Magnesium in PDB 7mz2: Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of 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 Dza at N-1 of the Template Base Paired with Incoming Dttp, PDB code: 7mz2 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) 19.87 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.809, 80.181, 55.414, 90, 107.56, 90
R / Rfree (%) 19.7 / 24.3

Other elements in 7mz2:

The structure of Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of 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 Dza at N-1 of the Template Base Paired with Incoming Dttp (pdb code 7mz2). 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 Dza at N-1 of the Template Base Paired with Incoming Dttp, PDB code: 7mz2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7mz2

Go back to Magnesium Binding Sites List in 7mz2
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of 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 Dza at N-1 of the Template Base Paired with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:9.2
occ:1.00
 O1G A:0KX405 2.0 10.0 1.0
OD2 A:ASP192 2.0 9.7 1.0
OD1 A:ASP190 2.0 10.5 1.0
O2A A:0KX405 2.1 9.3 1.0
O A:HOH520 2.1 8.8 1.0
O1B A:0KX405 2.1 8.1 1.0
CG A:ASP192 3.0 10.2 1.0
PB A:0KX405 3.1 9.6 1.0
CG A:ASP190 3.2 9.4 1.0
PA A:0KX405 3.2 10.3 1.0
PG A:0KX405 3.4 11.0 1.0
OD1 A:ASP192 3.4 10.8 1.0
N3A A:0KX405 3.6 9.8 1.0
MG A:MG402 3.6 18.6 1.0
O3B A:0KX405 3.6 9.8 1.0
OD2 A:ASP190 3.7 14.4 1.0
O A:ASP190 3.9 12.2 1.0
C5' A:0KX405 4.1 10.0 1.0
O2G A:0KX405 4.1 9.7 1.0
O5' A:0KX405 4.2 10.7 1.0
C A:ASP190 4.2 10.2 1.0
N A:ASP190 4.2 8.7 1.0
O A:HOH532 4.3 12.6 1.0
CB A:ASP192 4.4 12.3 1.0
CB A:ASP190 4.4 12.0 1.0
O1A A:0KX405 4.4 10.8 1.0
O3G A:0KX405 4.4 12.2 1.0
OG A:SER180 4.5 13.6 1.0
CA A:ASP190 4.5 8.0 1.0
N A:SER180 4.5 10.6 1.0
O2B A:0KX405 4.6 8.6 1.0
CA A:GLY179 4.6 9.4 1.0
N A:ASP192 4.9 12.1 1.0
N A:MET191 4.9 8.8 1.0
O A:HOH501 4.9 30.0 1.0
C A:MET191 5.0 12.4 1.0

Magnesium binding site 2 out of 2 in 7mz2

Go back to Magnesium Binding Sites List in 7mz2
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of 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 Dza at N-1 of the Template Base Paired with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:18.6
occ:1.00
 OD2 A:ASP190 2.2 14.4 1.0
O2A A:0KX405 2.3 9.3 1.0
OD2 A:ASP256 2.4 17.4 1.0
OD1 A:ASP192 2.5 10.8 1.0
O A:HOH501 2.5 30.0 1.0
CG A:ASP190 3.0 9.4 1.0
O3' P:DT10 3.1 22.9 1.0
OD1 A:ASP190 3.1 10.5 1.0
PA A:0KX405 3.3 10.3 1.0
CG A:ASP192 3.5 10.2 1.0
CG A:ASP256 3.6 16.9 1.0
MG A:MG401 3.6 9.2 1.0
C3' P:DT10 3.6 13.7 1.0
O1A A:0KX405 3.7 10.8 1.0
OD2 A:ASP192 3.7 9.7 1.0
O5' A:0KX405 3.8 10.7 1.0
C5' A:0KX405 4.1 10.0 1.0
CB A:ASP256 4.3 14.2 1.0
CB A:ASP190 4.3 12.0 1.0
OP1 P:DT10 4.4 9.9 1.0
C5' P:DT10 4.4 12.4 1.0
C4' P:DT10 4.5 15.0 1.0
OD1 A:ASP256 4.5 14.5 1.0
O1G A:0KX405 4.6 10.0 1.0
O5' P:DT10 4.6 14.9 1.0
NH2 A:ARG254 4.7 16.3 1.0
O A:MET191 4.8 10.0 1.0
CB A:ASP192 4.8 12.3 1.0
C2' P:DT10 4.9 15.1 1.0
O A:HOH546 4.9 25.3 1.0
N3A A:0KX405 4.9 9.8 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp To Be Published.
Page generated: Thu Oct 3 01:11:38 2024

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