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Magnesium in PDB 7mz4: Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp, PDB code: 7mz4 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) 20.09 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.706, 80.183, 54.927, 90, 108.64, 90
R / Rfree (%) 21.6 / 27

Other elements in 7mz4:

The structure of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp 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 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp (pdb code 7mz4). 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 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp, PDB code: 7mz4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7mz4

Go back to Magnesium Binding Sites List in 7mz4
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp


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 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:33.1
occ:1.00
 O1A A:1FZ404 2.3 28.8 1.0
OD2 A:ASP190 2.3 27.6 1.0
O A:HOH572 2.5 29.7 1.0
O3' P:DA10 2.6 28.8 1.0
OD1 A:ASP192 2.8 39.2 1.0
CG A:ASP190 2.9 25.1 1.0
OD1 A:ASP190 3.0 22.3 1.0
OD2 A:ASP192 3.1 41.1 1.0
C3' P:DA10 3.2 32.8 1.0
CG A:ASP192 3.3 31.5 1.0
PA A:1FZ404 3.4 31.9 1.0
MG A:MG401 3.4 28.2 1.0
O5' A:1FZ404 3.8 30.7 1.0
O2A A:1FZ404 3.9 32.9 1.0
C4' P:DA10 4.1 31.9 1.0
C5' A:1FZ404 4.2 28.1 1.0
O A:HOH501 4.2 39.1 1.0
CB A:ASP190 4.3 18.4 1.0
C2' P:DA10 4.4 33.7 1.0
O1G A:1FZ404 4.5 28.8 1.0
O P:HOH102 4.6 31.9 1.0
C5' P:DA10 4.6 26.4 1.0
O P:HOH101 4.7 27.0 1.0
OD2 A:ASP256 4.8 23.2 1.0
CB A:ASP192 4.8 20.7 1.0
O2B A:1FZ404 4.9 24.0 1.0
O5' P:DA10 4.9 29.2 1.0
N3A A:1FZ404 5.0 26.7 1.0

Magnesium binding site 2 out of 2 in 7mz4

Go back to Magnesium Binding Sites List in 7mz4
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp


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 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:28.2
occ:1.00
 O1G A:1FZ404 1.9 28.8 1.0
O A:HOH501 2.0 39.1 1.0
OD1 A:ASP190 2.0 22.3 1.0
O2B A:1FZ404 2.1 24.0 1.0
O1A A:1FZ404 2.2 28.8 1.0
O A:HOH533 2.2 25.3 1.0
OD2 A:ASP192 3.1 41.1 1.0
CG A:ASP190 3.1 25.1 1.0
PB A:1FZ404 3.1 25.6 1.0
PG A:1FZ404 3.2 30.8 1.0
PA A:1FZ404 3.3 31.9 1.0
MG A:MG400 3.4 33.1 1.0
O3B A:1FZ404 3.5 29.6 1.0
OD2 A:ASP190 3.6 27.6 1.0
N3A A:1FZ404 3.6 26.7 1.0
O3G A:1FZ404 3.9 31.2 1.0
CG A:ASP192 4.1 31.5 1.0
O A:ASP190 4.1 23.2 1.0
N A:ASP190 4.1 26.1 1.0
O2A A:1FZ404 4.3 32.9 1.0
C A:ASP190 4.3 21.6 1.0
O2G A:1FZ404 4.3 26.5 1.0
CB A:ASP190 4.3 18.4 1.0
O5' A:1FZ404 4.4 30.7 1.0
C5' A:1FZ404 4.4 28.1 1.0
CA A:ASP190 4.5 19.4 1.0
O1B A:1FZ404 4.5 25.2 1.0
OG A:SER180 4.6 26.7 1.0
O A:HOH537 4.6 25.8 1.0
N A:SER180 4.6 27.4 1.0
OD1 A:ASP192 4.6 39.2 1.0
CA A:GLY179 4.7 25.5 1.0
N A:MET191 4.9 24.2 1.0
N A:GLY189 5.0 25.6 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3-Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp To Be Published.
Page generated: Thu Oct 3 01:11:46 2024

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