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Sodium in PDB 2x7f: Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor

Enzymatic activity of Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor

All present enzymatic activity of Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor, PDB code: 2x7f was solved by M.Vollmar, I.Alfano, B.Shrestha, J.Bray, J.R.C.Muniz, A.Roos, P.Filippakopoulos, N.Burgess-Brown, E.Ugochukwu, O.Gileadi, C.Phillips, P.Mahajan, A.C.W.Pike, O.Fedorov, A.Chaikuad, F.Von Delft, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.Edwards, S.Knapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.32 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.972, 79.074, 214.159, 90.00, 91.87, 90.00
R / Rfree (%) 20.9 / 22.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor (pdb code 2x7f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor, PDB code: 2x7f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2x7f

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Sodium binding site 1 out of 5 in the Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor


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 the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1315

b:70.1
occ:1.00
 OG1 A:THR84 2.3 72.2 1.0
O A:ILE82 2.4 66.0 1.0
O A:HIS79 2.4 79.3 1.0
O A:SER77 2.6 74.2 1.0
C A:HIS79 3.4 80.4 1.0
CB A:THR84 3.5 60.9 1.0
N A:HIS79 3.6 73.7 1.0
N A:THR84 3.6 60.6 1.0
C A:ILE82 3.6 65.8 1.0
C A:SER77 3.7 72.8 1.0
CA A:THR84 3.8 58.7 1.0
OE1 A:GLU106 4.0 0.9 1.0
C A:HIS78 4.1 76.8 1.0
CA A:HIS78 4.1 69.3 1.0
C A:ALA83 4.1 65.8 1.0
CA A:HIS79 4.2 75.1 1.0
N A:ARG80 4.3 78.5 1.0
CG2 A:THR84 4.3 52.2 1.0
N A:HIS78 4.4 70.1 1.0
NZ A:LYS168 4.4 85.8 1.0
CA A:ARG80 4.5 79.0 1.0
N A:ILE82 4.5 70.0 1.0
CA A:ILE82 4.5 66.1 1.0
N A:ALA83 4.5 61.4 1.0
CA A:ALA83 4.6 60.2 1.0
O A:ALA83 4.6 66.4 1.0
CB A:ILE82 4.8 68.6 1.0
C A:ARG80 4.8 82.4 1.0
O A:HIS78 4.9 79.6 1.0
CA A:SER77 4.9 65.0 1.0

Sodium binding site 2 out of 5 in 2x7f

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Sodium binding site 2 out of 5 in the Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor


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 the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1315

b:56.4
occ:1.00
 O B:HOH2008 2.3 47.9 1.0
O B:HIS79 2.3 43.8 1.0
O B:SER77 2.4 47.7 1.0
OG1 B:THR84 2.4 39.0 1.0
O B:ILE82 2.6 40.8 1.0
C B:HIS79 3.3 40.6 1.0
N B:HIS79 3.4 35.8 1.0
CB B:THR84 3.5 28.5 1.0
C B:SER77 3.6 46.8 1.0
N B:THR84 3.8 33.1 1.0
CA B:THR84 3.8 32.2 1.0
C B:ILE82 3.8 38.9 1.0
CA B:HIS78 3.8 44.9 1.0
C B:HIS78 3.8 48.3 1.0
CA B:HIS79 4.0 32.9 1.0
CG2 B:THR84 4.1 22.6 1.0
N B:HIS78 4.1 45.1 1.0
N B:ARG80 4.2 36.6 1.0
OE1 B:GLU106 4.3 56.0 1.0
C B:ALA83 4.3 37.5 1.0
CA B:ARG80 4.4 36.5 1.0
N B:ILE82 4.6 33.6 1.0
CA B:ILE82 4.6 32.5 1.0
NZ B:LYS168 4.7 53.2 1.0
O B:HIS78 4.7 55.1 1.0
CA B:SER77 4.8 39.1 1.0
CB B:ILE82 4.8 34.6 1.0
N B:ALA83 4.8 33.3 1.0
O B:ALA83 4.8 39.5 1.0
C B:ARG80 4.9 47.4 1.0
CA B:ALA83 4.9 30.1 1.0

Sodium binding site 3 out of 5 in 2x7f

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Sodium binding site 3 out of 5 in the Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor


