Magnesium in PDB 5j2i: Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus, PDB code: 5j2i was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.11 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.630, 80.150, 55.460, 90.00, 107.51, 90.00
R / Rfree (%) 18.2 / 26.9

Other elements in 5j2i:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus (pdb code 5j2i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus, PDB code: 5j2i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5j2i

Go back to Magnesium Binding Sites List in 5j2i
Magnesium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:27.5
occ:1.00
OD1 A:ASP190 2.0 24.7 1.0
O2A A:DUP401 2.0 23.7 1.0
O3G A:DUP401 2.0 30.2 1.0
O2B A:DUP401 2.1 25.1 1.0
OD2 A:ASP192 2.2 28.0 1.0
O A:HOH547 2.4 30.5 1.0
CG A:ASP190 3.1 29.3 1.0
PB A:DUP401 3.1 24.3 1.0
PG A:DUP401 3.2 25.8 1.0
CG A:ASP192 3.2 32.1 1.0
PA A:DUP401 3.3 26.5 1.0
OD2 A:ASP190 3.6 30.0 1.0
N3A A:DUP401 3.6 30.3 1.0
O3B A:DUP401 3.6 32.8 1.0
MG A:MG403 3.6 30.0 1.0
OD1 A:ASP192 3.7 32.1 1.0
O2G A:DUP401 3.9 30.4 1.0
O A:ASP190 4.0 28.7 1.0
C5' A:DUP401 4.2 24.7 1.0
OG A:SER180 4.2 35.3 1.0
C A:ASP190 4.2 31.8 1.0
O5' A:DUP401 4.3 28.6 1.0
N A:ASP190 4.3 28.4 1.0
CB A:ASP190 4.3 29.8 1.0
O1A A:DUP401 4.3 31.2 1.0
O A:HOH533 4.4 33.2 1.0
N A:SER180 4.4 26.9 1.0
CA A:GLY179 4.5 29.6 1.0
CA A:ASP190 4.5 29.4 1.0
CB A:ASP192 4.5 30.4 1.0
O1B A:DUP401 4.5 31.8 1.0
O A:HOH665 4.5 41.3 1.0
O1G A:DUP401 4.6 30.3 1.0
N A:ASP192 4.8 29.8 1.0
N A:MET191 4.8 29.2 1.0
O A:HOH508 4.8 32.2 1.0
O P:HOH101 4.9 47.0 1.0

Magnesium binding site 2 out of 2 in 5j2i

Go back to Magnesium Binding Sites List in 5j2i
Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:C Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:30.0
occ:1.00
OD2 A:ASP190 2.1 30.0 1.0
OD1 A:ASP192 2.1 32.1 1.0
OD2 A:ASP256 2.2 35.5 1.0
O2A A:DUP401 2.2 23.7 1.0
O A:HOH508 2.3 32.2 1.0
CG A:ASP190 3.0 29.3 1.0
CG A:ASP192 3.1 32.1 1.0
PA A:DUP401 3.3 26.5 1.0
OD1 A:ASP190 3.3 24.7 1.0
CG A:ASP256 3.4 30.0 1.0
OD2 A:ASP192 3.4 28.0 1.0
O1A A:DUP401 3.4 31.2 1.0
MG A:MG402 3.6 27.5 1.0
O5' A:DUP401 3.6 28.6 1.0
C5' A:DUP401 4.0 24.7 1.0
CB A:ASP256 4.0 30.1 1.0
OD1 A:ASP256 4.3 27.9 1.0
CB A:ASP190 4.4 29.8 1.0
CB A:ASP192 4.5 30.4 1.0
O P:HOH103 4.6 38.3 1.0
O A:HOH665 4.6 41.3 1.0
OP1 P:DC10 4.6 67.6 1.0
O3G A:DUP401 4.6 30.2 1.0
N3A A:DUP401 4.8 30.3 1.0
OP2 P:DC10 4.8 61.8 1.0
O2B A:DUP401 4.9 25.1 1.0

Reference:

V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Mispaired Dna Termini Transitioning to Pre-Catalytic Complexes Support An Induced-Fit Fidelity Mechanism. Structure V. 24 1863 2016.
ISSN: ISSN 0969-2126
PubMed: 27642161
DOI: 10.1016/J.STR.2016.08.006
Page generated: Mon Dec 14 20:32:28 2020

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