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Magnesium in PDB 1xsl: Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap

Enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap, PDB code: 1xsl was solved by M.Garcia-Diaz, K.Bebenek, J.M.Krahn, T.A.Kunkel, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.47 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 191.504, 98.812, 104.519, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.2

Other elements in 1xsl:

The structure of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap also contains other interesting chemical elements:

Arsenic (As) 1 atom
Sodium (Na) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap (pdb code 1xsl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap, PDB code: 1xsl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1xsl

Go back to Magnesium Binding Sites List in 1xsl
Magnesium binding site 1 out of 3 in the Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg991

b:62.5
occ:1.00
 O B:HOH700 2.0 40.1 1.0
O B:HOH704 2.1 38.4 1.0
O B:HOH702 2.1 48.4 1.0
O B:HOH703 2.1 57.0 1.0
O D:HOH701 2.1 58.3 1.0
O B:HOH705 2.6 38.2 1.0
N7 B:DG2 4.0 37.7 1.0
O6 B:DG3 4.1 26.3 1.0
O6 B:DG2 4.3 36.1 1.0
N4 D:DC2 4.4 24.7 1.0
O6 D:DG1 4.4 35.1 1.0
O B:HOH291 4.5 41.5 1.0
O B:HOH750 4.8 49.4 1.0
C5 B:DG2 4.8 36.1 1.0
C6 B:DG2 4.9 37.1 1.0
C8 B:DG2 5.0 37.1 1.0

Magnesium binding site 2 out of 3 in 1xsl

Go back to Magnesium Binding Sites List in 1xsl
Magnesium binding site 2 out of 3 in the Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg992

b:50.9
occ:1.00
 O H:HOH856 1.9 54.8 1.0
O F:HOH857 1.9 40.2 1.0
O F:HOH859 2.2 36.6 1.0
O F:HOH858 2.2 44.2 1.0
O H:HOH855 2.2 55.4 1.0
O F:HOH854 2.3 55.0 1.0
O6 F:DG3 4.4 37.2 1.0
N7 F:DG2 4.4 46.2 1.0
O6 F:DG2 4.5 44.2 1.0
O F:HOH588 4.5 40.2 1.0
N4 H:DC2 4.5 40.0 1.0
O6 H:DG1 4.5 46.6 1.0
O F:HOH897 4.6 50.8 1.0

Magnesium binding site 3 out of 3 in 1xsl

Go back to Magnesium Binding Sites List in 1xsl
Magnesium binding site 3 out of 3 in the Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg993

b:85.8
occ:1.00
 O H:HOH868 1.6 0.4 1.0
O H:HOH874 1.9 66.3 1.0
O H:HOH873 1.9 68.4 1.0
O H:HOH871 2.3 54.2 1.0
O L:HOH870 2.4 64.8 1.0
O H:HOH872 2.7 72.1 1.0
O E:HOH1026 4.1 47.0 1.0
O H:HOH882 4.2 46.6 1.0
O6 H:DG4 4.2 46.2 1.0
O L:HOH612 4.2 46.9 1.0
O6 L:DG4 4.4 49.3 1.0
N7 L:DG4 4.5 51.3 1.0
O H:HOH375 4.5 32.8 1.0
N7 H:DG4 4.8 47.7 1.0
O H:HOH365 4.8 40.4 1.0
O E:HOH989 4.9 42.6 1.0
C5 H:DC3 5.0 51.2 1.0
C5 L:DC3 5.0 49.0 1.0

Reference:

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, T.A.Kunkel, L.C.Pedersen. A Closed Conformation For the Pol Lambda Catalytic Cycle. Nat.Struct.Mol.Biol. V. 12 97 2005.
ISSN: ISSN 1545-9993
PubMed: 15608652
DOI: 10.1038/NSMB876
Page generated: Tue Aug 13 18:22:52 2024

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