Magnesium in PDB 4bwj: Klentaq Mutant in Complex with Dna and Ddctp

All present enzymatic activity of Klentaq Mutant in Complex with Dna and Ddctp:
2.7.7.7;

The structure of Klentaq Mutant in Complex with Dna and Ddctp, PDB code: 4bwj was solved by N.Blatter, K.Bergen, W.Welte, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.827 / 1.55
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.143, 108.143, 89.810, 90.00, 90.00, 120.00
R / Rfree (%)	15.83 / 20.14

The binding sites of Magnesium atom in the Klentaq Mutant in Complex with Dna and Ddctp (pdb code 4bwj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Klentaq Mutant in Complex with Dna and Ddctp, PDB code: 4bwj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Klentaq Mutant in Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Klentaq Mutant in Complex with Dna and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1834 b:32.7 occ:1.00 O3G A:DCT1833 2.0 35.0 1.0 OD2 A:ASP785 2.1 32.9 1.0 O A:TYR611 2.1 28.5 1.0 O2B A:DCT1833 2.1 36.3 1.0 OD1 A:ASP610 2.2 35.2 1.0 O2A A:DCT1833 2.2 32.6 1.0 CG A:ASP785 3.2 31.9 1.0 PB A:DCT1833 3.2 33.8 1.0 PG A:DCT1833 3.2 36.9 1.0 CG A:ASP610 3.3 46.1 1.0 C A:TYR611 3.3 27.9 1.0 PA A:DCT1833 3.4 34.0 1.0 O3B A:DCT1833 3.5 38.3 1.0 MG A:MG1835 3.5 34.8 1.0 H5'' A:DCT1833 3.5 41.2 1.0 OD1 A:ASP785 3.6 29.6 1.0 O3A A:DCT1833 3.7 31.1 1.0 OD2 A:ASP610 3.8 57.9 1.0 HA A:SER612 3.8 38.3 1.0 O A:HOH2303 3.8 37.5 1.0 H A:GLN613 3.9 43.4 1.0 HG23 A:ILE614 4.0 43.1 1.0 O A:HOH2304 4.0 38.1 1.0 H A:ILE614 4.1 41.7 1.0 N A:TYR611 4.1 26.1 1.0 O2G A:DCT1833 4.1 36.7 1.0 H A:TYR611 4.1 31.3 1.0 HB2 A:TYR611 4.1 32.2 1.0 CA A:TYR611 4.2 27.8 1.0 N A:SER612 4.2 28.6 1.0 C5' A:DCT1833 4.3 34.4 1.0 O1G A:DCT1833 4.3 35.9 1.0 O5' A:DCT1833 4.3 31.0 1.0 CA A:SER612 4.4 31.9 1.0 HB A:ILE614 4.4 41.8 1.0 N A:GLN613 4.4 36.2 1.0 HB2 A:ASP785 4.4 35.4 1.0 C A:ASP610 4.4 27.2 1.0 CB A:ASP785 4.4 29.4 1.0 H5' A:DCT1833 4.5 41.2 1.0 CB A:ASP610 4.5 29.7 1.0 HZ1 A:LYS663 4.5 49.4 1.0 O1A A:DCT1833 4.5 33.9 1.0 O1B A:DCT1833 4.5 33.1 1.0 HG3 A:GLU786 4.6 32.3 0.4 CB A:TYR611 4.6 26.8 1.0 C A:SER612 4.6 35.0 1.0 HB3 A:ASP610 4.7 35.6 1.0 HG22 A:ILE614 4.7 43.1 1.0 CG2 A:ILE614 4.7 35.9 1.0 O A:ASP785 4.7 26.1 1.0 HB3 A:TYR611 4.8 32.2 1.0 HA A:ASP610 4.8 31.8 1.0 CA A:ASP610 4.9 26.5 1.0 N A:ILE614 4.9 34.8 1.0 HB3 A:ASP785 4.9 35.4 1.0 O A:ASP610 4.9 28.8 1.0 O A:HOH2305 5.0 36.8 1.0

