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Sodium in PDB 4pf4: 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277

Enzymatic activity of 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277

All present enzymatic activity of 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277:
2.7.11.1;

Protein crystallography data

The structure of 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277, PDB code: 4pf4 was solved by K.Temmerman, B.Simon, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.76 / 1.13
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.516, 62.005, 88.375, 90.00, 90.00, 90.00
R / Rfree (%) 11.7 / 15

Other elements in 4pf4:

The structure of 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277 (pdb code 4pf4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277, PDB code: 4pf4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4pf4

Go back to Sodium Binding Sites List in 4pf4
Sodium binding site 1 out of 2 in the 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:19.5
occ:1.00
OE1 A:GLU32 2.6 14.8 1.0
OH A:TYR39 2.7 10.8 1.0
HG1 A:THR35 2.9 12.5 1.0
HD11 A:LEU37 3.0 12.5 1.0
HE2 A:TYR39 3.1 7.6 1.0
HD13 A:LEU37 3.1 11.9 1.0
HB2 A:LEU37 3.1 10.7 1.0
HE2 A:HIS80 3.2 12.8 1.0
HH A:TYR39 3.2 10.1 1.0
OG1 A:THR35 3.3 12.9 1.0
HG22 A:THR35 3.3 14.2 1.0
HE1 A:HIS80 3.4 13.2 1.0
HG23 A:THR35 3.4 14.1 1.0
CD1 A:LEU37 3.5 12.3 1.0
NE2 A:HIS80 3.5 14.6 1.0
CZ A:TYR39 3.6 8.3 1.0
CD A:GLU32 3.6 13.6 1.0
CE1 A:HIS80 3.6 13.8 1.0
CE2 A:TYR39 3.6 7.6 1.0
CG2 A:THR35 3.7 14.3 1.0
CB A:THR35 3.9 12.9 1.0
CB A:LEU37 4.0 10.0 1.0
HB3 A:GLU32 4.0 10.7 1.0
HB A:THR35 4.1 13.3 1.0
HB3 A:LEU37 4.2 10.3 1.0
OE2 A:GLU32 4.2 13.9 1.0
CG A:LEU37 4.3 10.6 1.0
HD12 A:LEU37 4.3 11.9 1.0
HB2 A:GLU32 4.3 10.9 1.0
HG A:LEU37 4.4 10.6 1.0
CB A:GLU32 4.5 10.7 1.0
CG A:GLU32 4.5 11.4 1.0
CD2 A:HIS80 4.6 11.9 1.0
HG21 A:THR35 4.6 14.0 1.0
ND1 A:HIS80 4.7 10.4 1.0
H A:LEU37 4.7 10.9 1.0
HG2 A:GLU32 4.7 11.4 1.0
CE1 A:TYR39 4.8 8.5 1.0
CD2 A:TYR39 4.9 7.6 1.0
HH A:TYR13 5.0 10.9 1.0

Sodium binding site 2 out of 2 in 4pf4

Go back to Sodium Binding Sites List in 4pf4
Sodium binding site 2 out of 2 in the 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:39.9
occ:1.00
OE1 A:GLN72 1.9 44.0 1.0
O A:HOH497 2.9 31.9 1.0
CD A:GLN72 3.1 27.5 1.0
O A:HOH402 3.2 18.2 1.0
H A:HIS73 3.4 8.9 1.0
HA A:PRO74 3.4 11.1 1.0
C A:HIS73 3.4 7.7 1.0
O A:HIS73 3.5 9.4 1.0
O A:HOH536 3.6 37.7 1.0
N A:HIS73 3.6 8.6 1.0
HG3 A:GLN72 3.7 18.2 1.0
N A:PRO74 3.7 8.9 1.0
HZ1 A:LYS158 3.8 21.4 1.0
HG22 A:THR78 3.9 12.3 1.0
CA A:HIS73 3.9 7.9 1.0
CG A:GLN72 4.0 17.8 1.0
HA A:HIS73 4.0 8.3 1.0
NE2 A:GLN72 4.0 24.3 1.0
CA A:PRO74 4.0 10.3 1.0
HE22 A:GLN72 4.1 25.2 1.0
HD3 A:PRO74 4.1 9.8 1.0
HA A:GLN72 4.2 10.8 1.0
HG3 A:PRO74 4.2 13.0 1.0
C A:GLN72 4.3 8.5 1.0
HG23 A:THR78 4.3 12.7 1.0
CD A:PRO74 4.4 10.1 1.0
NZ A:LYS158 4.5 27.2 1.0
HZ2 A:LYS158 4.5 18.2 1.0
HZ3 A:LYS158 4.5 22.1 1.0
CG2 A:THR78 4.5 12.9 1.0
CA A:GLN72 4.7 10.5 1.0
HE21 A:GLN72 4.7 22.9 1.0
HG2 A:GLN72 4.7 18.4 1.0
CG A:PRO74 4.7 13.3 1.0
O A:HOH458 4.9 21.2 1.0
CB A:GLN72 4.9 12.8 1.0
HG21 A:THR78 4.9 12.1 1.0
CB A:PRO74 5.0 13.2 1.0
O A:GLN72 5.0 10.1 1.0

Reference:

K.Temmerman, B.Simon, M.Wilmanns. 1.1A X-Ray Structure of the Apo Catalytic Domain of Death-Associated Protein Kinase 1, Aa 1-277 To Be Published.
Page generated: Tue Dec 15 06:58:08 2020

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