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Sodium in PDB 4ymn: Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4ymn 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) 19.76 / 2.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.907, 79.020, 55.019, 90.00, 107.92, 90.00
R / Rfree (%) 20 / 26.9

Other elements in 4ymn:

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp also contains other interesting chemical elements:

Fluorine (F) 1 atom
Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp (pdb code 4ymn). 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 Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4ymn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4ymn

Go back to Sodium Binding Sites List in 4ymn
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp


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 Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:23.1
occ:1.00
 O A:THR101 2.3 21.6 1.0
OP1 P:DG9 2.3 18.5 1.0
O A:ILE106 2.6 18.3 1.0
O A:VAL103 2.9 22.1 1.0
O A:HOH554 3.0 24.1 1.0
P P:DG9 3.3 15.9 1.0
O A:HOH553 3.3 30.4 1.0
C A:THR101 3.3 18.3 1.0
OP2 P:DG9 3.4 27.7 1.0
C A:ILE106 3.6 19.7 1.0
C A:VAL103 3.7 17.3 1.0
CA A:THR101 4.0 15.7 1.0
CA A:SER104 4.0 16.5 1.0
N A:ILE106 4.1 16.7 1.0
N A:SER104 4.2 16.2 1.0
O P:HOH112 4.2 22.3 1.0
N A:GLY105 4.2 20.1 1.0
O5' P:DG9 4.3 20.0 1.0
N A:ARG102 4.4 19.8 1.0
CA A:ILE106 4.4 15.0 1.0
O3' P:DC8 4.4 22.8 1.0
C A:ARG102 4.4 18.3 1.0
N A:VAL103 4.4 13.6 1.0
CB A:THR101 4.4 20.6 1.0
N A:GLY107 4.5 15.8 1.0
C A:SER104 4.5 20.7 1.0
CA A:ARG102 4.6 17.3 1.0
CA A:GLY107 4.7 17.7 1.0
CA A:VAL103 4.7 15.4 1.0
O A:ARG102 4.8 18.4 1.0
CB A:ILE106 4.9 17.9 1.0
C A:GLY105 4.9 18.6 1.0

Sodium binding site 2 out of 2 in 4ymn

Go back to Sodium Binding Sites List in 4ymn
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp


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 Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:29.9
occ:1.00
 O A:LYS60 2.4 34.1 1.0
O A:LEU62 2.6 29.4 1.0
OP1 D:DC3 2.9 26.6 1.0
O A:VAL65 2.9 25.8 1.0
C A:LEU62 3.3 27.0 1.0
C A:LYS60 3.6 25.9 1.0
C A:LYS61 3.7 26.5 1.0
O A:LYS61 3.7 29.9 1.0
N A:LEU62 3.8 27.6 1.0
N A:PRO63 3.9 27.7 1.0
CA A:PRO63 4.0 25.7 1.0
C A:VAL65 4.0 26.0 1.0
P D:DC3 4.0 23.4 1.0
CA A:LEU62 4.2 26.4 1.0
OP2 D:DC3 4.2 20.6 1.0
CA A:LYS61 4.2 24.8 1.0
N A:VAL65 4.2 21.8 1.0
N A:LYS61 4.3 22.2 1.0
N A:GLY64 4.4 24.6 1.0
CA A:VAL65 4.6 21.1 1.0
CA A:LYS60 4.6 27.6 1.0
C A:PRO63 4.6 25.4 1.0
CB A:VAL65 4.8 26.2 1.0
CG A:LYS60 4.9 26.2 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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