Magnesium binding site 2 out of 5 in the Klentaq Mutant in Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Klentaq Mutant in Complex with Dna and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1835 b:34.8 occ:1.00 CD A:GLU786 2.3 34.7 0.4 OD1 A:ASP785 2.3 29.6 1.0 HG3 A:GLU786 2.5 32.3 0.4 OE2 A:GLU786 2.5 30.9 0.4 OD2 A:ASP610 2.5 57.9 1.0 O2A A:DCT1833 2.5 32.6 1.0 O A:HOH2305 2.5 36.8 1.0 OE1 A:GLU786 2.6 25.5 0.4 CG A:GLU786 2.8 26.9 0.4 H3'1 B:DOC112 2.8 33.5 1.0 OD1 A:ASP610 3.1 35.2 1.0 CG A:ASP610 3.1 46.1 1.0 CG A:ASP785 3.2 31.9 1.0 HG2 A:GLU786 3.2 32.3 0.4 HB2 A:GLU786 3.4 33.6 0.6 OD2 A:ASP785 3.5 32.9 1.0 MG A:MG1834 3.5 32.7 1.0 H5'' B:DOC112 3.5 34.2 1.0 PA A:DCT1833 3.6 34.0 1.0 O A:HOH2304 3.6 38.1 1.0 HZ2 A:LYS831 3.7 72.5 1.0 C3' B:DOC112 3.7 27.9 1.0 H3'2 B:DOC112 3.8 33.5 1.0 O1A A:DCT1833 3.9 33.9 1.0 H5' A:DCT1833 4.0 41.2 1.0 O5' A:DCT1833 4.0 31.0 1.0 HB3 A:GLU786 4.1 33.6 0.6 CB A:GLU786 4.1 28.0 0.6 HZ3 A:LYS831 4.2 72.5 1.0 CB A:GLU786 4.2 26.8 0.4 H4' B:DOC112 4.2 36.0 1.0 NZ A:LYS831 4.3 60.4 1.0 HB2 A:GLU786 4.3 32.1 0.4 H A:ASP785 4.3 28.9 1.0 C4' B:DOC112 4.3 30.0 1.0 C5' B:DOC112 4.3 28.5 1.0 H5'' A:DCT1833 4.3 41.2 1.0 OE1 A:GLU786 4.3 33.1 0.6 C5' A:DCT1833 4.4 34.4 1.0 HZ1 A:LYS831 4.4 72.5 1.0 CB A:ASP610 4.4 29.7 1.0 O3G A:DCT1833 4.5 35.0 1.0 C A:ASP785 4.5 25.4 1.0 O A:VAL783 4.6 26.3 1.0 HB2 A:ASP610 4.6 35.6 1.0 CB A:ASP785 4.6 29.4 1.0 O A:ASP785 4.6 26.1 1.0 N A:GLU786 4.7 27.9 1.0 HA A:ASP610 4.8 31.8 1.0 O5' B:DOC112 4.8 25.9 1.0 HB3 A:GLU786 4.8 32.1 0.4 HZ1 A:LYS663 4.8 49.4 1.0 C2' B:DOC112 4.9 28.5 1.0 H2' B:DOC112 4.9 34.2 1.0 CA A:GLU786 4.9 24.1 0.4 CA A:ASP785 4.9 26.3 1.0 N A:ASP785 5.0 24.1 1.0 O3A A:DCT1833 5.0 31.1 1.0 HB3 A:ASP785 5.0 35.4 1.0 CA A:GLU786 5.0 22.3 0.6 OP2 B:DOC112 5.0 30.7 1.0 H A:GLU786 5.0 33.5 0.6

