Manganese in PDB 5kt5: Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MN2+

All present enzymatic activity of Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MN2+:
2.7.7.7;

The structure of Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MN2+, PDB code: 5kt5 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)	42.48 / 2.80
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.111, 98.111, 202.761, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 26.6

The binding sites of Manganese atom in the Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MN2+ (pdb code 5kt5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MN2+, PDB code: 5kt5:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn901 b:28.4 occ:0.35 O2A A:0KX501 1.9 24.4 1.0 O3' P:DC873 2.2 32.8 1.0 OE2 A:GLU152 2.3 28.2 1.0 OD1 A:ASP59 2.3 32.2 1.0 OD1 A:ASP151 2.5 36.0 1.0 OD2 A:ASP151 2.9 29.4 1.0 CG A:ASP151 3.0 31.9 1.0 CG A:ASP59 3.1 26.5 1.0 PA A:0KX501 3.1 31.1 1.0 MN A:MN502 3.2 32.8 1.0 CD A:GLU152 3.2 31.1 1.0 OD2 A:ASP59 3.3 31.5 1.0 CG A:GLU152 3.4 26.2 1.0 O1A A:0KX501 3.6 31.2 1.0 C3' P:DC873 3.6 36.6 1.0 O5' A:0KX501 3.7 32.5 1.0 O A:HOH601 3.9 23.6 1.0 C5' A:0KX501 3.9 28.2 1.0 C4' P:DC873 4.1 36.5 1.0 O2B A:0KX501 4.2 28.8 1.0 C2' P:DC873 4.2 33.8 1.0 CB A:ASP59 4.4 23.3 1.0 O1G A:0KX501 4.4 28.3 1.0 OE1 A:GLU152 4.4 32.8 1.0 N3A A:0KX501 4.5 36.1 1.0 CB A:ASP151 4.6 33.9 1.0 C5' P:DC873 4.7 31.9 1.0 CB A:GLU152 4.8 22.3 1.0 O A:ASP151 4.9 27.2 1.0 C A:ASP151 4.9 27.7 1.0

Manganese binding site 2 out of 2 in the Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:32.8 occ:1.00 O2B A:0KX501 1.9 28.8 1.0 OD2 A:ASP59 2.0 31.5 1.0 O1G A:0KX501 2.1 28.3 1.0 OD2 A:ASP151 2.1 29.4 1.0 O A:LEU60 2.2 28.1 1.0 O2A A:0KX501 2.4 24.4 1.0 CG A:ASP59 3.0 26.5 1.0 PB A:0KX501 3.1 31.1 1.0 MN P:MN901 3.2 28.4 0.3 CG A:ASP151 3.3 31.9 1.0 C A:LEU60 3.3 24.4 1.0 PG A:0KX501 3.4 27.5 1.0 OD1 A:ASP59 3.5 32.2 1.0 PA A:0KX501 3.5 31.1 1.0 O3B A:0KX501 3.6 40.9 1.0 N A:LEU60 3.7 30.6 1.0 N3A A:0KX501 3.7 36.1 1.0 OD1 A:ASP151 3.9 36.0 1.0 C5' A:0KX501 4.0 28.2 1.0 CA A:LEU60 4.0 27.4 1.0 C A:ASP59 4.2 29.5 1.0 O5' A:0KX501 4.3 32.5 1.0 O3G A:0KX501 4.3 40.1 1.0 CB A:ASP59 4.3 23.3 1.0 CB A:ASP151 4.4 33.9 1.0 N A:ASP61 4.4 20.5 1.0 O2G A:0KX501 4.4 24.2 1.0 O1B A:0KX501 4.4 36.6 1.0 N A:CYS62 4.5 29.3 1.0 CB A:LEU60 4.6 23.2 1.0 CA A:ASP59 4.7 28.8 1.0 CA A:ASP61 4.7 25.0 1.0 O A:ASP59 4.7 34.2 1.0 N A:PHE63 4.8 36.3 1.0 C A:ASP61 4.8 34.4 1.0 O1A A:0KX501 4.8 31.2 1.0 CB A:PHE63 4.9 32.7 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