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Sodium in PDB 4m47: Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

Enzymatic activity of Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

All present enzymatic activity of Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 4m47 was solved by M.C.Koag, K.Min, A.F.Monzingo, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.82 / 2.37
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.175, 79.267, 55.294, 90.00, 107.80, 90.00
R / Rfree (%) 20.9 / 27.3

Other elements in 4m47:

The structure of Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp also contains other interesting chemical elements:

Bromine (Br) 1 atom
Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp (pdb code 4m47). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 4m47:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4m47

Go back to Sodium Binding Sites List in 4m47
Sodium binding site 1 out of 3 in the Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp


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 Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:41.4
occ:1.00
 OD1 A:ASP192 2.3 29.2 1.0
O1A A:XG4401 2.4 41.2 1.0
OD2 A:ASP190 2.4 35.8 1.0
O A:HOH513 2.6 38.9 1.0
CG A:ASP190 3.1 35.6 1.0
CG A:ASP192 3.3 33.1 1.0
OD1 A:ASP190 3.3 34.1 1.0
PA A:XG4401 3.4 44.0 1.0
OD2 A:ASP192 3.6 32.9 1.0
MG A:MG402 3.6 34.9 1.0
O2A A:XG4401 3.7 39.9 1.0
O5' A:XG4401 3.7 42.2 1.0
O3' P:DA10 4.1 60.3 1.0
OD2 A:ASP256 4.2 28.3 1.0
C3' P:DA10 4.2 57.2 1.0
C5' A:XG4401 4.3 41.3 1.0
C5' P:DA10 4.3 53.2 1.0
O A:HOH502 4.4 47.0 1.0
CB A:ASP190 4.4 34.1 1.0
CG A:ASP256 4.4 31.6 1.0
C4' P:DA10 4.4 55.8 1.0
O A:HOH544 4.5 40.6 1.0
OP1 P:DA10 4.6 39.5 1.0
O1G A:XG4401 4.6 28.0 1.0
CB A:ASP192 4.7 32.5 1.0
OD1 A:ASP256 4.7 34.0 1.0
O A:MET191 4.9 28.2 1.0
N3A A:XG4401 4.9 35.4 1.0

Sodium binding site 2 out of 3 in 4m47

Go back to Sodium Binding Sites List in 4m47
Sodium binding site 2 out of 3 in the Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp


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 Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:32.1
occ:1.00
 O A:ILE106 2.2 29.3 1.0
OP1 P:DG9 2.2 29.4 1.0
O A:THR101 2.3 35.5 1.0
O A:HOH507 2.5 21.9 1.0
O A:VAL103 2.5 26.7 1.0
O P:HOH102 2.6 33.3 1.0
P P:DG9 3.3 29.4 1.0
C A:ILE106 3.3 28.7 1.0
C A:THR101 3.3 32.0 1.0
C A:VAL103 3.3 27.7 1.0
OP2 P:DG9 3.5 28.3 1.0
N A:ILE106 3.8 30.1 1.0
CA A:SER104 3.8 27.9 1.0
N A:SER104 3.9 27.1 1.0
CA A:THR101 3.9 29.2 1.0
N A:GLY105 4.0 27.6 1.0
CA A:ILE106 4.1 28.4 1.0
N A:VAL103 4.1 29.4 1.0
O3' P:DC8 4.3 27.9 1.0
N A:GLY107 4.3 30.8 1.0
C A:SER104 4.3 26.0 1.0
C A:ARG102 4.3 32.1 1.0
CA A:VAL103 4.4 29.1 1.0
N A:ARG102 4.4 33.3 1.0
O5' P:DG9 4.4 28.0 1.0
CB A:THR101 4.5 27.9 1.0
CB A:ILE106 4.6 28.1 1.0
CA A:GLY107 4.6 30.5 1.0
CA A:ARG102 4.6 31.1 1.0
C A:GLY105 4.6 27.9 1.0
O A:LEU100 4.8 23.1 1.0
O A:ARG102 4.9 32.2 1.0
CA A:GLY105 4.9 29.1 1.0

Sodium binding site 3 out of 3 in 4m47

Go back to Sodium Binding Sites List in 4m47
Sodium binding site 3 out of 3 in the Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Human Dna Polymerase Complexed with 8-Brg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:43.0
occ:1.00
 O A:LYS60 2.3 31.8 1.0
O A:VAL65 2.4 35.2 1.0
O A:LEU62 2.6 39.3 1.0
OP1 D:DC3 3.1 39.2 1.0
C A:LYS60 3.4 34.9 1.0
C A:VAL65 3.5 35.1 1.0
OP2 D:DC3 3.6 31.6 1.0
C A:LEU62 3.6 35.6 1.0
P D:DC3 3.8 37.3 1.0
N A:VAL65 4.1 31.6 1.0
CA A:LYS60 4.1 38.0 1.0
C A:LYS61 4.1 35.0 1.0
N A:LEU62 4.2 34.1 1.0
CA A:VAL65 4.2 33.0 1.0
CG A:LYS60 4.2 44.1 1.0
O A:LYS61 4.3 40.7 1.0
CA A:PRO63 4.4 34.5 1.0
N A:PRO63 4.4 35.8 1.0
CB A:VAL65 4.4 33.4 1.0
N A:LYS61 4.5 37.2 1.0
N A:GLY66 4.5 34.9 1.0
N A:GLY64 4.5 35.9 1.0
NZ A:LYS60 4.5 49.8 1.0
CA A:LEU62 4.5 37.1 1.0
CA A:LYS61 4.6 36.8 1.0
O3' D:DT2 4.6 35.7 1.0
CA A:GLY66 4.7 30.6 1.0
CB A:LYS60 4.8 41.0 1.0
C A:PRO63 4.9 35.1 1.0
O A:ALA59 5.0 44.7 1.0

Reference:

M.C.Koag, K.Min, S.Lee. Structural Basis For Promutagenicity of 8-Halogenated Guanine. J.Biol.Chem. V. 289 6289 2014.
ISSN: ISSN 0021-9258
PubMed: 24425881
DOI: 10.1074/JBC.M113.537803
Page generated: Mon Oct 7 16:54:43 2024

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