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Sodium in PDB 4rt2: Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp, PDB code: 4rt2 was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.24 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.587, 79.409, 55.315, 90.00, 107.27, 90.00
R / Rfree (%) 17.6 / 21.1

Other elements in 4rt2:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp (pdb code 4rt2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp, PDB code: 4rt2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4rt2

Go back to Sodium Binding Sites List in 4rt2
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:21.6
occ:1.00
 OD1 A:ASP192 2.1 18.5 1.0
OD2 A:ASP190 2.1 22.2 1.0
O A:HOH665 2.1 25.3 1.0
OD2 A:ASP256 2.1 23.6 1.0
O1A A:N6T406 2.4 16.2 1.0
CG A:ASP190 3.1 20.5 1.0
CG A:ASP192 3.1 17.0 1.0
CG A:ASP256 3.3 23.4 1.0
OD1 A:ASP190 3.3 18.4 1.0
OD2 A:ASP192 3.4 15.5 1.0
PA A:N6T406 3.4 19.9 1.0
MG A:MG401 3.6 15.6 1.0
C3' P:DOC10 3.8 25.6 1.0
O2A A:N6T406 3.8 20.4 1.0
O5' A:N6T406 3.9 21.2 1.0
CB A:ASP256 3.9 21.7 1.0
C5' P:DOC10 4.1 26.6 1.0
C4' P:DOC10 4.2 30.0 1.0
C5' A:N6T406 4.2 18.7 1.0
OD1 A:ASP256 4.3 23.8 1.0
CB A:ASP192 4.4 17.2 1.0
CB A:ASP190 4.4 17.8 1.0
O A:HOH771 4.5 28.7 1.0
OP1 P:DOC10 4.6 26.2 1.0
O5' P:DOC10 4.7 25.5 1.0
NH2 A:ARG254 4.7 21.4 1.0
O A:MET191 4.8 18.3 1.0
O3G A:N6T406 4.8 18.5 1.0
CA A:ASP192 5.0 17.8 1.0
O2B A:N6T406 5.0 15.6 1.0

Sodium binding site 2 out of 3 in 4rt2

Go back to Sodium Binding Sites List in 4rt2
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:24.6
occ:1.00
 O A:THR101 2.3 21.2 1.0
O A:ILE106 2.4 20.5 1.0
OP1 P:DG9 2.4 24.0 1.0
O P:HOH101 2.5 25.9 1.0
O A:VAL103 2.5 20.1 1.0
O A:HOH553 2.8 27.5 1.0
C A:THR101 3.3 19.6 1.0
C A:VAL103 3.4 19.5 1.0
C A:ILE106 3.4 21.1 1.0
P P:DG9 3.5 23.8 1.0
OP2 P:DG9 3.7 19.9 1.0
O A:HOH638 3.7 36.0 1.0
N A:ILE106 3.8 19.2 1.0
CA A:THR101 3.9 20.9 1.0
N A:GLY105 4.0 19.1 1.0
CA A:SER104 4.0 20.4 1.0
N A:SER104 4.1 17.5 1.0
CA A:ILE106 4.1 19.5 1.0
N A:VAL103 4.2 18.2 1.0
C A:ARG102 4.3 20.7 1.0
N A:ARG102 4.4 20.7 1.0
C A:SER104 4.4 18.6 1.0
CB A:THR101 4.4 23.1 1.0
O3' P:DC8 4.4 21.2 1.0
N A:GLY107 4.4 18.7 1.0
CA A:VAL103 4.4 20.6 1.0
CB A:ILE106 4.5 20.4 1.0
CA A:ARG102 4.6 24.1 1.0
CA A:GLY107 4.7 21.1 1.0
O A:HOH656 4.7 41.5 1.0
C A:GLY105 4.7 20.2 1.0
O A:ARG102 4.7 21.4 1.0
O5' P:DG9 4.8 25.7 1.0
O A:LEU100 4.9 20.7 1.0
CA A:GLY105 4.9 21.4 1.0

Sodium binding site 3 out of 3 in 4rt2

Go back to Sodium Binding Sites List in 4rt2
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-CH2-(Beta,Gamma)-Nh-Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:27.1
occ:1.00
 O A:LEU62 2.3 27.4 1.0
O A:HOH533 2.4 31.7 1.0
O A:LYS60 2.4 26.9 1.0
O A:VAL65 2.5 28.2 1.0
OP1 D:DC3 2.7 27.0 1.0
O D:HOH112 2.7 32.8 1.0
C A:LEU62 3.3 26.5 1.0
C A:LYS60 3.5 29.9 1.0
C A:VAL65 3.5 26.9 1.0
P D:DC3 3.7 26.3 1.0
N A:VAL65 3.8 24.8 1.0
OP2 D:DC3 3.9 27.7 1.0
N A:LEU62 3.9 26.1 1.0
C A:LYS61 4.0 31.6 1.0
CA A:PRO63 4.0 29.5 1.0
O A:HOH804 4.0 36.2 1.0
N A:PRO63 4.1 30.9 1.0
CA A:VAL65 4.1 24.6 1.0
N A:GLY64 4.1 26.1 1.0
CA A:LEU62 4.2 27.4 1.0
CA A:LYS60 4.3 27.9 1.0
O A:LYS61 4.3 30.2 1.0
CB A:VAL65 4.4 22.6 1.0
N A:LYS61 4.4 30.7 1.0
C A:PRO63 4.5 29.3 1.0
CA A:LYS61 4.5 29.2 1.0
CG A:LYS60 4.6 29.1 1.0
O3' D:DT2 4.6 29.2 1.0
N A:GLY66 4.6 25.1 1.0
C A:GLY64 4.8 26.5 1.0
O A:ALA59 4.8 25.1 1.0
CA A:GLY66 4.9 27.1 1.0
O5' D:DC3 4.9 33.1 1.0

Reference:

A.P.Kadina, B.A.Kashemirov, K.Oertell, V.K.Batra, S.H.Wilson, M.F.Goodman, C.E.Mckenna. Two Scaffolds From Two Flips: (Alpha, Beta)/(Beta, Gamma) CH2/Nh "Met-Im" Analogues of Dttp. Org.Lett. V. 17 2586 2015.
ISSN: ISSN 1523-7060
PubMed: 25970636
DOI: 10.1021/ACS.ORGLETT.5B00799
Page generated: Mon Oct 7 18:21:14 2024

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