Sodium in PDB 2fmq: Sodium in Active Site of Dna Polymerase Beta

All present enzymatic activity of Sodium in Active Site of Dna Polymerase Beta:
2.7.7.7;

The structure of Sodium in Active Site of Dna Polymerase Beta, PDB code: 2fmq 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)	48.45 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.800, 80.200, 55.300, 90.00, 107.50, 90.00
R / Rfree (%)	19 / 24.2

The structure of Sodium in Active Site of Dna Polymerase Beta also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Sodium in Active Site of Dna Polymerase Beta (pdb code 2fmq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Sodium in Active Site of Dna Polymerase Beta, PDB code: 2fmq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Sodium in Active Site of Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sodium in Active Site of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na340 b:30.3 occ:1.00 OD1 A:ASP192 2.2 25.7 1.0 O1A A:DUP338 2.5 16.8 1.0 OD2 A:ASP190 2.6 29.3 1.0 OD2 A:ASP256 2.7 30.2 1.0 OD1 A:ASP190 2.9 21.6 1.0 CG A:ASP190 3.0 24.5 1.0 CG A:ASP192 3.2 23.9 1.0 C3' C:DC10 3.4 36.2 1.0 MG A:MG339 3.4 18.8 1.0 OD2 A:ASP192 3.4 24.9 1.0 O3' C:DC10 3.5 37.8 1.0 PA A:DUP338 3.6 21.9 1.0 CG A:ASP256 3.6 25.7 1.0 O5' A:DUP338 3.8 21.1 1.0 CB A:ASP256 4.1 24.2 1.0 O2A A:DUP338 4.1 23.0 1.0 C5' A:DUP338 4.2 21.7 1.0 CB A:ASP190 4.4 22.4 1.0 C4' C:DC10 4.4 35.8 1.0 O A:MET191 4.4 22.9 1.0 C2' C:DC10 4.4 34.7 1.0 C5' C:DC10 4.5 35.4 1.0 CB A:ASP192 4.5 24.8 1.0 OD1 A:ASP256 4.6 27.9 1.0 O5' C:DC10 4.7 34.9 1.0 NH2 A:ARG254 4.7 24.9 1.0 O3G A:DUP338 4.7 19.3 1.0 C A:MET191 4.9 24.3 1.0 O2B A:DUP338 4.9 16.7 1.0 OP1 C:DC10 4.9 36.4 1.0 CA A:ASP192 4.9 24.0 1.0 O A:HOH566 5.0 38.5 1.0

Sodium binding site 2 out of 3 in the Sodium in Active Site of Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sodium in Active Site of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:28.7 occ:1.00 O A:THR101 2.4 27.0 1.0 OP1 C:DG9 2.4 26.7 1.0 O A:HOH552 2.5 35.4 1.0 O A:VAL103 2.5 20.0 1.0 O A:ILE106 2.6 19.8 1.0 O C:HOH55 2.7 30.9 1.0 C A:THR101 3.3 25.9 1.0 C A:VAL103 3.4 23.2 1.0 P C:DG9 3.5 26.9 1.0 C A:ILE106 3.6 21.9 1.0 OP2 C:DG9 3.7 27.8 1.0 N A:ILE106 3.8 22.2 1.0 CA A:THR101 3.9 25.1 1.0 CA A:SER104 3.9 24.2 1.0 N A:GLY105 4.0 24.4 1.0 N A:SER104 4.0 22.5 1.0 N A:VAL103 4.1 24.4 1.0 CA A:ILE106 4.2 20.9 1.0 N A:ARG102 4.3 25.2 1.0 C A:SER104 4.3 23.1 1.0 C A:ARG102 4.3 25.6 1.0 CA A:VAL103 4.4 24.0 1.0 CB A:THR101 4.4 23.0 1.0 CB A:ILE106 4.5 22.4 1.0 N A:GLY107 4.6 22.5 1.0 O5' C:DG9 4.6 26.9 1.0 O3' C:DC8 4.6 25.0 1.0 CA A:ARG102 4.6 26.0 1.0 C A:GLY105 4.7 24.0 1.0 CA A:GLY107 4.8 23.5 1.0 O A:LEU100 4.8 23.5 1.0 O A:ARG102 4.9 28.8 1.0 CA A:GLY105 5.0 24.4 1.0

Sodium binding site 3 out of 3 in the Sodium in Active Site of Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sodium in Active Site of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:42.3 occ:1.00 O A:LEU62 2.4 35.7 1.0 O A:VAL65 2.4 28.6 1.0 OP1 D:DC3 2.4 34.5 1.0 O A:HOH491 2.5 36.4 1.0 O D:HOH9 2.6 37.5 1.0 O A:LYS60 2.7 36.9 1.0 C A:LEU62 3.4 34.6 1.0 C A:VAL65 3.5 28.8 1.0 P D:DC3 3.5 35.8 1.0 C A:LYS60 3.6 36.2 1.0 N A:VAL65 3.7 29.4 1.0 OP2 D:DC3 3.8 34.0 1.0 N A:GLY64 4.0 32.9 1.0 CA A:PRO63 4.0 34.8 1.0 CA A:VAL65 4.1 29.2 1.0 N A:PRO63 4.1 34.5 1.0 C A:LYS61 4.2 36.5 1.0 N A:LEU62 4.2 35.3 1.0 CA A:LYS60 4.3 33.9 1.0 O A:LYS61 4.4 37.4 1.0 O3' D:DT2 4.4 34.7 1.0 C A:PRO63 4.4 34.3 1.0 CB A:VAL65 4.4 29.8 1.0 CA A:LEU62 4.5 34.2 1.0 N A:LYS61 4.5 36.1 1.0 CG A:LYS60 4.5 35.5 1.0 N A:GLY66 4.5 28.9 1.0 CA A:LYS61 4.6 36.5 1.0 C A:GLY64 4.6 31.1 1.0 O5' D:DC3 4.8 36.3 1.0 CA A:GLY66 4.8 28.3 1.0 O A:ALA59 4.9 28.5 1.0 CA A:GLY64 4.9 33.2 1.0

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