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Sodium in PDB 2a2a: High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase

Enzymatic activity of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase

All present enzymatic activity of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase:
2.7.1.37;

Protein crystallography data

The structure of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase, PDB code: 2a2a was solved by P.Kursula, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.47
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.300, 60.650, 98.710, 92.16, 103.45, 94.25
R / Rfree (%) 15 / 20.7

Other elements in 2a2a:

The structure of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase (pdb code 2a2a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase, PDB code: 2a2a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 2a2a

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Sodium binding site 1 out of 8 in the High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3152

b:32.1
occ:1.00
 O B:HOH4029 2.1 27.4 1.0
O A:HOH3353 2.2 26.5 1.0
O B:HOH3790 2.5 20.4 1.0
O B:ASN190 2.5 22.6 1.0
O A:ASN190 2.6 23.5 1.0
C B:ASN190 3.2 18.7 1.0
C A:ASN190 3.3 16.9 1.0
O B:HOH3904 3.4 34.7 1.0
O A:HOH3494 3.4 38.7 1.0
CA B:ASN190 3.6 18.9 1.0
CA A:ASN190 3.7 18.2 1.0
O B:HOH3848 3.8 31.2 1.0
O A:HOH3436 3.8 30.2 1.0
CB B:ASN190 4.2 16.7 1.0
CB A:TYR191 4.2 17.9 1.0
N B:TYR191 4.2 18.1 1.0
N A:TYR191 4.3 18.6 1.0
CB A:ASN190 4.3 18.1 1.0
CB B:TYR191 4.3 19.8 1.0
OD1 B:ASN190 4.3 21.1 1.0
OD1 A:ASN190 4.5 23.2 1.0
O B:VAL189 4.6 22.4 1.0
O A:VAL189 4.7 20.9 1.0
CA A:TYR191 4.7 20.8 1.0
CA B:TYR191 4.7 17.0 1.0
CG B:ASN190 4.7 21.8 1.0
N B:ASN190 4.8 20.4 1.0
CG A:ASN190 4.8 17.3 1.0
N A:ASN190 4.9 18.3 1.0

Sodium binding site 2 out of 8 in 2a2a

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Sodium binding site 2 out of 8 in the High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3178

b:43.6
occ:1.00
 OG1 A:THR244 2.3 26.7 1.0
O A:HOH3364 2.4 25.6 1.0
O A:LEU211 2.8 21.5 1.0
O A:HOH3361 2.9 25.1 1.0
O A:HOH3477 3.2 34.4 1.0
CB A:THR244 3.4 21.8 1.0
CA A:THR244 3.7 22.4 1.0
C A:LEU211 3.7 18.4 1.0
N A:THR244 3.7 22.4 1.0
CB A:LEU211 3.9 19.8 1.0
CG2 A:THR244 3.9 22.1 1.0
O A:VAL290 4.1 23.9 1.0
C A:HIS243 4.2 23.9 1.0
CA A:LEU211 4.2 18.5 1.0
CA A:VAL291 4.4 26.8 1.0
O A:PHE240 4.4 24.2 1.0
CB A:HIS243 4.5 24.3 1.0
OE1 A:GLU113 4.6 20.4 1.0
CG2 A:VAL291 4.6 25.6 1.0
O A:HIS243 4.6 25.4 1.0
N A:SER212 4.8 20.2 1.0
CD2 A:PHE241 4.8 25.6 1.0
CD2 A:LEU211 4.8 22.3 1.0
CA A:HIS243 4.8 23.9 1.0
CG A:LEU211 4.8 20.3 1.0
CB A:VAL291 4.9 26.3 1.0
C A:VAL290 4.9 21.1 1.0
N A:HIS243 4.9 21.6 1.0
CA A:SER212 5.0 23.0 1.0
CA A:PHE241 5.0 23.6 1.0
CG1 A:VAL291 5.0 27.0 1.0

Sodium binding site 3 out of 8 in 2a2a

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Sodium binding site 3 out of 8 in the High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3763

b:52.9
occ:1.00
 OE2 B:GLU60 2.2 35.0 1.0
CD B:GLU60 3.0 39.0 1.0
N B:SER57 3.1 30.4 1.0
OE1 B:GLU60 3.2 40.3 1.0
O B:HOH4040 3.3 37.0 1.0
CA B:VAL56 3.6 34.2 1.0
C B:VAL56 3.8 32.4 1.0
CB B:SER57 3.9 29.0 1.0
OG B:SER57 3.9 29.0 1.0
CA B:SER57 4.0 29.5 1.0
CG1 B:VAL56 4.1 30.9 1.0
O B:GLY55 4.1 42.2 1.0
O B:HOH3957 4.2 44.1 1.0
CG B:GLU60 4.3 33.5 1.0
CB B:VAL56 4.3 33.9 1.0
NH1 B:ARG47 4.4 36.2 1.0
O B:HOH3946 4.7 40.1 1.0
N B:VAL56 4.7 36.2 1.0
CB B:GLU60 4.7 27.7 1.0
CG2 B:VAL56 4.8 32.8 1.0
C B:GLY55 4.8 40.4 1.0
CD B:ARG47 4.8 40.2 1.0

