Atomistry » Magnesium » PDB 2bhd-2bt1 » 2bpf
Atomistry »
  Magnesium »
    PDB 2bhd-2bt1 »
      2bpf »

Magnesium in PDB 2bpf: Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp

Protein crystallography data

The structure of Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp, PDB code: 2bpf was solved by H.Pelletier, M.R.Sawaya, A.Kumar, S.H.Wilson, J.Kraut, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.90
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 94.900, 94.900, 117.600, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp (pdb code 2bpf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp, PDB code: 2bpf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2bpf

Go back to Magnesium Binding Sites List in 2bpf
Magnesium binding site 1 out of 2 in the Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg339

b:6.0
occ:1.00
O2B A:DCT338 1.7 10.0 1.0
OD1 A:ASP190 2.1 14.9 1.0
O1G A:DCT338 2.3 21.7 1.0
OD2 A:ASP192 2.5 15.8 1.0
O A:HOH419 2.5 31.8 1.0
O1A A:DCT338 3.0 1.0 1.0
O A:ASP190 3.1 4.5 1.0
PB A:DCT338 3.2 17.0 1.0
CG A:ASP190 3.3 15.0 1.0
PG A:DCT338 3.4 22.7 1.0
CG A:ASP192 3.5 16.5 1.0
OG A:SER188 3.5 35.9 1.0
OG A:SER180 3.5 13.0 1.0
O3B A:DCT338 3.7 20.1 1.0
N A:ASP190 3.7 17.9 1.0
C A:ASP190 3.7 8.4 1.0
N A:SER180 3.8 5.8 1.0
O2G A:DCT338 4.0 17.6 1.0
PA A:DCT338 4.1 18.6 1.0
O3A A:DCT338 4.1 20.2 1.0
OD1 A:ASP192 4.1 16.8 1.0
OD2 A:ASP190 4.1 22.7 1.0
O1B A:DCT338 4.1 6.5 1.0
CA A:ASP190 4.2 9.5 1.0
CB A:SER180 4.2 13.3 1.0
CB A:ASP192 4.3 14.4 1.0
CB A:ASP190 4.3 11.3 1.0
O5' A:DCT338 4.4 19.9 1.0
CA A:GLY179 4.4 7.8 1.0
N A:ASP192 4.5 18.7 1.0
CA A:SER180 4.6 12.3 1.0
N A:MET191 4.6 11.0 1.0
C A:GLY179 4.6 4.3 1.0
N A:GLY189 4.6 20.6 1.0
O3G A:DCT338 4.6 27.7 1.0
MG A:MG340 4.7 79.1 1.0
CB A:SER188 4.7 32.9 1.0
C A:GLY189 4.8 24.4 1.0
C A:MET191 4.9 17.9 1.0
CA A:MET191 4.9 14.3 1.0
CA A:GLY189 4.9 21.4 1.0

Magnesium binding site 2 out of 2 in 2bpf

Go back to Magnesium Binding Sites List in 2bpf
Magnesium binding site 2 out of 2 in the Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg340

b:79.1
occ:1.00
OD2 A:ASP190 2.0 22.7 1.0
OD1 A:ASP192 2.5 16.8 1.0
O1A A:DCT338 2.6 1.0 1.0
CG A:ASP190 3.1 15.0 1.0
CG A:ASP192 3.1 16.5 1.0
OD2 A:ASP256 3.2 43.0 1.0
OD2 A:ASP192 3.2 15.8 1.0
OD1 A:ASP190 3.4 14.9 1.0
PA A:DCT338 3.4 18.6 1.0
O5' A:DCT338 3.5 19.9 1.0
O A:HOH403 3.8 41.7 1.0
OP1 P:DC7 3.8 20.2 1.0
O2A A:DCT338 3.9 19.2 1.0
C3' P:DC7 3.9 18.2 1.0
O5' P:DC7 3.9 21.4 1.0
CG A:ASP256 4.1 35.4 1.0
CB A:ASP190 4.3 11.3 1.0
P P:DC7 4.4 18.6 1.0
NH2 A:ARG254 4.4 58.5 1.0
C5' A:DCT338 4.4 14.9 1.0
C5' P:DC7 4.5 22.2 1.0
CB A:ASP256 4.5 16.7 1.0
C4' P:DC7 4.6 20.2 1.0
CB A:ASP192 4.6 14.4 1.0
O2B A:DCT338 4.6 10.0 1.0
MG A:MG339 4.7 6.0 1.0
O1G A:DCT338 4.8 21.7 1.0
OP2 P:DC7 4.9 23.5 1.0
O3A A:DCT338 4.9 20.2 1.0

Reference:

H.Pelletier, M.R.Sawaya, A.Kumar, S.H.Wilson, J.Kraut. Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp. Science V. 264 1891 1994.
ISSN: ISSN 0036-8075
PubMed: 7516580
Page generated: Tue Aug 13 21:58:55 2024

Last articles

Mg in 7XKW
Mg in 7XMV
Mg in 7XMU
Mg in 7XQX
Mg in 7XQV
Mg in 7XMB
Mg in 7XML
Mg in 7XM0
Mg in 7XMA
Mg in 7XD7
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy