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Sodium in PDB 2fmp: Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site

Enzymatic activity of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site

All present enzymatic activity of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site, PDB code: 2fmp was solved by V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.18 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.900, 80.400, 55.300, 90.00, 107.50, 90.00
R / Rfree (%) 17.9 / 21.7

Other elements in 2fmp:

The structure of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site (pdb code 2fmp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site, PDB code: 2fmp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2fmp

Go back to Sodium Binding Sites List in 2fmp
Sodium binding site 1 out of 5 in the Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1340

b:15.4
occ:1.00
 OD1 A:ASP192 2.2 12.7 1.0
OD2 A:ASP190 2.3 21.5 1.0
OD2 A:ASP256 2.4 22.1 1.0
O1A A:DCT1338 2.5 14.8 1.0
O P:HOH11 2.5 38.4 1.0
OD1 A:ASP190 2.9 12.2 1.0
CG A:ASP190 2.9 16.6 1.0
CG A:ASP192 3.2 10.8 1.0
MG A:MG1339 3.4 11.1 1.0
OD2 A:ASP192 3.5 13.6 1.0
CG A:ASP256 3.5 21.0 1.0
PA A:DCT1338 3.6 13.1 1.0
C3' P:DOC10 3.7 19.5 1.0
O5' A:DCT1338 3.8 12.0 1.0
C5' A:DCT1338 4.0 10.3 1.0
CB A:ASP256 4.2 11.8 1.0
O2A A:DCT1338 4.2 13.4 1.0
C5' P:DOC10 4.2 17.4 1.0
O A:HOH1453 4.3 19.9 1.0
C4' P:DOC10 4.3 20.0 1.0
CB A:ASP190 4.3 11.9 1.0
O A:MET191 4.5 11.2 0.5
CB A:ASP192 4.5 8.6 1.0
O A:HOH1408 4.6 9.6 0.5
OD1 A:ASP256 4.6 17.5 1.0
O1G A:DCT1338 4.6 27.0 0.5
O A:MET191 4.8 10.3 0.5
O A:HOH1568 4.8 28.1 1.0
OP1 P:DOC10 4.8 16.7 1.0
O5' P:DOC10 4.9 17.7 1.0
C A:MET191 4.9 10.7 0.5
NH2 A:ARG254 4.9 14.4 1.0
CA A:ASP192 4.9 9.5 1.0
C A:MET191 5.0 11.9 0.5
O3A A:DCT1338 5.0 11.1 1.0
O2B A:DCT1338 5.0 11.4 1.0

Sodium binding site 2 out of 5 in 2fmp

Go back to Sodium Binding Sites List in 2fmp
Sodium binding site 2 out of 5 in the Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1341

b:17.6
occ:1.00
 O P:HOH12 2.3 24.4 1.0
O A:THR101 2.4 16.2 1.0
O A:HOH1410 2.5 20.3 1.0
O A:ILE106 2.5 16.1 1.0
O A:VAL103 2.5 13.5 1.0
OP1 P:DG9 2.6 18.7 1.0
C A:THR101 3.4 16.0 1.0
C A:VAL103 3.5 14.1 1.0
C A:ILE106 3.5 13.2 1.0
P P:DG9 3.6 17.1 1.0
OP2 P:DG9 3.7 17.2 1.0
N A:ILE106 3.8 12.2 1.0
CA A:THR101 4.0 13.6 1.0
N A:GLY105 4.0 12.1 1.0
CA A:SER104 4.0 11.5 1.0
O A:HOH1838 4.1 45.7 1.0
N A:VAL103 4.1 13.1 1.0
N A:SER104 4.1 11.7 1.0
CA A:ILE106 4.2 11.8 1.0
O P:HOH24 4.2 35.5 1.0
C A:SER104 4.3 15.1 1.0
C A:ARG102 4.4 17.9 1.0
N A:ARG102 4.4 14.8 1.0
O3' P:DC8 4.5 17.8 1.0
CA A:VAL103 4.5 11.3 1.0
N A:GLY107 4.5 11.9 1.0
CB A:THR101 4.5 13.2 1.0
CB A:ILE106 4.6 14.8 1.0
CA A:ARG102 4.7 13.2 1.0
C A:GLY105 4.7 11.3 1.0
CA A:GLY107 4.7 15.3 1.0
O A:HOH1720 4.8 37.6 1.0
O A:ARG102 4.8 18.4 1.0
O A:HOH1895 4.9 58.1 1.0
CA A:GLY105 4.9 14.8 1.0
O5' P:DG9 4.9 17.5 1.0
O A:LEU100 4.9 13.0 1.0

