Atomistry » Sodium » PDB 4yil-4z48 » 4ymn
Atomistry »
  Sodium »
    PDB 4yil-4z48 »
      4ymn »

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: Tue Dec 15 10:04:15 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy