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Magnesium in PDB 3pml: Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T

Enzymatic activity of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T

All present enzymatic activity of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T, PDB code: 3pml 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) 25.02 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.038, 191.570, 59.084, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 27.1

Other elements in 3pml:

The structure of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T (pdb code 3pml). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T, PDB code: 3pml:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3pml

Go back to Magnesium Binding Sites List in 3pml
Magnesium binding site 1 out of 4 in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T


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 A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:30.4
occ:1.00
 OD2 A:ASP427 1.9 38.3 1.0
O2A A:1GC701 2.0 38.6 1.0
O2B A:1GC701 2.0 43.0 1.0
OD1 A:ASP429 2.1 34.2 1.0
O A:HOH42 2.3 28.9 1.0
O1G A:1GC701 2.5 38.1 1.0
CG A:ASP427 2.9 38.1 1.0
CG A:ASP429 3.0 33.7 1.0
PB A:1GC701 3.1 41.3 1.0
PA A:1GC701 3.1 42.1 1.0
OD1 A:ASP427 3.3 40.6 1.0
OD2 A:ASP429 3.3 32.8 1.0
MG A:MG2 3.4 27.2 1.0
C3A A:1GC701 3.5 38.3 1.0
O3B A:1GC701 3.6 41.7 1.0
PG A:1GC701 3.6 40.8 1.0
C5' A:1GC701 3.6 43.1 1.0
O5' A:1GC701 3.9 42.8 1.0
O3G A:1GC701 4.3 38.2 1.0
O A:HOH80 4.3 49.8 1.0
CB A:ASP427 4.3 34.6 1.0
C A:ASP427 4.3 33.1 1.0
O A:ASP427 4.4 30.2 1.0
CB A:ASP429 4.4 31.8 1.0
N A:SER417 4.4 30.8 1.0
O1B A:1GC701 4.4 42.0 1.0
O1A A:1GC701 4.4 42.1 1.0
CA A:GLY416 4.4 30.8 1.0
N A:ASP427 4.5 32.1 1.0
O A:HOH21 4.6 66.0 1.0
OG A:SER417 4.6 29.8 1.0
CA A:ASP427 4.6 34.2 1.0
N A:ASP429 4.7 30.1 1.0
N A:VAL428 4.7 31.3 1.0
O H:HOH12 4.8 23.2 1.0
O2G A:1GC701 4.8 40.4 1.0
C4' A:1GC701 4.9 44.5 1.0
C A:VAL428 5.0 30.1 1.0
C A:GLY416 5.0 31.4 1.0

Magnesium binding site 2 out of 4 in 3pml

Go back to Magnesium Binding Sites List in 3pml
Magnesium binding site 2 out of 4 in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T


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 A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:27.2
occ:1.00
 OD1 A:ASP427 2.0 40.6 1.0
O2A A:1GC701 2.1 38.6 1.0
OD2 A:ASP429 2.2 32.8 1.0
O H:HOH12 2.3 23.2 1.0
O3' H:DC6 2.4 40.2 1.0
OD2 A:ASP490 2.6 33.8 1.0
PA A:1GC701 3.1 42.1 1.0
CG A:ASP427 3.1 38.1 1.0
CG A:ASP429 3.2 33.7 1.0
MG A:MG1 3.4 30.4 1.0
C3' H:DC6 3.4 41.3 1.0
O1A A:1GC701 3.4 42.1 1.0
OD2 A:ASP427 3.5 38.3 1.0
O5' A:1GC701 3.5 42.8 1.0
OD1 A:ASP429 3.5 34.2 1.0
C5' A:1GC701 3.6 43.1 1.0
CG A:ASP490 3.7 29.4 1.0
C4' H:DC6 4.2 39.5 1.0
C5' H:DC6 4.3 38.4 1.0
O5' H:DC6 4.3 36.1 1.0
CB A:ASP490 4.3 29.6 1.0
CB A:ASP427 4.4 34.6 1.0
CB A:ASP429 4.5 31.8 1.0
OP1 H:DC6 4.6 30.0 1.0
O A:HOH21 4.7 66.0 1.0
C2' H:DC6 4.7 38.7 1.0
OD1 A:ASP490 4.7 29.4 1.0
C3A A:1GC701 4.7 38.3 1.0
O2B A:1GC701 4.8 43.0 1.0
O1G A:1GC701 4.8 38.1 1.0
NH2 A:ARG488 4.9 38.9 1.0