Sodium binding site 3 out of 5 in 2fmp

Go back to Sodium Binding Sites List in 2fmp
Sodium binding site 3 out of 5 in the Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1342

b:20.0
occ:1.00
 O A:LYS60 2.3 25.1 1.0
O A:LEU62 2.3 20.4 1.0
O A:VAL65 2.4 17.3 1.0
O A:HOH1411 2.4 28.2 1.0
OP1 D:DC3 2.6 20.0 0.5
O D:HOH6 2.6 25.8 1.0
OP1 D:DC3 2.7 16.5 0.5
C A:LEU62 3.4 19.2 1.0
C A:LYS60 3.4 23.9 1.0
C A:VAL65 3.5 16.1 1.0
P D:DC3 3.6 16.4 0.5
OP2 D:DC3 3.7 16.5 0.5
P D:DC3 3.7 24.0 0.5
N A:VAL65 3.8 14.0 1.0
OP2 D:DC3 4.0 26.0 0.5
N A:LEU62 4.0 20.4 1.0
O D:HOH14 4.0 33.2 1.0
N A:GLY64 4.1 19.3 1.0
CA A:PRO63 4.1 22.9 1.0
CA A:VAL65 4.1 14.6 1.0
C A:LYS61 4.1 23.9 1.0
N A:PRO63 4.1 26.4 1.0
CA A:LYS60 4.2 19.5 1.0
CA A:LEU62 4.3 21.4 1.0
CB A:VAL65 4.3 18.6 1.0
CG A:LYS60 4.4 27.0 1.0
O A:LYS61 4.4 24.0 1.0
N A:LYS61 4.4 20.9 1.0
O3' D:DT2 4.5 17.9 1.0
C A:PRO63 4.5 19.7 1.0
CA A:LYS61 4.6 20.3 1.0
N A:GLY66 4.6 16.3 1.0
C A:GLY64 4.8 17.1 1.0
O A:ALA59 4.9 19.7 1.0
O5' D:DC3 4.9 23.0 0.5
CA A:GLY66 4.9 22.5 1.0
CB A:LYS60 4.9 23.8 1.0
O5' D:DC3 4.9 22.9 0.5

Sodium binding site 4 out of 5 in 2fmp

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Sodium binding site 4 out of 5 in the Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1402

b:24.8
occ:1.00
 O A:HOH1526 2.3 26.2 1.0
O A:HOH1569 2.3 27.6 1.0
O A:HOH1493 2.4 23.8 1.0
O A:HOH1510 2.4 25.0 1.0
O A:HOH1501 2.5 24.5 1.0
O A:ARG126 2.6 26.1 1.0
NA A:NA1406 3.2 22.6 1.0
C A:ARG126 3.7 23.6 1.0
O A:HOH1614 4.0 31.3 1.0
OE2 A:GLU129 4.0 20.2 0.5
O A:HOH1459 4.0 21.2 1.0
OE1 A:GLU129 4.3 48.6 0.5
CA A:LYS127 4.4 22.8 1.0
CB A:ARG126 4.4 18.8 1.0
N A:LYS127 4.4 20.2 1.0
CA A:ARG126 4.6 19.1 1.0
O A:HOH1528 4.6 25.8 1.0
CD A:GLU129 4.7 15.8 0.5
OE1 A:GLU129 4.8 15.6 0.5
CB A:LYS127 4.9 30.7 1.0

Sodium binding site 5 out of 5 in 2fmp

Go back to Sodium Binding Sites List in 2fmp
Sodium binding site 5 out of 5 in the Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1406

b:22.6
occ:1.00
 O A:HOH1528 2.3 25.8 1.0
O A:HOH1499 2.4 25.2 1.0
O A:HOH1558 2.4 27.1 1.0
O A:HOH1501 2.5 24.5 1.0
O A:HOH1526 2.5 26.2 1.0
O A:HOH1510 2.7 25.0 1.0
NA A:NA1402 3.2 24.8 1.0
O A:HOH1459 4.1 21.2 1.0
O A:HOH1504 4.2 23.8 1.0
OE2 A:GLU129 4.5 20.2 0.5
OE1 A:GLU129 4.5 48.6 0.5
O A:HOH1493 5.0 23.8 1.0

Reference:

V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, S.H.Wilson. Magnesium-Induced Assembly of A Complete Dna Polymerase Catalytic Complex. Structure V. 14 757 2006.
ISSN: ISSN 0969-2126
PubMed: 16615916
DOI: 10.1016/J.STR.2006.01.011
Page generated: Tue Dec 15 05:49:07 2020

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