Sodium binding site 4 out of 8 in 2a2a

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Sodium binding site 4 out of 8 in the High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3221

b:40.7
occ:1.00
 OG1 B:THR244 2.2 25.4 1.0
O B:HOH3797 2.4 26.4 1.0
O B:HOH3801 2.8 24.7 1.0
O B:LEU211 2.8 20.8 1.0
O B:HOH3943 3.2 38.8 1.0
CB B:THR244 3.3 16.6 1.0
CA B:THR244 3.7 18.3 1.0
C B:LEU211 3.8 19.2 1.0
N B:THR244 3.8 18.4 1.0
CG2 B:THR244 3.9 16.9 1.0
CB B:LEU211 3.9 17.9 1.0
O B:VAL290 3.9 23.0 1.0
C B:HIS243 4.2 19.2 1.0
CA B:LEU211 4.3 18.1 1.0
CA B:VAL291 4.3 24.1 1.0
O B:PHE240 4.4 21.7 1.0
CB B:HIS243 4.5 20.8 1.0
OE1 B:GLU113 4.6 18.8 1.0
O B:HIS243 4.6 23.3 1.0
CG2 B:VAL291 4.7 29.4 1.0
CD2 B:PHE241 4.7 19.2 1.0
CA B:HIS243 4.7 17.9 1.0
N B:SER212 4.8 19.5 1.0
C B:VAL290 4.8 21.0 1.0
CD2 B:LEU211 4.9 18.6 1.0
CG B:LEU211 4.9 17.8 1.0
CA B:PHE241 4.9 20.2 1.0
CB B:VAL291 4.9 24.8 1.0
N B:ASN292 5.0 28.8 1.0
N B:HIS243 5.0 19.0 1.0
CA B:SER212 5.0 19.8 1.0

Sodium binding site 5 out of 8 in 2a2a

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Sodium binding site 5 out of 8 in the High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3158

b:31.8
occ:1.00
 O D:HOH3286 2.1 29.4 1.0
O D:HOH3188 2.5 17.9 1.0
O C:ASN190 2.6 17.9 1.0
O D:ASN190 2.7 19.5 1.0
C C:ASN190 3.2 16.8 1.0
C D:ASN190 3.3 16.2 1.0
O C:HOH3390 3.4 33.6 1.0
CA C:ASN190 3.6 18.9 1.0
CA D:ASN190 3.6 17.9 1.0
O D:HOH3313 3.6 37.7 1.0
O D:HOH3238 3.9 29.7 1.0
O C:HOH3369 4.1 29.4 1.0
CB C:ASN190 4.2 17.8 1.0
CB C:TYR191 4.3 19.1 1.0
N D:TYR191 4.3 18.2 1.0
CB D:ASN190 4.3 17.2 1.0
N C:TYR191 4.3 16.7 1.0
CB D:TYR191 4.3 18.5 1.0
OD1 C:ASN190 4.4 19.0 1.0
OD1 D:ASN190 4.4 19.5 1.0
O D:VAL189 4.6 18.6 1.0
O C:VAL189 4.6 19.1 1.0
CA C:TYR191 4.8 17.9 1.0
CG C:ASN190 4.8 20.4 1.0
CA D:TYR191 4.8 16.8 1.0
CG D:ASN190 4.9 19.4 1.0
N C:ASN190 4.9 17.8 1.0
N D:ASN190 4.9 16.6 1.0

Sodium binding site 6 out of 8 in 2a2a

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Sodium binding site 6 out of 8 in the High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3281

b:66.3
occ:1.00
 OE2 C:GLU60 2.4 35.3 1.0
O C:HOH3480 2.9 46.0 1.0
O C:HOH3503 3.2 47.5 1.0
CD C:GLU60 3.3 34.6 1.0
N C:SER57 3.5 26.7 1.0
OE1 C:GLU60 3.6 41.8 1.0
CA C:VAL56 3.9 28.4 1.0
O C:GLY55 4.0 35.1 1.0
C C:VAL56 4.2 28.6 1.0
O C:HOH3623 4.2 48.9 1.0
CB C:SER57 4.2 28.1 1.0
CG1 C:VAL56 4.3 28.3 1.0
NH1 C:ARG47 4.4 35.8 1.0
O C:HOH3396 4.5 40.1 1.0
OG C:SER57 4.5 27.0 1.0
CA C:SER57 4.5 27.1 1.0
CB C:VAL56 4.6 25.9 1.0
CG C:GLU60 4.7 28.6 1.0
N C:VAL56 4.8 30.2 1.0
C C:GLY55 4.8 35.5 1.0
CD C:ARG47 4.9 41.4 1.0

