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Sodium in PDB 1zjn: Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp

Enzymatic activity of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp, PDB code: 1zjn was solved by V.K.Batra, W.A.Beard, D.D.Shock, 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) 30.39 / 2.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.100, 79.500, 55.100, 90.00, 106.20, 90.00
R / Rfree (%) 22.8 / 23.4

Other elements in 1zjn:

The structure of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp (pdb code 1zjn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp, PDB code: 1zjn:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1zjn

Go back to Sodium Binding Sites List in 1zjn
Sodium binding site 1 out of 3 in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na340

b:37.0
occ:1.00
 OD2 A:ASP256 2.7 37.0 1.0
CG A:ASP190 2.7 35.4 1.0
OD1 A:ASP190 2.7 35.9 1.0
OD2 A:ASP190 2.7 35.5 1.0
OD1 A:ASP192 2.8 35.8 1.0
O1A A:DGT338 3.5 28.6 1.0
CB A:ASP190 3.6 34.2 1.0
CG A:ASP256 3.7 33.2 1.0
O5' P:DA10 3.7 78.6 1.0
CG A:ASP192 3.8 34.5 1.0
MG A:MG339 4.1 46.5 1.0
OD2 A:ASP192 4.1 38.6 1.0
C5' P:DA10 4.2 82.9 1.0
CB A:ASP256 4.3 33.4 1.0
OP1 P:DA10 4.3 78.2 1.0
O A:MET191 4.3 36.4 1.0
NH2 A:ARG254 4.5 39.6 1.0
OD1 A:ASP256 4.6 31.5 1.0
N A:MET191 4.6 31.1 1.0
C A:MET191 4.7 31.8 1.0
PA A:DGT338 4.7 31.1 1.0
P P:DA10 4.8 75.9 1.0
O A:HOH349 4.8 29.6 1.0
C4' P:DA10 4.8 85.6 1.0
CA A:ASP190 4.9 33.0 1.0
C5' A:DGT338 4.9 38.6 1.0
N A:ASP256 4.9 32.1 1.0
C A:ASP190 5.0 32.4 1.0

Sodium binding site 2 out of 3 in 1zjn

Go back to Sodium Binding Sites List in 1zjn
Sodium binding site 2 out of 3 in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:38.7
occ:1.00
 O A:THR101 2.0 35.4 1.0
O A:VAL103 2.2 37.0 1.0
OP1 P:DG9 2.6 44.2 1.0
O P:HOH11 2.8 28.6 1.0
O A:ILE106 2.8 29.4 1.0
C A:THR101 3.0 35.1 1.0
C A:VAL103 3.1 34.4 1.0
N A:VAL103 3.5 35.4 1.0
P P:DG9 3.6 44.0 1.0
OP2 P:DG9 3.6 42.6 1.0
C A:ILE106 3.6 29.1 1.0
N A:ILE106 3.7 29.1 1.0
CA A:THR101 3.9 36.7 1.0
N A:SER104 3.9 33.0 1.0
C A:ARG102 3.9 36.5 1.0
N A:ARG102 4.0 34.2 1.0
CA A:SER104 4.0 31.4 1.0
CA A:VAL103 4.0 33.9 1.0
N A:GLY105 4.0 30.1 1.0
CA A:ILE106 4.1 29.6 1.0
CA A:ARG102 4.1 36.9 1.0
C A:SER104 4.3 30.2 1.0
CB A:ILE106 4.4 30.2 1.0
CB A:THR101 4.5 34.1 1.0
O5' P:DG9 4.6 47.7 1.0
N A:GLY107 4.6 28.3 1.0
O A:ARG102 4.7 35.5 1.0
O3' P:DC8 4.7 43.3 1.0
O A:LEU100 4.7 36.1 1.0
C A:GLY105 4.7 30.7 1.0
CB A:VAL103 4.9 32.8 1.0
CA A:GLY105 5.0 29.6 1.0
CA A:GLY107 5.0 27.2 1.0

Sodium binding site 3 out of 3 in 1zjn

Go back to Sodium Binding Sites List in 1zjn
Sodium binding site 3 out of 3 in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:27.8
occ:1.00
 O A:LYS60 2.1 39.6 1.0
O A:LEU62 2.4 40.9 1.0
OP1 D:DC3 2.7 39.0 1.0
O A:VAL65 2.9 35.5 1.0
C A:LEU62 3.3 40.9 1.0
C A:LYS60 3.3 39.6 1.0
P D:DC3 3.6 40.5 1.0
OP2 D:DC3 3.6 39.9 1.0
C A:VAL65 3.9 35.7 1.0
CA A:PRO63 3.9 41.5 1.0
C A:LYS61 4.0 42.0 1.0
N A:PRO63 4.0 41.0 1.0
N A:LEU62 4.1 41.6 1.0
N A:VAL65 4.1 39.0 1.0
O A:LYS61 4.1 42.5 1.0
CG A:LYS60 4.1 38.2 1.0
CA A:LYS60 4.1 37.5 1.0
N A:GLY64 4.3 41.0 1.0
CA A:LEU62 4.3 41.1 1.0
N A:LYS61 4.3 40.6 1.0
CA A:LYS61 4.5 41.3 1.0
CA A:VAL65 4.5 36.4 1.0
C A:PRO63 4.5 41.8 1.0
CB A:VAL65 4.6 37.2 1.0
O3' D:DT2 4.7 39.3 1.0
CB A:LYS60 4.7 37.5 1.0
O5' D:DC3 4.8 40.0 1.0
N A:GLY66 4.8 36.0 1.0
CA A:GLY66 5.0 36.5 1.0

Reference:

V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson. Nucleotide-Induced Dna Polymerase Active Site Motions Accommodating A Mutagenic Dna Intermediate. Structure V. 13 1225 2005.
ISSN: ISSN 0969-2126
PubMed: 16084394
DOI: 10.1016/J.STR.2005.05.010
Page generated: Mon Oct 7 01:42:22 2024

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