Magnesium in PDB 5kt6: Teranry Complex of Human Dna Polymerase Iota(1-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+

All present enzymatic activity of Teranry Complex of Human Dna Polymerase Iota(1-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+:
2.7.7.7;

The structure of Teranry Complex of Human Dna Polymerase Iota(1-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+, PDB code: 5kt6 was solved by J.Y.Choi, A.Patra, M.Yeom, Y.S.Lee, Q.Zhang, M.Egli, F.P.Guengerich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.74 / 3.54
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.269, 98.269, 201.656, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 24.4

The binding sites of Magnesium atom in the Teranry Complex of Human Dna Polymerase Iota(1-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+ (pdb code 5kt6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Teranry Complex of Human Dna Polymerase Iota(1-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+, PDB code: 5kt6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Teranry Complex of Human Dna Polymerase Iota(1-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Teranry Complex of Human Dna Polymerase Iota(1-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:34.1 occ:1.00 OD2 A:ASP59 2.0 42.0 1.0 O A:LEU60 2.0 54.7 1.0 O2B A:0KX501 2.1 37.0 1.0 OD2 A:ASP151 2.2 52.8 1.0 O2A A:0KX501 2.2 43.3 1.0 O1G A:0KX501 2.3 48.5 1.0 MG A:MG503 3.0 55.6 0.6 CG A:ASP59 3.1 57.9 1.0 C A:LEU60 3.2 48.7 1.0 PB A:0KX501 3.3 47.1 1.0 CG A:ASP151 3.4 54.2 1.0 PA A:0KX501 3.5 52.6 1.0 PG A:0KX501 3.6 59.5 1.0 OD1 A:ASP59 3.6 74.9 1.0 N A:LEU60 3.7 44.4 1.0 O3B A:0KX501 3.7 56.6 1.0 N3A A:0KX501 3.7 65.3 1.0 C5' A:0KX501 4.0 51.4 1.0 CA A:LEU60 4.0 39.5 1.0 OD1 A:ASP151 4.1 58.0 1.0 C A:ASP59 4.2 51.2 1.0 O5' A:0KX501 4.2 51.7 1.0 N A:ASP61 4.3 50.7 1.0 O3G A:0KX501 4.3 56.5 1.0 CB A:ASP59 4.4 44.2 1.0 CB A:ASP151 4.4 52.0 1.0 CA A:ASP61 4.5 61.2 1.0 O1B A:0KX501 4.6 56.5 1.0 N A:CYS62 4.6 43.6 1.0 CA A:ASP59 4.6 40.6 1.0 CB A:LEU60 4.6 42.1 1.0 O2G A:0KX501 4.7 48.9 1.0 O1A A:0KX501 4.7 48.7 1.0 O A:ASP59 4.7 58.9 1.0 C A:ASP61 4.8 51.5 1.0 O3' P:DC873 4.8 51.2 1.0 N A:PHE63 5.0 49.7 1.0

Magnesium binding site 2 out of 2 in the Teranry Complex of Human Dna Polymerase Iota(1-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Teranry Complex of Human Dna Polymerase Iota(1-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:55.6 occ:0.61 O2A A:0KX501 2.0 43.3 1.0 O3' P:DC873 2.2 51.2 1.0 OE2 A:GLU152 2.3 46.7 1.0 OD2 A:ASP151 2.7 52.8 1.0 OD1 A:ASP151 2.7 58.0 1.0 OD2 A:ASP59 2.9 42.0 1.0 OD1 A:ASP59 2.9 74.9 1.0 MG A:MG502 3.0 34.1 1.0 CG A:ASP151 3.0 54.2 1.0 CG A:ASP59 3.1 57.9 1.0 CD A:GLU152 3.2 59.4 1.0 PA A:0KX501 3.2 52.6 1.0 CG A:GLU152 3.2 57.7 1.0 C3' P:DC873 3.5 57.5 1.0 O1A A:0KX501 3.7 48.7 1.0 O5' A:0KX501 3.9 51.7 1.0 C5' A:0KX501 4.0 51.4 1.0 C4' P:DC873 4.1 62.5 1.0 C2' P:DC873 4.3 64.8 1.0 O2B A:0KX501 4.3 37.0 1.0 OE1 A:GLU152 4.4 60.4 1.0 O1G A:0KX501 4.4 48.5 1.0 CB A:ASP59 4.4 44.2 1.0 CB A:ASP151 4.5 52.0 1.0 N3A A:0KX501 4.6 65.3 1.0 C5' P:DC873 4.7 59.9 1.0 CB A:GLU152 4.7 52.9 1.0 O A:LEU60 4.9 54.7 1.0 C A:ASP151 4.9 46.5 1.0 CA A:ASP59 4.9 40.6 1.0 N A:GLU152 5.0 47.4 1.0

J.Y.Choi, A.Patra, M.Yeom, Y.S.Lee, Q.Zhang, M.Egli, F.P.Guengerich. Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human Dna Polymerase Iota. J.Biol.Chem. V. 291 21063 2016.
ISSN: ESSN 1083-351X
PubMed: 27555320
DOI: 10.1074/JBC.M116.748285