Magnesium in PDB 3bf3: Type III Pantothenate Kinase From Thermotoga Maritima Complexed with Product Phosphopantothenate

All present enzymatic activity of Type III Pantothenate Kinase From Thermotoga Maritima Complexed with Product Phosphopantothenate:
2.7.1.33;

The structure of Type III Pantothenate Kinase From Thermotoga Maritima Complexed with Product Phosphopantothenate, PDB code: 3bf3 was solved by K.Yang, C.Huerta, E.Strauss, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.82 / 1.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.091, 137.256, 75.248, 90.00, 110.44, 90.00
R / Rfree (%)	18.4 / 22.7

The binding sites of Magnesium atom in the Type III Pantothenate Kinase From Thermotoga Maritima Complexed with Product Phosphopantothenate (pdb code 3bf3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Type III Pantothenate Kinase From Thermotoga Maritima Complexed with Product Phosphopantothenate, PDB code: 3bf3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Type III Pantothenate Kinase From Thermotoga Maritima Complexed with Product Phosphopantothenate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Type III Pantothenate Kinase From Thermotoga Maritima Complexed with Product Phosphopantothenate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg247 b:23.4 occ:1.00 O F:HOH504 2.1 28.3 1.0 O D:HOH432 2.2 38.8 1.0 NE2 A:HIS42 2.2 24.1 1.0 O A:HOH392 2.2 37.5 1.0 NE2 D:HIS42 2.3 23.2 1.0 NE2 F:HIS42 2.3 23.9 1.0 CE1 A:HIS42 3.0 24.6 1.0 CE1 D:HIS42 3.1 22.0 1.0 CE1 F:HIS42 3.1 23.1 1.0 CD2 D:HIS42 3.4 21.0 1.0 CD2 A:HIS42 3.4 23.6 1.0 CD2 F:HIS42 3.4 22.6 1.0 ND1 A:HIS42 4.2 23.4 1.0 ND1 D:HIS42 4.3 21.7 1.0 ND1 F:HIS42 4.3 22.2 1.0 OE1 F:GLU38 4.4 26.4 1.0 CG A:HIS42 4.4 20.6 1.0 CG D:HIS42 4.4 18.6 1.0 OE1 A:GLU38 4.5 27.6 1.0 CG F:HIS42 4.5 19.1 1.0 OE1 D:GLU38 4.6 25.6 1.0 O D:HOH488 4.7 55.2 1.0 CG F:GLU38 4.9 20.2 1.0 NE2 F:GLN34 4.9 35.5 1.0

Magnesium binding site 2 out of 2 in the Type III Pantothenate Kinase From Thermotoga Maritima Complexed with Product Phosphopantothenate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Type III Pantothenate Kinase From Thermotoga Maritima Complexed with Product Phosphopantothenate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg247 b:24.2 occ:1.00 O B:HOH551 2.1 34.3 1.0 O E:HOH377 2.2 37.8 1.0 NE2 E:HIS42 2.2 25.5 1.0 NE2 C:HIS42 2.3 23.7 1.0 O C:HOH333 2.3 33.2 1.0 NE2 B:HIS42 2.3 22.8 1.0 CE1 E:HIS42 3.0 25.7 1.0 CE1 C:HIS42 3.1 22.8 1.0 CE1 B:HIS42 3.1 23.0 1.0 CD2 E:HIS42 3.3 23.9 1.0 CD2 C:HIS42 3.4 22.1 1.0 CD2 B:HIS42 3.4 22.9 1.0 O E:HOH534 4.2 88.2 1.0 ND1 E:HIS42 4.2 24.6 1.0 ND1 C:HIS42 4.2 23.1 1.0 ND1 B:HIS42 4.2 20.5 1.0 CG E:HIS42 4.4 21.2 1.0 OE1 E:GLU38 4.4 29.8 1.0 CG C:HIS42 4.4 19.1 1.0 CG B:HIS42 4.4 18.7 1.0 OE1 B:GLU38 4.5 27.0 1.0 OE2 C:GLU38 4.7 26.4 1.0 NE2 B:GLN34 4.9 34.2 1.0 O B:HOH518 4.9 50.5 1.0 CG B:GLU38 5.0 18.4 1.0

K.Yang, E.Strauss, C.Huerta, H.Zhang. Structural Basis For Substrate Binding and the Catalytic Mechanism of Type III Pantothenate Kinase. Biochemistry V. 47 1369 2008.
ISSN: ISSN 0006-2960
PubMed: 18186650
DOI: 10.1021/BI7018578