Chlorine in PDB 3pmn: Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

Enzymatic activity of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

All present enzymatic activity of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site, PDB code: 3pmn was solved by K.Bebenek, 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) 25.27 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.390, 62.417, 139.881, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.3

Other elements in 3pmn:

The structure of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Manganese (Mn) 3 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site (pdb code 3pmn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site, PDB code: 3pmn:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3pmn

Go back to Chlorine Binding Sites List in 3pmn
Chlorine binding site 1 out of 2 in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8

b:55.1
occ:1.00
 O A:HOH588 3.0 21.1 1.0
MN A:MN6 3.0 45.3 1.0
CE1 A:HIS486 3.7 30.6 1.0
ND1 A:HIS486 3.9 28.3 1.0
O A:HOH589 4.1 33.7 1.0
O A:HOH590 4.2 38.3 1.0
NH1 A:ARG478 4.6 39.1 1.0
OD1 A:ASP382 4.7 28.8 1.0
ND1 A:HIS379 4.8 26.3 1.0
CE A:LYS378 4.9 47.6 1.0
NE2 A:HIS486 4.9 31.4 1.0
CE1 A:HIS379 4.9 27.9 1.0

Chlorine binding site 2 out of 2 in 3pmn

Go back to Chlorine Binding Sites List in 3pmn
Chlorine binding site 2 out of 2 in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl9

b:54.0
occ:1.00
 NH2 A:ARG514 3.2 25.6 1.0
O B:HOH12 3.2 27.3 1.0
O A:HOH49 3.3 28.1 1.0
NH1 A:ARG514 3.5 23.0 1.0
CZ A:ARG514 3.8 26.9 1.0
CD1 A:LEU277 4.3 27.0 1.0
CE A:LYS273 4.3 48.3 1.0
CZ3 A:TRP274 4.4 27.8 1.0
CD2 A:LEU277 4.7 26.5 1.0
CB A:LEU277 4.7 28.7 1.0
O A:LYS273 4.8 31.9 1.0
NZ A:LYS273 4.8 52.6 1.0
CG A:LEU277 4.8 28.7 1.0
CB A:LYS273 4.8 35.7 1.0
CE3 A:TRP274 4.8 29.5 1.0

Reference:

K.Bebenek, L.C.Pedersen, T.A.Kunkel. Replication Infidelity Via A Mismatch with Watson-Crick Geometry. Proc.Natl.Acad.Sci.Usa V. 108 1862 2011.
ISSN: ISSN 0027-8424
PubMed: 21233421
DOI: 10.1073/PNAS.1012825108
Page generated: Sat Dec 12 10:02:54 2020

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