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Sodium in PDB 4yn4: Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site, PDB code: 4yn4 was solved by S.Lee, M.-C.Koag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.774, 79.179, 55.031, 90.00, 106.53, 90.00
R / Rfree (%) 20.3 / 25.5

Other elements in 4yn4:

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site also contains other interesting chemical elements:

Fluorine (F) 1 atom
Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site (pdb code 4yn4). 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 Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site, PDB code: 4yn4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4yn4

Go back to Sodium Binding Sites List in 4yn4
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site


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 Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:33.2
occ:1.00
 O D:HOH104 2.4 31.8 1.0
O A:VAL65 2.4 34.5 1.0
O A:HOH546 2.4 36.3 1.0
O A:LEU62 2.5 34.4 1.0
O A:LYS60 2.5 35.7 1.0
OP1 D:DC3 2.6 33.3 1.0
C A:LEU62 3.4 33.5 1.0
C A:VAL65 3.5 29.9 1.0
C A:LYS60 3.5 36.4 1.0
N A:VAL65 3.7 30.5 1.0
P D:DC3 3.7 25.9 1.0
N A:LEU62 4.0 34.0 1.0
CA A:VAL65 4.0 26.0 1.0
OP2 D:DC3 4.0 25.8 1.0
C A:LYS61 4.0 36.5 1.0
N A:GLY64 4.1 32.0 1.0
N A:PRO63 4.1 32.1 1.0
CA A:PRO63 4.2 34.2 1.0
CB A:VAL65 4.3 29.1 1.0
CA A:LYS60 4.3 33.0 1.0
O A:LYS61 4.3 40.7 1.0
CA A:LEU62 4.3 35.9 1.0
N A:LYS61 4.4 31.8 1.0
CA A:LYS61 4.5 33.8 1.0
N A:GLY66 4.5 22.8 1.0
C A:PRO63 4.5 30.4 1.0
CG A:LYS60 4.5 34.8 1.0
O3' D:DT2 4.6 30.5 1.0
C A:GLY64 4.8 27.5 1.0
CA A:GLY66 4.8 23.7 1.0
O5' D:DC3 4.9 25.2 1.0
O A:ALA59 5.0 32.0 1.0

Sodium binding site 2 out of 2 in 4yn4

Go back to Sodium Binding Sites List in 4yn4
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site


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 Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:19.4
occ:1.00
 O A:THR101 2.3 24.6 1.0
OP1 P:DG9 2.4 20.8 1.0
O A:ILE106 2.4 19.2 1.0
O A:VAL103 2.5 20.4 1.0
O A:HOH582 2.5 23.9 1.0
O P:HOH111 2.6 22.3 1.0
C A:THR101 3.2 22.7 1.0
C A:VAL103 3.3 23.4 1.0
O A:HOH583 3.3 17.4 1.0
C A:ILE106 3.4 20.1 1.0
P P:DG9 3.6 22.8 1.0
N A:ILE106 3.8 19.2 1.0
CA A:SER104 3.8 20.5 1.0
CA A:THR101 3.9 20.4 1.0
N A:SER104 3.9 20.3 1.0
OP2 P:DG9 3.9 22.7 1.0
N A:GLY105 3.9 14.5 1.0
N A:VAL103 4.1 21.6 1.0
CA A:ILE106 4.1 18.5 1.0
C A:ARG102 4.2 23.9 1.0
N A:ARG102 4.2 23.9 1.0
C A:SER104 4.3 17.1 1.0
CA A:VAL103 4.3 18.8 1.0
N A:GLY107 4.4 22.1 1.0
CB A:THR101 4.4 22.4 1.0
CB A:ILE106 4.5 17.1 1.0
CA A:ARG102 4.5 23.0 1.0
O3' P:DC8 4.6 23.0 1.0
O5' P:DG9 4.6 24.1 1.0
O A:ARG102 4.6 23.8 1.0
CA A:GLY107 4.6 19.5 1.0
C A:GLY105 4.6 17.5 1.0
O P:HOH109 4.8 26.2 1.0
O A:LEU100 4.9 18.7 1.0
CA A:GLY105 4.9 18.9 1.0

Reference:

Y.Kou, M.C.Koag, S.Lee. Structural and Kinetic Studies of the Effect of Guanine-N7 Alkylation and Metal Cofactors on Dna Replication. Biochemistry 2018.
ISSN: ISSN 1520-4995
PubMed: 29957995
DOI: 10.1021/ACS.BIOCHEM.8B00331
Page generated: Mon Oct 7 19:33:16 2024

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