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 the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1315

b:68.7
occ:1.00
 OG1 C:THR84 2.2 68.5 1.0
O C:ILE82 2.4 68.2 1.0
O C:HIS79 2.5 77.5 1.0
O C:SER77 3.2 85.5 1.0
OE1 C:GLU106 3.4 77.3 1.0
CB C:THR84 3.5 69.1 1.0
N C:THR84 3.5 63.0 1.0
C C:HIS79 3.5 77.9 1.0
C C:ILE82 3.6 66.3 1.0
NZ C:LYS168 3.7 87.3 1.0
CA C:THR84 3.8 62.9 1.0
N C:HIS79 4.1 75.4 1.0
C C:ALA83 4.2 65.6 1.0
CA C:ARG80 4.2 72.7 1.0
N C:ARG80 4.2 73.8 1.0
CG2 C:THR84 4.4 65.8 1.0
C C:SER77 4.4 85.6 1.0
N C:ILE82 4.4 63.1 1.0
CA C:ALA83 4.5 59.3 1.0
N C:ALA83 4.5 60.8 1.0
C C:ARG80 4.5 76.8 1.0
CD C:GLU106 4.5 90.3 1.0
CA C:HIS79 4.5 74.1 1.0
CA C:ILE82 4.6 62.4 1.0
C C:HIS78 4.7 83.6 1.0
O C:ARG80 4.7 77.9 1.0
CA C:HIS78 4.7 82.4 1.0
O C:ALA83 4.9 65.9 1.0
OE2 C:GLU106 5.0 93.0 1.0

Sodium binding site 4 out of 5 in 2x7f

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Sodium binding site 4 out of 5 in the Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor


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 the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1308

b:94.7
occ:1.00
 OG1 D:THR84 2.2 0.6 1.0
O D:HIS79 2.2 98.3 1.0
O D:SER77 2.5 94.2 1.0
O D:ILE82 2.8 93.2 1.0
C D:HIS79 3.2 98.1 1.0
N D:HIS79 3.2 91.8 1.0
CB D:THR84 3.4 0.1 1.0
C D:SER77 3.7 95.1 1.0
C D:HIS78 3.7 96.5 1.0
CA D:THR84 3.8 93.5 1.0
N D:THR84 3.8 93.3 1.0
CA D:HIS78 3.8 91.0 1.0
CA D:HIS79 3.8 92.3 1.0
CG2 D:THR84 4.0 0.1 1.0
C D:ILE82 4.0 92.9 1.0
OE1 D:GLU106 4.1 0.9 1.0
N D:ARG80 4.1 94.6 1.0
N D:HIS78 4.2 91.7 1.0
CA D:ARG80 4.4 94.1 1.0
O D:HIS78 4.6 97.8 1.0
C D:ALA83 4.7 94.8 1.0
N D:ILE82 4.7 89.0 1.0
CA D:ILE82 4.8 88.0 1.0
CA D:SER77 4.9 92.0 1.0
C D:ARG80 4.9 97.7 1.0
CB D:ILE82 5.0 90.7 1.0
CB D:HIS79 5.0 93.0 1.0

Sodium binding site 5 out of 5 in 2x7f

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Sodium binding site 5 out of 5 in the Crystal Structure of the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor


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 the Kinase Domain of Human TRAF2- and Nck- Interacting Kinase with WEE1CHK1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1311

b:83.4
occ:1.00
 O E:SER77 2.2 0.8 1.0
O E:HIS79 2.3 0.6 1.0
OG1 E:THR84 2.4 0.2 1.0
O E:ILE82 2.4 0.6 1.0
C E:HIS79 3.2 0.6 1.0
N E:HIS79 3.3 0.8 1.0
C E:SER77 3.4 0.0 1.0
CB E:THR84 3.5 0.3 1.0
C E:ILE82 3.6 0.1 1.0
N E:THR84 3.6 0.4 1.0
CA E:THR84 3.7 98.7 1.0
CA E:HIS78 3.8 0.1 1.0
C E:HIS78 3.9 0.2 1.0
CA E:HIS79 3.9 0.4 1.0
OE1 E:GLU106 4.0 95.3 1.0
N E:HIS78 4.1 0.1 1.0
CG2 E:THR84 4.1 0.2 1.0
C E:ALA83 4.2 0.3 1.0
N E:ARG80 4.2 0.9 1.0
CA E:ILE82 4.4 0.3 1.0
N E:ILE82 4.4 0.7 1.0
CA E:ARG80 4.5 0.1 1.0
CB E:ILE82 4.6 0.2 1.0
N E:ALA83 4.6 0.3 1.0
CA E:SER77 4.6 0.8 1.0
O E:ALA83 4.7 0.8 1.0
CA E:ALA83 4.7 0.4 1.0
O E:HIS78 4.8 0.8 1.0
C E:ARG80 4.8 1.0 1.0
CB E:SER77 4.9 0.0 1.0
CB E:HIS79 5.0 1.0 1.0

Reference:

M.Vollmar, I.Alfano, B.Shrestha, J.Bray, J.R.C.Muniz, A.Roos, P.Filippakopoulos, N.Burgess-Brown, E.Ugochukwu, O.Gileadi, C.Phillips, P.Mahajan, A.C.W.Pike, O.Fedorov, A.Chaikuad, F.Von Delft, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.Edwards, S.Knapp. Crystal Structure of the Kinase Domain of Human TRAF2- and Nck-Interacting Kinase with WEE1CHK1 Inhibitor To Be Published.
Page generated: Mon Oct 7 05:04:55 2024

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