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Magnesium in PDB 4rt3: Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp, PDB code: 4rt3 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) 22.26 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.735, 79.909, 55.337, 90.00, 107.52, 90.00
R / Rfree (%) 18 / 22.6

Other elements in 4rt3:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp (pdb code 4rt3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp, PDB code: 4rt3:

Magnesium binding site 1 out of 1 in 4rt3

Go back to Magnesium Binding Sites List in 4rt3
Magnesium binding site 1 out of 1 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp


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 (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:16.6
occ:1.00
 OD1 A:ASP190 2.0 19.4 1.0
OD2 A:ASP192 2.0 18.2 1.0
O2B A:C6T408 2.0 18.4 1.0
O A:HOH501 2.1 18.3 1.0
O3G A:C6T408 2.1 20.4 1.0
O1A A:C6T408 2.1 21.6 1.0
CG A:ASP192 3.0 18.4 1.0
CG A:ASP190 3.1 20.2 1.0
PB A:C6T408 3.2 20.5 1.0
PG A:C6T408 3.3 23.6 1.0
PA A:C6T408 3.3 20.1 1.0
OD1 A:ASP192 3.4 18.2 1.0
NA A:NA402 3.5 6.5 1.0
N3A A:C6T408 3.6 21.2 1.0
O2G A:C6T408 3.7 22.8 1.0
OD2 A:ASP190 3.7 20.6 1.0
C3B A:C6T408 3.8 21.6 1.0
O A:ASP190 4.0 23.5 1.0
C5' A:C6T408 4.2 21.2 1.0
O A:HOH505 4.2 26.9 1.0
N A:ASP190 4.2 20.5 1.0
C A:ASP190 4.2 22.4 1.0
O5' A:C6T408 4.3 21.5 1.0
O A:HOH510 4.3 21.4 1.0
CB A:ASP192 4.3 22.4 1.0
CB A:ASP190 4.3 18.5 1.0
O2A A:C6T408 4.4 20.8 1.0
CA A:ASP190 4.5 19.4 1.0
CA A:GLY179 4.5 19.4 1.0
N A:SER180 4.5 23.0 1.0
O1G A:C6T408 4.6 28.6 1.0
O1B A:C6T408 4.6 21.4 1.0
OG A:SER180 4.6 26.7 1.0
O P:HOH501 4.7 17.4 1.0
N A:ASP192 4.7 21.6 1.0
N A:MET191 4.8 19.3 1.0
C A:MET191 5.0 19.9 1.0

Reference:

A.P.Kadina, B.A.Kashemirov, K.Oertell, V.K.Batra, S.H.Wilson, M.F.Goodman, C.E.Mckenna. Two Scaffolds From Two Flips: (Alpha, Beta)/(Beta, Gamma) CH2/Nh "Met-Im" Analogues of Dttp. Org.Lett. V. 17 2586 2015.
ISSN: ISSN 1523-7060
PubMed: 25970636
DOI: 10.1021/ACS.ORGLETT.5B00799
Page generated: Tue Aug 20 03:29:42 2024

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