Sodium binding site 7 out of 8 in 2a2a

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Sodium binding site 7 out of 8 in the High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3291

b:46.6
occ:1.00
 OG1 C:THR244 2.1 27.1 1.0
O C:HOH3355 2.5 27.2 1.0
O C:HOH3332 2.8 25.8 1.0
O C:LEU211 2.9 21.1 1.0
O C:HOH3472 3.2 35.9 1.0
CB C:THR244 3.3 23.8 1.0
CA C:THR244 3.6 18.8 1.0
N C:THR244 3.7 22.2 1.0
C C:LEU211 3.8 18.2 1.0
CG2 C:THR244 3.8 22.5 1.0
CB C:LEU211 3.9 18.2 1.0
O C:VAL290 3.9 22.1 1.0
C C:HIS243 4.1 23.4 1.0
CA C:LEU211 4.3 16.0 1.0
CB C:HIS243 4.3 25.3 1.0
CA C:VAL291 4.3 27.5 1.0
O C:PHE240 4.6 23.2 1.0
OE1 C:GLU113 4.6 20.6 1.0
O C:HIS243 4.6 28.1 1.0
CA C:HIS243 4.7 22.6 1.0
N C:SER212 4.7 19.4 1.0
N C:HIS243 4.8 20.4 1.0
C C:VAL290 4.8 20.7 1.0
N C:ASN292 4.8 34.1 1.0
CA C:PHE241 4.8 22.0 1.0
CG C:LEU211 4.9 19.2 1.0
CD2 C:LEU211 4.9 21.0 1.0
CG2 C:VAL291 4.9 23.7 1.0
CD2 C:PHE241 4.9 24.4 1.0
CA C:SER212 5.0 19.7 1.0
N C:VAL291 5.0 26.6 1.0

Sodium binding site 8 out of 8 in 2a2a

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Sodium binding site 8 out of 8 in the High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of High-Resolution Crystallographic Analysis of the Autoinhibited Conformation of A Human Death-Associated Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3175

b:46.9
occ:1.00
 O D:HOH3212 2.2 26.9 1.0
OG1 D:THR244 2.3 25.9 1.0
O D:LEU211 2.7 19.2 1.0
O D:HOH3227 2.8 25.6 1.0
O D:HOH3328 2.8 32.3 1.0
CB D:THR244 3.5 19.6 1.0
C D:LEU211 3.6 18.4 1.0
O D:VAL290 3.7 27.3 1.0
CA D:THR244 3.8 19.4 1.0
CB D:LEU211 3.9 17.9 1.0
N D:THR244 3.9 20.7 1.0
CA D:VAL291 4.0 25.9 1.0
CA D:LEU211 4.1 16.8 1.0
CG2 D:THR244 4.2 16.8 1.0
C D:HIS243 4.2 23.3 1.0
CB D:HIS243 4.2 24.8 1.0
CG2 D:VAL291 4.5 31.2 1.0
N D:ASN292 4.5 30.0 1.0
O D:HIS243 4.5 23.2 1.0
CB D:VAL291 4.6 23.6 1.0
C D:VAL290 4.6 24.2 1.0
N D:SER212 4.6 18.7 1.0
CG1 D:VAL291 4.7 29.1 1.0
N D:VAL291 4.7 24.4 1.0
OE1 D:GLU113 4.7 20.6 1.0
CA D:HIS243 4.7 21.7 1.0
O D:PHE240 4.7 23.8 1.0
C D:VAL291 4.8 25.6 1.0
CD2 D:LEU211 4.8 21.5 1.0
CA D:SER212 4.9 18.6 1.0
CG D:LEU211 4.9 15.5 1.0

Reference:

B.Simon, A.S.Huart, K.Temmerman, J.Vahokoski, H.D.Mertens, D.Komadina, J.E.Hoffmann, H.Yumerefendi, D.I.Svergun, P.Kursula, C.Schultz, A.A.Mccarthy, D.J.Hart, M.Wilmanns. Death-Associated Protein Kinase Activity Is Regulated By Coupled Calcium/Calmodulin Binding to Two Distinct Sites Structure 2016.
ISSN: ISSN 0969-2126
PubMed: 27133022
DOI: 10.1016/J.STR.2016.03.020
Page generated: Mon Oct 7 01:46:58 2024

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