Magnesium binding site 3 out of 4 in 3pml

Go back to Magnesium Binding Sites List in 3pml
Magnesium binding site 3 out of 4 in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T


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 A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3

b:52.1
occ:1.00
 O1G B:1GC702 2.0 63.5 1.0
OD1 B:ASP429 2.2 51.3 1.0
O2B B:1GC702 2.2 60.5 1.0
O B:HOH116 2.4 50.9 1.0
OD2 B:ASP427 2.4 55.8 1.0
O2A B:1GC702 2.5 62.6 1.0
CG B:ASP427 2.8 55.9 1.0
OD1 B:ASP427 2.8 56.2 1.0
O B:ASP427 3.1 53.2 1.0
CG B:ASP429 3.2 52.1 1.0
PB B:1GC702 3.3 62.4 1.0
PG B:1GC702 3.4 64.4 1.0
C B:ASP427 3.6 53.2 1.0
O3B B:1GC702 3.6 64.2 1.0
PA B:1GC702 3.7 62.7 1.0
OD2 B:ASP429 3.7 51.5 1.0
C3A B:1GC702 3.8 60.7 1.0
CB B:ASP427 4.0 53.9 1.0
CA B:ASP427 4.1 53.3 1.0
N B:ASP427 4.1 53.2 1.0
O3G B:1GC702 4.1 65.0 1.0
OG B:SER417 4.2 41.1 1.0
MG B:MG4 4.2 44.9 1.0
CA B:GLY416 4.2 33.1 1.0
N B:SER417 4.3 36.3 1.0
C5' B:1GC702 4.3 58.9 1.0
N B:VAL428 4.3 51.9 1.0
N B:ASP429 4.5 48.7 1.0
CB B:ASP429 4.5 50.3 1.0
O2G B:1GC702 4.5 64.8 1.0
O5' B:1GC702 4.5 61.4 1.0
CA B:VAL428 4.7 49.5 1.0
O1B B:1GC702 4.7 61.1 1.0
C B:VAL428 4.7 49.1 1.0
C B:GLY416 4.8 34.3 1.0
O1A B:1GC702 4.8 61.7 1.0

Magnesium binding site 4 out of 4 in 3pml

Go back to Magnesium Binding Sites List in 3pml
Magnesium binding site 4 out of 4 in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4

b:44.9
occ:1.00
 O B:HOH117 1.9 36.9 1.0
OD2 B:ASP429 2.0 51.5 1.0
OD2 B:ASP490 2.2 55.0 1.0
O2A B:1GC702 2.4 62.6 1.0
OD2 B:ASP427 2.7 55.8 1.0
O3' F:DC6 2.8 60.0 1.0
CG B:ASP429 3.1 52.1 1.0
PA B:1GC702 3.2 62.7 1.0
O1A B:1GC702 3.3 61.7 1.0
CG B:ASP490 3.3 52.3 1.0
CG B:ASP427 3.4 55.9 1.0
OD1 B:ASP429 3.6 51.3 1.0
O5' B:1GC702 3.6 61.4 1.0
C3' F:DC6 3.8 57.3 1.0
C5' B:1GC702 3.8 58.9 1.0
OD1 B:ASP427 3.9 56.2 1.0
CB B:ASP490 4.0 50.0 1.0
O5' F:DC6 4.2 51.5 1.0
C5' F:DC6 4.2 53.9 1.0
MG B:MG3 4.2 52.1 1.0
OD1 B:ASP490 4.3 54.0 1.0
CB B:ASP429 4.3 50.3 1.0
C4' F:DC6 4.4 56.8 1.0
CB B:ASP427 4.5 53.9 1.0
OP1 F:DC6 4.7 51.9 1.0
CE1 B:PHE506 4.8 37.1 0.5
C3A B:1GC702 4.9 60.7 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: Mon Aug 11 02:06:57 2025

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