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Sodium 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:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2fms

Go back to Sodium Binding Sites List in 2fms
Sodium 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 Sodium with other atoms in the Na 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:Na341

b:25.4
occ:1.00
OP1 P:DG9 2.3 25.4 1.0
O A:THR101 2.3 24.0 1.0
O P:HOH25 2.4 31.9 1.0
O A:ILE106 2.5 23.6 1.0
O A:VAL103 2.5 24.1 1.0
O A:HOH433 2.6 30.6 1.0
C A:THR101 3.3 24.5 1.0
P P:DG9 3.4 27.1 1.0
C A:VAL103 3.4 23.0 1.0
OP2 P:DG9 3.5 25.1 1.0
C A:ILE106 3.6 22.6 1.0
N A:ILE106 3.8 23.2 1.0
O A:HOH501 3.9 42.2 1.0
CA A:SER104 4.0 22.9 1.0
CA A:THR101 4.0 24.7 1.0
N A:GLY105 4.0 24.7 1.0
N A:SER104 4.1 22.7 1.0
N A:VAL103 4.1 24.1 1.0
CA A:ILE106 4.2 21.9 1.0
C A:ARG102 4.3 26.6 1.0
C A:SER104 4.3 24.3 1.0
N A:ARG102 4.3 24.9 1.0
O3' P:DC8 4.4 26.1 1.0
CA A:VAL103 4.4 24.3 1.0
O5' P:DG9 4.5 27.1 1.0
CB A:THR101 4.6 24.0 1.0
N A:GLY107 4.6 22.6 1.0
CA A:ARG102 4.6 25.6 1.0
CB A:ILE106 4.6 23.3 1.0
C A:GLY105 4.7 25.0 1.0
CA A:GLY107 4.8 23.4 1.0
O A:ARG102 4.8 26.8 1.0
O A:LEU100 4.9 24.9 1.0
CA A:GLY105 5.0 24.5 1.0

Sodium binding site 2 out of 2 in 2fms

Go back to Sodium Binding Sites List in 2fms
Sodium 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 Sodium with other atoms in the Na 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:Na342

b:34.6
occ:1.00
O A:LEU62 2.3 39.3 1.0
O D:HOH132 2.3 48.5 1.0
O A:LYS60 2.4 33.3 1.0
O A:VAL65 2.5 31.4 1.0
OP1 D:DC3 2.6 34.0 1.0
C A:LEU62 3.3 38.2 1.0
C A:LYS60 3.5 36.5 1.0
C A:VAL65 3.5 32.7 1.0
P D:DC3 3.6 36.2 1.0
N A:VAL65 3.7 34.4 1.0
OP2 D:DC3 3.8 34.6 1.0
CA A:PRO63 4.0 36.3 1.0
N A:PRO63 4.0 38.7 1.0
CA A:VAL65 4.0 32.6 1.0
N A:GLY64 4.1 34.4 1.0
N A:LEU62 4.1 38.6 1.0
C A:LYS61 4.2 39.9 1.0
CA A:LYS60 4.2 34.8 1.0
CB A:VAL65 4.3 32.9 1.0
CA A:LEU62 4.3 38.4 1.0
CG A:LYS60 4.4 37.3 1.0
C A:PRO63 4.4 36.0 1.0
O A:LYS61 4.4 38.4 1.0
N A:LYS61 4.5 37.9 1.0
O3' D:DT2 4.6 38.0 1.0
N A:GLY66 4.6 32.9 1.0
CA A:LYS61 4.7 39.9 1.0
C A:GLY64 4.7 35.6 1.0
O A:ALA59 4.8 34.7 1.0
O5' D:DC3 4.8 38.8 1.0
CA A:GLY66 4.9 33.1 1.0
CB A:LYS60 4.9 34.4 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: Tue Dec 15 05:49:07 2020

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