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Sodium in PDB 4rt3: Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp

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

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

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp, PDB code: 4rt3 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) 22.26 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.735, 79.909, 55.337, 90.00, 107.52, 90.00
R / Rfree (%) 18 / 22.6

Other elements in 4rt3:

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

Magnesium (Mg) 1 atom
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp (pdb code 4rt3). 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)-Nh-(Beta,Gamma)-CH2-Dttp, PDB code: 4rt3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4rt3

Go back to Sodium Binding Sites List in 4rt3
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-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)-Nh-(Beta,Gamma)-CH2-Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:6.5
occ:1.00
 OD2 A:ASP256 2.1 23.2 1.0
OD1 A:ASP192 2.1 18.2 1.0
OD2 A:ASP190 2.1 20.6 1.0
O P:HOH501 2.2 17.4 1.0
O1A A:C6T408 2.3 21.6 1.0
CG A:ASP190 2.9 20.2 1.0
CG A:ASP192 3.1 18.4 1.0
OD1 A:ASP190 3.1 19.4 1.0
CG A:ASP256 3.2 22.5 1.0
PA A:C6T408 3.3 20.1 1.0
OD2 A:ASP192 3.4 18.2 1.0
MG A:MG401 3.5 16.6 1.0
O2A A:C6T408 3.6 20.8 1.0
O5' A:C6T408 3.6 21.5 1.0
CB A:ASP256 3.8 22.6 1.0
C3' P:DOC10 3.9 24.0 1.0
C5' A:C6T408 4.1 21.2 1.0
OD1 A:ASP256 4.2 22.0 1.0
CB A:ASP190 4.3 18.5 1.0
CB A:ASP192 4.4 22.4 1.0
C5' P:DOC10 4.4 21.0 1.0
C4' P:DOC10 4.5 22.7 1.0
O A:HOH505 4.5 26.9 1.0
O3G A:C6T408 4.5 20.4 1.0
OP1 P:DOC10 4.5 21.6 1.0
O A:MET191 4.7 21.9 1.0
NH2 A:ARG254 4.7 24.6 1.0
N3A A:C6T408 4.8 21.2 1.0
N A:ASP256 4.9 20.9 1.0
O5' P:DOC10 4.9 23.1 1.0
O2B A:C6T408 4.9 18.4 1.0
CA A:ASP192 5.0 20.5 1.0
C A:MET191 5.0 19.9 1.0

Sodium binding site 2 out of 3 in 4rt3

Go back to Sodium Binding Sites List in 4rt3
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-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)-Nh-(Beta,Gamma)-CH2-Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:27.2
occ:1.00
 O A:THR101 2.3 26.4 1.0
O A:ILE106 2.5 23.4 1.0
O P:HOH502 2.5 30.9 1.0
O A:VAL103 2.5 26.4 1.0
O A:HOH535 2.5 30.2 1.0
OP1 P:DG9 2.6 27.8 1.0
C A:THR101 3.3 24.9 1.0
C A:VAL103 3.4 26.2 1.0
C A:ILE106 3.5 26.2 1.0
P P:DG9 3.6 29.2 1.0
O A:HOH595 3.6 39.1 1.0
OP2 P:DG9 3.6 27.9 1.0
N A:ILE106 3.8 24.2 1.0
CA A:THR101 3.9 29.0 1.0
N A:GLY105 4.0 25.6 1.0
CA A:SER104 4.0 26.7 1.0
N A:VAL103 4.1 23.6 1.0
N A:SER104 4.1 25.0 1.0
CA A:ILE106 4.2 22.8 1.0
C A:ARG102 4.3 26.4 1.0
N A:ARG102 4.3 25.8 1.0
C A:SER104 4.4 26.0 1.0
CA A:VAL103 4.4 23.6 1.0
N A:GLY107 4.5 25.4 1.0
O3' P:DC8 4.5 29.0 1.0
CA A:ARG102 4.5 28.6 1.0
CB A:THR101 4.5 29.5 1.0
CB A:ILE106 4.6 24.9 1.0
C A:GLY105 4.7 28.7 1.0
O A:ARG102 4.7 28.2 1.0
CA A:GLY107 4.7 25.0 1.0
O A:HOH702 4.8 44.1 1.0
O A:HOH713 4.8 36.3 1.0
O A:LEU100 4.8 24.9 1.0
O5' P:DG9 4.9 31.3 1.0
CA A:GLY105 4.9 29.2 1.0
O A:HOH639 4.9 40.0 1.0

Sodium binding site 3 out of 3 in 4rt3

Go back to Sodium Binding Sites List in 4rt3
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-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)-Nh-(Beta,Gamma)-CH2-Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:38.0
occ:1.00
 O A:LYS60 2.4 34.5 1.0
O A:LEU62 2.4 36.4 1.0
O A:VAL65 2.4 35.3 1.0
OP1 D:DC3 2.6 35.1 1.0
C A:LEU62 3.4 34.1 1.0
C A:LYS60 3.5 34.2 1.0
C A:VAL65 3.6 34.4 1.0
P D:DC3 3.7 38.3 1.0
OP2 D:DC3 3.9 34.6 1.0
N A:VAL65 4.0 35.2 1.0
CA A:PRO63 4.0 36.8 1.0
C A:LYS61 4.0 40.3 1.0
N A:PRO63 4.1 35.2 1.0
N A:LEU62 4.1 33.5 1.0
O A:LYS61 4.2 37.9 1.0
CA A:VAL65 4.2 32.7 1.0
N A:GLY64 4.3 33.9 1.0
CA A:LYS60 4.3 35.3 1.0
CG A:LYS60 4.3 35.3 1.0
N A:LYS61 4.4 38.5 1.0
CA A:LEU62 4.4 35.4 1.0
CB A:VAL65 4.4 30.3 1.0
CA A:LYS61 4.5 34.8 1.0
C A:PRO63 4.6 34.7 1.0
N A:GLY66 4.6 34.4 1.0
O3' D:DT2 4.7 39.8 1.0
O5' D:DC3 4.9 43.9 1.0
CA A:GLY66 4.9 34.3 1.0
NZ A:LYS60 4.9 42.5 1.0
CB A:LYS60 4.9 35.6 1.0
C A:GLY64 5.0 34.4 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 18:21:16 2024

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