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Magnesium in PDB 5kt4: Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MG2+

Enzymatic activity of Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MG2+

All present enzymatic activity of Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MG2+:
2.7.7.7;

Protein crystallography data

The structure of Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MG2+, PDB code: 5kt4 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) 49.06 / 2.78
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 98.119, 98.119, 202.720, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MG2+ (pdb code 5kt4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Teranry Complex of Human Dna Polymerase Iota R96G Inserting Dcmpnpp Opposite Template G in the Presence of MG2+, PDB code: 5kt4:

Magnesium binding site 1 out of 1 in 5kt4

Go back to Magnesium Binding Sites List in 5kt4
Magnesium binding site 1 out of 1 in the Teranry Complex of Human Dna Polymerase Iota R96G 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 R96G Inserting Dcmpnpp Opposite Template G in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:40.7
occ:1.00
 O2B A:0KX501 2.0 40.6 1.0
O1G A:0KX501 2.1 48.4 1.0
OD2 A:ASP59 2.1 49.9 1.0
OD2 A:ASP151 2.1 50.0 1.0
O A:LEU60 2.2 41.2 1.0
O1A A:0KX501 2.3 36.5 1.0
CG A:ASP59 3.2 44.3 1.0
PB A:0KX501 3.3 45.2 1.0
CG A:ASP151 3.3 47.4 1.0
C A:LEU60 3.3 35.8 1.0
PG A:0KX501 3.4 45.6 1.0
PA A:0KX501 3.6 54.1 1.0
OD1 A:ASP59 3.7 56.9 1.0
O3B A:0KX501 3.7 58.5 1.0
N A:LEU60 3.7 42.8 1.0
N3A A:0KX501 3.9 53.6 1.0
O A:HOH609 4.0 49.3 1.0
OD1 A:ASP151 4.0 53.9 1.0
CA A:LEU60 4.1 38.2 1.0
C5' A:0KX501 4.1 44.3 1.0
O3G A:0KX501 4.1 51.5 1.0
C A:ASP59 4.2 44.3 1.0
O5' A:0KX501 4.3 47.9 1.0
CB A:ASP151 4.4 49.6 1.0
N A:ASP61 4.4 27.9 1.0
CB A:ASP59 4.4 33.0 1.0
O2G A:0KX501 4.5 55.9 1.0
N A:CYS62 4.6 42.1 1.0
O1B A:0KX501 4.6 55.8 1.0
CB A:LEU60 4.6 39.6 1.0
CA A:ASP61 4.7 34.8 1.0
CA A:ASP59 4.7 36.7 1.0
O A:ASP59 4.7 52.6 1.0
C A:ASP61 4.8 48.6 1.0
O2A A:0KX501 4.8 51.4 1.0
N A:PHE63 4.9 46.9 1.0
O3' P:DC873 4.9 57.6 1.0

Reference:

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
Page generated: Tue Aug 12 13:17:41 2025

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