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Magnesium in PDB 4nlk: Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4nlk was solved by M.-C.Koag, K.Min, A.F.Monzingo, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.01 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.807, 79.706, 55.683, 90.00, 107.83, 90.00
R / Rfree (%) 19.4 / 27

Other elements in 4nlk:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp also contains other interesting chemical elements:

Bromine (Br) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp (pdb code 4nlk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4nlk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4nlk

Go back to Magnesium Binding Sites List in 4nlk
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:17.6
occ:1.00
 O2G A:0KX405 1.9 21.9 1.0
OD1 A:ASP190 1.9 18.2 1.0
O2A A:0KX405 2.0 22.0 1.0
O1B A:0KX405 2.0 21.9 1.0
OD2 A:ASP192 2.0 22.6 1.0
O A:HOH502 2.4 19.5 1.0
PB A:0KX405 3.0 23.4 1.0
CG A:ASP190 3.0 20.0 1.0
CG A:ASP192 3.0 21.7 1.0
PA A:0KX405 3.2 23.6 1.0
OD1 A:ASP192 3.3 23.8 1.0
MG A:MG402 3.4 31.6 1.0
PG A:0KX405 3.4 21.8 1.0
OD2 A:ASP190 3.4 20.6 1.0
N3A A:0KX405 3.5 23.2 1.0
O3B A:0KX405 3.7 21.1 1.0
C5' A:0KX405 4.0 20.9 1.0
O A:ASP190 4.1 23.1 1.0
O5' A:0KX405 4.1 23.5 1.0
O A:HOH549 4.2 26.9 1.0
O1G A:0KX405 4.2 21.1 1.0
CB A:ASP190 4.3 20.3 1.0
O3G A:0KX405 4.3 22.6 1.0
CA A:GLY179 4.4 19.7 1.0
O2B A:0KX405 4.4 22.9 1.0
CB A:ASP192 4.4 20.7 1.0
C A:ASP190 4.4 22.0 1.0
N A:SER180 4.4 20.7 1.0
OG A:SER180 4.5 22.7 1.0
O1A A:0KX405 4.5 23.0 1.0
N A:ASP190 4.6 21.1 1.0
CA A:ASP190 4.7 20.6 1.0
N A:ASP192 4.9 22.3 1.0
C A:GLY179 4.9 20.5 1.0
N A:MET191 5.0 22.0 1.0

Magnesium binding site 2 out of 2 in 4nlk

Go back to Magnesium Binding Sites List in 4nlk
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with 8BRG in the Template Base-Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:31.6
occ:1.00
 OD2 A:ASP190 2.0 20.6 1.0
O2A A:0KX405 2.2 22.0 1.0
OD2 A:ASP256 2.3 24.9 1.0
OD1 A:ASP192 2.4 23.8 1.0
O3' P:DA10 2.6 29.5 1.0
CG A:ASP190 2.9 20.0 1.0
PA A:0KX405 3.1 23.6 1.0
OD1 A:ASP190 3.2 18.2 1.0
CG A:ASP192 3.4 21.7 1.0
MG A:MG401 3.4 17.6 1.0
O5' A:0KX405 3.5 23.5 1.0
CG A:ASP256 3.5 24.8 1.0
OD2 A:ASP192 3.6 22.6 1.0
C3' P:DA10 3.6 27.7 1.0
O1A A:0KX405 3.7 23.0 1.0
C5' A:0KX405 3.9 20.9 1.0
CB A:ASP190 4.3 20.3 1.0
OP1 P:DA10 4.3 29.1 1.0
CB A:ASP256 4.3 22.5 1.0
OD1 A:ASP256 4.5 25.2 1.0
C4' P:DA10 4.5 27.2 1.0
O2G A:0KX405 4.6 21.9 1.0
O5' P:DA10 4.7 24.8 1.0
N3A A:0KX405 4.7 23.2 1.0
C5' P:DA10 4.7 26.7 1.0
CB A:ASP192 4.7 20.7 1.0
O1B A:0KX405 4.8 21.9 1.0
C2' P:DA10 4.8 27.6 1.0
O A:MET191 4.8 25.1 1.0
O A:HOH552 4.9 32.9 1.0

Reference:

M.C.Koag, K.Min, S.Lee. Structural Basis For Promutagenicity of 8-Halogenated Guanine. J.Biol.Chem. V. 289 6289 2014.
ISSN: ISSN 0021-9258
PubMed: 24425881
DOI: 10.1074/JBC.M113.537803
Page generated: Mon Aug 19 23:39:27 2024

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