 1.0
CB B:PHE128 4.6 47.2 1.0
CA B:GLU125 4.7 55.8 1.0
N B:PRO126 4.8 50.7 1.0
CA B:PRO124 4.8 58.0 1.0
O B:PRO124 4.8 58.4 1.0
N B:PRO124 4.8 58.5 1.0
CA B:PRO126 4.9 48.9 1.0
N B:PHE129 4.9 47.7 1.0
C B:PRO126 4.9 47.6 1.0
CA B:GLU123 4.9 60.8 1.0

Sodium binding site 3 out of 6 in 1x27

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Sodium binding site 3 out of 6 in the Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na14

b:44.5
occ:1.00
 O C:PHE128 2.6 50.9 1.0
O C:GLU123 2.6 60.4 1.0
O C:GLU125 2.7 52.2 1.0
C C:PHE128 3.6 50.6 1.0
C C:GLU123 3.7 61.2 1.0
C C:GLU125 3.8 53.2 1.0
CB C:PHE128 4.0 51.0 1.0
CA C:PHE128 4.1 49.8 1.0
N C:PHE128 4.1 47.5 1.0
O C:HOH232 4.1 50.2 1.0
C C:PRO124 4.2 60.9 1.0
N C:GLU125 4.2 59.3 1.0
O C:LEU122 4.4 59.8 1.0
O C:PRO124 4.4 62.5 1.0
CA C:GLU123 4.5 63.6 1.0
CA C:GLU125 4.6 56.5 1.0
CE1 C:PHE129 4.6 55.2 1.0
CA C:PRO124 4.6 59.5 1.0
CD1 C:PHE129 4.7 54.8 1.0
N C:PRO124 4.7 59.5 1.0
N C:PHE129 4.7 53.3 1.0
N C:PRO126 4.8 51.5 1.0
C C:PRO126 4.8 47.6 1.0
O C:PRO126 4.9 47.2 1.0
CD2 C:PHE128 4.9 55.1 1.0
CG C:PHE128 4.9 53.5 1.0
CA C:PRO126 5.0 48.6 1.0

Sodium binding site 4 out of 6 in 1x27

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Sodium binding site 4 out of 6 in the Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na10

b:50.5
occ:1.00
 O D:GLU125 2.7 60.2 1.0
O D:GLU123 2.8 67.4 1.0
O D:PHE128 2.8 68.9 1.0
C D:GLU125 3.7 60.4 1.0
O D:PRO124 3.8 64.8 1.0
C D:PHE128 3.9 67.1 1.0
C D:GLU123 4.0 67.7 1.0
C D:PRO124 4.1 64.4 1.0
N D:GLU125 4.4 64.1 1.0
CE1 D:PHE129 4.4 73.6 1.0
N D:PHE128 4.5 60.1 1.0
N D:PRO126 4.5 57.9 1.0
CD1 D:PHE129 4.6 72.3 1.0
CA D:PHE128 4.6 64.4 1.0
CB D:PHE128 4.6 65.3 1.0
CA D:GLU125 4.6 62.6 1.0
CA D:PRO126 4.6 55.3 1.0
O D:PRO126 4.6 54.5 1.0
C D:PRO126 4.7 54.3 1.0
CA D:PRO124 4.7 64.2 1.0
O D:LEU122 4.8 69.2 1.0
N D:PRO124 4.8 64.7 1.0
CA D:GLU123 4.9 70.5 1.0
CZ D:PHE129 4.9 73.3 1.0
N D:PHE129 5.0 69.7 1.0

Sodium binding site 5 out of 6 in 1x27

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Sodium binding site 5 out of 6 in the Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na227

b:43.8
occ:1.00
 O E:PHE128 2.6 63.4 1.0
O E:GLU125 2.7 54.3 1.0
O E:GLU123 2.7 66.5 1.0
C E:GLU125 3.8 54.7 1.0
C E:PHE128 3.8 62.3 1.0
C E:GLU123 4.0 66.2 1.0
CE1 E:PHE129 4.0 75.0 1.0
CD1 E:PHE129 4.1 74.0 1.0
O E:PRO124 4.3 61.2 1.0
C E:PRO124 4.4 61.0 1.0
N E:PHE128 4.5 53.4 1.0
CA E:PRO126 4.5 51.8 1.0
N E:PRO126 4.5 53.0 1.0
N E:GLU125 4.6 59.6 1.0
CA E:PHE128 4.6 58.6 1.0
C E:PRO126 4.6 50.6 1.0
O E:PRO126 4.6 51.1 1.0
CA E:GLU125 4.8 57.2 1.0
CA E:GLU123 4.8 68.1 1.0
O E:LEU122 4.8 69.5 1.0
CZ E:PHE129 4.8 74.5 1.0
N E:PHE129 4.8 66.5 1.0
N E:PRO124 4.9 63.7 1.0
CB E:PHE128 4.9 58.8 1.0
CA E:PRO124 4.9 62.1 1.0
CA E:PHE129 5.0 70.0 1.0
CG E:PHE129 5.0 74.1 1.0

Sodium binding site 6 out of 6 in 1x27

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Sodium binding site 6 out of 6 in the Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Lck SH2-SH3 with SH2 Binding Site of P130CAS within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na21

b:27.7
occ:1.00
 O F:GLU125 2.6 38.0 1.0
O F:PHE128 2.6 54.4 1.0
O F:GLU123 2.6 43.6 1.0
C F:PHE128 3.7 52.5 1.0
C F:GLU125 3.7 41.5 1.0
CE1 F:PHE129 3.8 53.1 1.0
C F:GLU123 3.9 46.9 1.0
O F:PRO124 3.9 44.3 1.0
CD1 F:PHE129 4.0 53.5 1.0
C F:PRO124 4.0 42.4 1.0
N F:PHE128 4.3 46.1 1.0
CZ F:PHE129 4.4 53.3 1.0
N F:GLU125 4.4 42.4 1.0
CA F:PHE128 4.4 51.0 1.0
CA F:PRO124 4.6 41.7 1.0
N F:PRO126 4.6 40.2 1.0
CA F:PRO126 4.6 40.0 1.0
CA F:GLU125 4.6 43.4 1.0
CB F:PHE128 4.6 52.7 1.0
N F:PRO124 4.6 43.4 1.0
CG F:PHE129 4.7 55.5 1.0
C F:PRO126 4.7 42.0 1.0
N F:PHE129 4.7 54.3 1.0
O F:LEU122 4.7 52.5 1.0
CA F:PHE129 4.9 56.4 1.0
O F:PRO126 4.9 43.3 1.0
CA F:GLU123 4.9 51.6 1.0
CE2 F:PHE129 5.0 53.0 1.0

Reference:

F.Nasertorabi, K.Tars, K.Becherer, R.Kodandapani, L.Liljas, K.Vuori, K.R.Ely. Molecular Basis For Regulation of Src By the Docking Protein P130CAS J.Mol.Recog. V. 19 30 2006.
ISSN: ISSN 0952-3499
PubMed: 16245368
DOI: 10.1002/JMR.755
Page generated: Sun Aug 17 09:09:21 2025

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