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Magnesium in PDB 4phe: Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

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

Protein crystallography data

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

Resolution Low / High (Å) 20.00 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.535, 79.093, 54.796, 90.00, 105.78, 90.00
R / Rfree (%) 21.6 / 26.1

Other elements in 4phe:

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

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp (pdb code 4phe). 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 T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 4phe:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4phe

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


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 T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:30.9
occ:1.00
 O1A A:XG4405 1.9 54.2 1.0
O1G A:XG4405 2.0 42.8 1.0
O A:HOH543 2.1 36.0 1.0
OD1 A:ASP190 2.2 29.4 1.0
O1B A:XG4405 2.3 49.0 1.0
O A:HOH555 3.2 42.6 1.0
CG A:ASP190 3.3 31.3 1.0
PG A:XG4405 3.3 48.5 1.0
PA A:XG4405 3.3 68.8 1.0
PB A:XG4405 3.4 51.2 1.0
MG A:MG402 3.5 42.7 1.0
O3B A:XG4405 3.7 50.3 1.0
OD2 A:ASP190 3.8 27.9 1.0
N3A A:XG4405 3.8 60.1 1.0
O A:ASP190 3.9 27.1 1.0
O2G A:XG4405 3.9 45.5 1.0
O2A A:XG4405 4.1 66.7 1.0
C A:ASP190 4.3 29.0 1.0
N A:ASP190 4.4 26.4 1.0
O A:HOH531 4.4 26.2 1.0
CA A:GLY179 4.4 31.7 1.0
O3G A:XG4405 4.5 46.5 1.0
O5' A:XG4405 4.5 68.4 1.0
CB A:ASP190 4.5 24.7 1.0
CB A:ASP192 4.6 31.4 1.0
N A:SER180 4.6 35.8 1.0
CA A:ASP190 4.6 26.1 1.0
O2B A:XG4405 4.7 52.2 1.0
N A:ASP192 4.8 24.2 1.0
OG A:SER180 4.9 38.1 1.0
N A:MET191 4.9 24.5 1.0

Magnesium binding site 2 out of 2 in 4phe

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


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 T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:42.7
occ:1.00
 O A:HOH555 2.0 42.6 1.0
O3' P:DC10 2.5 49.5 1.0
OD2 A:ASP190 2.5 27.9 1.0
O1A A:XG4405 2.6 54.2 1.0
O2A A:XG4405 2.8 66.7 1.0
PA A:XG4405 3.1 68.8 1.0
CG A:ASP190 3.3 31.3 1.0
OD1 A:ASP190 3.4 29.4 1.0
MG A:MG401 3.5 30.9 1.0
C3' P:DC10 3.7 45.5 1.0
O5' A:XG4405 3.9 68.4 1.0
OD2 A:ASP256 4.2 30.0 1.0
CG A:ASP192 4.4 44.4 1.0
OD2 A:ASP192 4.4 45.8 1.0
C4' P:DC10 4.4 34.4 1.0
O1G A:XG4405 4.5 42.8 1.0
CB A:ASP192 4.5 31.4 1.0
N3A A:XG4405 4.7 60.1 1.0
C5' P:DC10 4.7 31.0 1.0
NH2 A:ARG258 4.7 43.6 1.0
OD1 A:ASP192 4.7 38.7 1.0
CB A:ASP190 4.8 24.7 1.0
C5' A:XG4405 4.8 76.5 1.0
O1B A:XG4405 4.8 49.0 1.0
C2' P:DC10 4.9 34.7 1.0

Reference:

M.C.Koag, S.Lee. The Spontaneous Base Substitution Mechanisms of Human Dna Polymerase Beta To Be Published.
Page generated: Tue Aug 20 01:21:26 2024

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