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Sodium in PDB 4z6f: Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese

Enzymatic activity of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese

All present enzymatic activity of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese, PDB code: 4z6f was solved by M.-C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.753, 79.558, 55.204, 90.00, 107.70, 90.00
R / Rfree (%) 19.5 / 24.8

Other elements in 4z6f:

The structure of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese (pdb code 4z6f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese, PDB code: 4z6f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4z6f

Go back to Sodium Binding Sites List in 4z6f
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:20.1
occ:1.00
 O A:THR101 2.4 19.2 1.0
OP1 P:DG9 2.4 18.9 1.0
O A:HOH509 2.4 21.6 1.0
O A:VAL103 2.5 20.2 1.0
O A:ILE106 2.5 13.9 1.0
P P:DG9 3.3 21.7 1.0
C A:VAL103 3.4 15.6 1.0
OP2 P:DG9 3.4 22.2 1.0
C A:THR101 3.4 20.2 1.0
C A:ILE106 3.5 17.6 1.0
N A:ILE106 3.6 17.8 1.0
CA A:SER104 3.7 15.4 1.0
N A:GLY105 3.7 14.6 1.0
N A:SER104 3.9 14.8 1.0
O A:HOH555 4.0 22.9 1.0
CA A:ILE106 4.0 15.8 1.0
C A:SER104 4.1 19.6 1.0
CA A:THR101 4.2 18.1 1.0
N A:VAL103 4.2 16.3 1.0
C A:ARG102 4.2 17.6 1.0
O3' P:DC8 4.3 17.1 1.0
N A:ARG102 4.4 16.0 1.0
CA A:VAL103 4.5 19.9 1.0
CB A:ILE106 4.5 16.0 1.0
C A:GLY105 4.5 18.8 1.0
N A:GLY107 4.5 15.1 1.0
O A:ARG102 4.5 22.4 1.0
O5' P:DG9 4.6 18.5 1.0
CA A:ARG102 4.6 18.5 1.0
CA A:GLY105 4.7 16.3 1.0
CB A:THR101 4.8 17.5 1.0
CA A:GLY107 4.9 18.8 1.0
O A:LEU100 4.9 19.4 1.0

Sodium binding site 2 out of 2 in 4z6f

Go back to Sodium Binding Sites List in 4z6f
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:33.0
occ:1.00
 O A:LEU62 2.4 35.3 1.0
OP1 D:DC3 2.5 32.4 1.0
O A:LYS60 2.5 33.0 1.0
O A:VAL65 2.6 28.8 1.0
C A:LEU62 3.3 34.2 1.0
C A:LYS60 3.6 33.4 1.0
C A:VAL65 3.7 28.9 1.0
P D:DC3 3.7 29.9 1.0
C A:LYS61 4.0 30.7 1.0
CA A:PRO63 4.0 29.4 1.0
O A:LYS61 4.0 31.4 1.0
N A:PRO63 4.0 31.4 1.0
N A:VAL65 4.0 23.0 1.0
OP2 D:DC3 4.1 35.5 1.0
N A:LEU62 4.1 29.3 1.0
N A:GLY64 4.2 27.0 1.0
CA A:VAL65 4.3 28.2 1.0
CA A:LEU62 4.3 31.7 1.0
N A:LYS61 4.5 31.9 1.0
C A:PRO63 4.5 32.3 1.0
CA A:LYS61 4.5 32.5 1.0
CA A:LYS60 4.5 29.0 1.0
CB A:VAL65 4.6 24.8 1.0
O5' D:DC3 4.7 40.6 1.0
N A:GLY66 4.8 26.9 1.0
O3' D:DT2 4.8 34.4 1.0
CG A:LYS60 4.9 30.8 1.0
C A:GLY64 5.0 32.1 1.0

Reference:

M.C.Koag, S.Lee. Insights Into the Effect of Minor Groove Interactions and Metal Cofactors on Mutagenic Replication By Human Dna Polymerase Beta. Biochem. J. V. 475 571 2018.
ISSN: ESSN 1470-8728
PubMed: 29301983
DOI: 10.1042/BCJ20170787
Page generated: Mon Oct 7 19:37:48 2024

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