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Sodium in PDB 2ihm: Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide

Enzymatic activity of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide

All present enzymatic activity of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide:
2.7.7.7;

Protein crystallography data

The structure of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide, PDB code: 2ihm was solved by A.F.Moon, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.028, 96.085, 73.090, 90.00, 106.55, 90.00
R / Rfree (%) 23 / 27.7

Other elements in 2ihm:

The structure of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide (pdb code 2ihm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide, PDB code: 2ihm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2ihm

Go back to Sodium Binding Sites List in 2ihm
Sodium binding site 1 out of 3 in the Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na900

b:42.8
occ:1.00
 O A:VAL246 2.4 41.3 1.0
O A:VAL243 2.5 35.3 1.0
O A:THR241 2.5 37.8 1.0
OP1 P:DA5 2.5 39.3 1.0
C A:VAL246 3.3 38.0 1.0
N A:VAL246 3.4 38.6 1.0
C A:VAL243 3.4 34.8 1.0
C A:THR241 3.5 37.2 1.0
P P:DA5 3.6 38.7 1.0
CA A:VAL246 3.8 38.4 1.0
N A:GLY245 3.8 36.8 1.0
OP2 P:DA5 3.8 39.7 1.0
N A:VAL243 4.0 36.2 1.0
CA A:PHE244 4.1 36.4 1.0
N A:PHE244 4.1 35.8 1.0
CB A:VAL246 4.1 37.1 1.0
CA A:THR241 4.1 37.4 1.0
C A:PHE244 4.2 36.2 1.0
C A:GLN242 4.3 36.8 1.0
C A:GLY245 4.4 40.1 1.0
N A:GLN242 4.4 36.8 1.0
O3' P:DT4 4.4 39.2 1.0
CA A:VAL243 4.4 37.4 1.0
N A:GLY247 4.5 40.5 1.0
CA A:GLN242 4.5 39.0 1.0
CA A:GLY245 4.7 37.6 1.0
O A:PHE240 4.7 39.7 1.0
O A:GLN242 4.8 35.7 1.0
CB A:THR241 4.9 36.9 1.0
O5' P:DA5 4.9 36.9 1.0
CA A:GLY247 4.9 38.3 1.0

Sodium binding site 2 out of 3 in 2ihm

Go back to Sodium Binding Sites List in 2ihm
Sodium binding site 2 out of 3 in the Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na902

b:40.4
occ:0.50
 OD2 A:ASP330 2.1 46.0 1.0
OD2 A:ASP420 2.8 53.8 1.0
O1A A:D3T538 2.9 30.3 1.0
OD1 A:ASP332 2.9 47.9 1.0
CG A:ASP330 3.0 43.1 1.0
OD1 A:ASP330 3.3 44.5 1.0
C3' P:DT6 3.4 36.6 1.0
C5' P:DT6 3.5 32.2 1.0
O5' A:D3T538 3.5 32.0 1.0
PA A:D3T538 3.7 34.8 1.0
CG A:ASP332 3.8 48.8 1.0
OD2 A:ASP332 3.8 48.8 1.0
O5' P:DT6 3.8 31.0 1.0
C5' A:D3T538 3.9 30.2 1.0
C4' P:DT6 3.9 36.3 1.0
CE1 A:HIS329 3.9 39.0 1.0
CG A:ASP420 4.1 52.3 1.0
MG A:MG700 4.1 34.5 1.0
OP1 P:DT6 4.3 31.8 1.0
NE2 A:HIS329 4.3 36.8 1.0
O2A A:D3T538 4.3 34.1 1.0
CB A:ASP330 4.4 41.0 1.0
NH2 A:ARG418 4.5 45.5 1.0
CZ3 A:TRP436 4.6 43.6 1.0
P P:DT6 4.7 30.6 1.0
C2' P:DT6 4.7 36.3 1.0
CB A:ASP420 4.9 46.3 1.0
OD1 A:ASP420 4.9 53.4 1.0
ND1 A:HIS329 4.9 40.4 1.0

Sodium binding site 3 out of 3 in 2ihm

Go back to Sodium Binding Sites List in 2ihm
Sodium binding site 3 out of 3 in the Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na901

b:47.0
occ:1.00
 O B:VAL246 2.3 44.9 1.0
OP1 Q:DA5 2.4 47.5 1.0
O B:THR241 2.7 47.2 1.0
O B:VAL243 2.9 52.5 1.0
P Q:DA5 3.2 46.4 1.0
OP2 Q:DA5 3.3 39.8 1.0
C B:VAL246 3.4 43.3 1.0
N B:VAL246 3.8 46.4 1.0
C B:THR241 3.8 47.5 1.0
C B:VAL243 4.0 51.8 1.0
N B:GLY245 4.0 50.1 1.0
CA B:VAL246 4.2 43.8 1.0
O5' Q:DA5 4.3 42.6 1.0
N B:GLY247 4.3 42.6 1.0
CA B:THR241 4.4 47.9 1.0
CA B:PHE244 4.4 52.0 1.0
O3' Q:DT4 4.4 47.6 1.0
CA B:GLY247 4.5 42.0 1.0
N B:PHE244 4.6 50.9 1.0
C B:PHE244 4.7 52.0 1.0
C B:GLY245 4.7 49.0 1.0
CB B:VAL246 4.7 43.6 1.0
C B:GLN242 4.7 50.1 1.0
N B:VAL243 4.8 49.8 1.0
N B:GLN242 4.9 48.7 1.0
CB B:THR241 4.9 46.4 1.0
O B:GLN242 4.9 49.0 1.0
CA B:GLY245 4.9 48.6 1.0

Reference:

A.F.Moon, M.Garcia-Diaz, K.Bebenek, B.J.Davis, X.Zhong, D.A.Ramsden, T.A.Kunkel, L.C.Pedersen. Structural Insight Into the Substrate Specificity of Dna Polymerase Mu. Nat.Struct.Mol.Biol. V. 14 45 2007.
ISSN: ISSN 1545-9993
PubMed: 17159995
DOI: 10.1038/NSMB1180
Page generated: Mon Oct 7 02:52:47 2024

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