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Magnesium in PDB 2fms: Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site

Enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site

All present enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site, PDB code: 2fms was solved by V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.91 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%) 19.6 / 24.4

Other elements in 2fms:

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site (pdb code 2fms). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site, PDB code: 2fms:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2fms

Go back to Magnesium Binding Sites List in 2fms
Magnesium binding site 1 out of 2 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg339

b:18.0
occ:1.00
OD1 A:ASP190 1.9 22.2 1.0
OD2 A:ASP192 2.0 19.0 1.0
O2B A:DUP338 2.0 18.1 1.0
O1A A:DUP338 2.1 17.1 1.0
O3G A:DUP338 2.1 20.4 1.0
O A:HOH347 2.3 19.7 1.0
CG A:ASP190 3.0 22.0 1.0
PB A:DUP338 3.0 20.6 1.0
CG A:ASP192 3.1 20.8 1.0
PA A:DUP338 3.2 22.0 1.0
N3A A:DUP338 3.2 19.3 1.0
PG A:DUP338 3.3 24.5 1.0
OD2 A:ASP190 3.4 22.9 1.0
MG A:MG340 3.4 22.1 1.0
OD1 A:ASP192 3.5 23.3 1.0
O3B A:DUP338 3.5 19.4 1.0
O A:HOH377 3.9 23.4 1.0
O2G A:DUP338 3.9 18.6 1.0
C5' A:DUP338 4.0 20.2 1.0
O5' A:DUP338 4.1 18.1 1.0
O A:ASP190 4.1 22.1 1.0
CB A:ASP190 4.3 18.8 1.0
N A:ASP190 4.3 18.5 1.0
C A:ASP190 4.3 20.7 1.0
O2A A:DUP338 4.3 20.2 1.0
O1G A:DUP338 4.4 24.1 1.0
CB A:ASP192 4.4 22.2 1.0
O1B A:DUP338 4.4 21.1 1.0
OG A:SER180 4.5 26.5 1.0
O A:HOH348 4.5 21.3 1.0
O A:HOH357 4.5 23.1 1.0
CA A:ASP190 4.6 18.8 1.0
N A:SER180 4.6 22.3 1.0
CA A:GLY179 4.6 20.3 1.0
N A:ASP192 4.8 21.3 1.0
O3' P:DC10 4.9 25.2 1.0
N A:MET191 4.9 21.0 1.0

Magnesium binding site 2 out of 2 in 2fms

Go back to Magnesium Binding Sites List in 2fms
Magnesium binding site 2 out of 2 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg340

b:22.1
occ:1.00
OD1 A:ASP192 2.0 23.3 1.0
OD2 A:ASP190 2.1 22.9 1.0
OD2 A:ASP256 2.2 22.7 1.0
O A:HOH348 2.2 21.3 1.0
O1A A:DUP338 2.2 17.1 1.0
O3' P:DC10 2.2 25.2 1.0
CG A:ASP192 3.0 20.8 1.0
CG A:ASP190 3.1 22.0 1.0
PA A:DUP338 3.3 22.0 1.0
CG A:ASP256 3.3 26.9 1.0
OD2 A:ASP192 3.3 19.0 1.0
OD1 A:ASP190 3.4 22.2 1.0
C3' P:DC10 3.4 25.1 1.0
MG A:MG339 3.4 18.0 1.0
O5' A:DUP338 3.6 18.1 1.0
O2A A:DUP338 3.8 20.2 1.0
CB A:ASP256 3.9 23.7 1.0
C4' P:DC10 4.0 26.8 1.0
C5' A:DUP338 4.0 20.2 1.0
C5' P:DC10 4.1 25.8 1.0
O A:HOH377 4.3 23.4 1.0
OD1 A:ASP256 4.3 25.8 1.0
CB A:ASP192 4.4 22.2 1.0
CB A:ASP190 4.4 18.8 1.0
O5' P:DC10 4.6 24.5 1.0
C2' P:DC10 4.7 26.1 1.0
OP1 P:DC10 4.7 23.8 1.0
N3A A:DUP338 4.7 19.3 1.0
O3G A:DUP338 4.7 20.4 1.0
NH2 A:ARG254 4.8 23.2 1.0
O A:MET191 4.9 21.6 1.0
CA A:ASP192 4.9 23.0 1.0
O2B A:DUP338 5.0 18.1 1.0

Reference:

V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, S.H.Wilson. Magnesium-Induced Assembly of A Complete Dna Polymerase Catalytic Complex. Structure V. 14 757 2006.
ISSN: ISSN 0969-2126
PubMed: 16615916
DOI: 10.1016/J.STR.2006.01.011
Page generated: Mon Dec 14 07:23:16 2020

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