Magnesium binding site 3 out of 5 in the Klentaq Mutant in Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Klentaq Mutant in Complex with Dna and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1836 b:37.8 occ:1.00 O A:HOH3001 2.1 42.6 1.0 O A:HOH3000 2.2 33.1 1.0 O A:HOH3003 2.2 49.9 1.0 O A:HOH3002 2.2 52.4 1.0 O A:HOH3004 2.2 40.5 1.0 OE1 A:GLU825 2.5 59.3 1.0 CD A:GLU825 3.3 50.0 1.0 HZ2 A:LYS793 3.7 54.0 1.0 HB3 A:GLU825 3.8 44.0 1.0 OE2 A:GLU825 3.9 45.6 1.0 HA A:GLU602 3.9 42.6 1.0 O A:HOH2403 4.0 40.7 1.0 O A:ALA600 4.1 31.3 1.0 HB1 A:ALA600 4.1 34.7 1.0 HZ1 A:LYS793 4.2 54.0 1.0 O A:HOH2402 4.3 42.1 1.0 O A:HOH2153 4.3 52.0 1.0 NZ A:LYS793 4.4 45.0 1.0 CG A:GLU825 4.4 40.4 1.0 HA A:GLU825 4.4 44.6 1.0 CB A:GLU825 4.5 36.7 1.0 O A:GLU601 4.5 29.2 1.0 HH12 A:ARG450 4.5 56.7 1.0 H A:GLY603 4.6 38.9 1.0 HG3 A:GLU825 4.6 48.4 1.0 O A:TRP604 4.6 30.6 1.0 HZ3 A:LYS793 4.7 54.0 1.0 O A:GLU825 4.8 34.5 1.0 H A:ALA600 4.8 35.4 1.0 CA A:GLU602 4.9 35.5 1.0 HG3 A:GLU602 4.9 68.2 1.0 HB A:ILE599 4.9 29.3 1.0 CA A:GLU825 4.9 37.2 1.0 C A:ALA600 5.0 29.4 1.0

Magnesium binding site 4 out of 5 in the Klentaq Mutant in Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Klentaq Mutant in Complex with Dna and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1112 b:54.2 occ:1.00 OP2 B:DA102 1.8 75.4 1.0 H5' B:DA102 2.0 63.0 1.0 H5'' B:DA102 2.6 63.0 1.0 C5' B:DA102 2.6 52.5 1.0 H2'' B:DG101 2.8 51.3 1.0 H3' B:DG101 2.9 81.0 1.0 H2' B:DG101 2.9 51.3 1.0 P B:DA102 3.0 76.3 1.0 C2' B:DG101 3.1 42.8 1.0 H8 B:DA102 3.2 61.0 1.0 O5' B:DA102 3.2 69.7 1.0 C3' B:DG101 3.2 67.5 1.0 O3' B:DG101 3.6 67.1 1.0 H3' B:DA102 3.8 65.0 1.0 C4' B:DA102 3.9 59.3 1.0 C8 B:DA102 4.1 50.8 1.0 OP1 B:DA102 4.3 75.1 1.0 O4' B:DA102 4.3 50.5 1.0 C3' B:DA102 4.4 54.2 1.0 C1' B:DG101 4.6 50.2 1.0 H4' B:DA102 4.6 71.1 1.0 C4' B:DG101 4.7 78.4 1.0 O5' B:DG101 4.8 85.0 1.0 N9 B:DA102 4.9 45.9 1.0 N7 B:DA102 4.9 50.7 1.0 H1' B:DG101 5.0 60.2 1.0

Magnesium binding site 5 out of 5 in the Klentaq Mutant in Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Klentaq Mutant in Complex with Dna and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1113 b:60.9 occ:1.00 H5' B:DC104 2.0 84.0 1.0 O3' B:DC103 2.0 77.3 1.0 H5'' B:DC104 2.1 84.0 1.0 OP1 B:DC104 2.2 72.5 1.0 C5' B:DC104 2.3 70.0 1.0 P B:DC104 2.3 84.4 1.0 O5' B:DC104 2.6 73.7 1.0 C3' B:DC103 3.3 57.9 1.0 H2'' B:DC103 3.3 53.7 1.0 H4' B:DC103 3.7 58.9 1.0 C4' B:DC104 3.8 63.6 1.0 OP2 B:DC104 3.8 63.5 1.0 C2' B:DC103 3.8 44.7 1.0 H3' B:DC103 3.9 69.5 1.0 H4' B:DC104 4.0 76.3 1.0 C4' B:DC103 4.1 49.1 1.0 H3' B:DC104 4.4 74.4 1.0 H1' B:DC103 4.4 43.5 1.0 O4' B:DC104 4.5 56.3 1.0 H2' B:DC103 4.6 53.7 1.0 C1' B:DC103 4.6 36.2 1.0 C3' B:DC104 4.7 62.0 1.0 O4' B:DC103 4.9 38.9 1.0

N.Blatter, K.Bergen, O.Nolte, W.Welte, K.Diederichs, J.Mayer, M.Wieland, A.Marx. Struktur Und Funktion Einer Rna-Lesenden Thermostabilen Dna-Polymerase Angew.Chem. V. 125 12154 2013.
ISSN: ISSN 1433-7851
DOI: 10.1002/ANGE.201306655