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Manganese in PDB 3upq: Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T.

Enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T.

All present enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T.:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T., PDB code: 3upq was solved by R.A.Gosavi, A.F.Moon, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.44 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.975, 63.660, 139.970, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.4

Other elements in 3upq:

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T. also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T. (pdb code 3upq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T., PDB code: 3upq:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 3upq

Go back to Manganese Binding Sites List in 3upq
Manganese binding site 1 out of 3 in the Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1

b:22.9
occ:1.00
OD1 A:ASP427 2.1 23.3 1.0
O1B A:ZAN0 2.2 21.7 1.0
OD2 A:ASP429 2.2 24.0 1.0
O2G A:ZAN0 2.2 18.9 1.0
O1A A:ZAN0 2.2 19.5 1.0
O A:HOH215 2.3 21.2 1.0
CG A:ASP427 3.1 21.5 1.0
CG A:ASP429 3.1 23.1 1.0
PB A:ZAN0 3.2 27.9 1.0
PA A:ZAN0 3.4 23.2 1.0
PG A:ZAN0 3.4 24.8 1.0
OD1 A:ASP429 3.4 20.4 1.0
OD2 A:ASP427 3.5 23.4 1.0
O3B A:ZAN0 3.6 25.9 1.0
MN A:MN2 3.6 26.3 1.0
N3A A:ZAN0 3.7 20.9 1.0
O A:HOH211 3.8 25.1 1.0
C5' A:ZAN0 3.9 26.1 1.0
O A:ASP427 4.0 24.4 1.0
O3G A:ZAN0 4.1 27.6 1.0
C A:ASP427 4.3 22.3 1.0
N A:ASP427 4.3 25.0 1.0
O5' A:ZAN0 4.3 24.5 1.0
OG A:SER417 4.4 23.0 1.0
CB A:ASP427 4.4 22.0 1.0
N A:SER417 4.4 21.0 1.0
CB A:ASP429 4.5 16.7 1.0
CA A:GLY416 4.5 18.7 1.0
O A:HOH214 4.5 23.3 1.0
O2A A:ZAN0 4.6 24.5 1.0
O1G A:ZAN0 4.6 25.5 1.0
CA A:ASP427 4.6 19.9 1.0
O2B A:ZAN0 4.6 27.5 1.0
N A:ASP429 4.7 20.9 1.0
O A:HOH213 4.7 28.6 1.0
N A:VAL428 4.9 21.9 1.0
C A:VAL428 5.0 18.5 1.0

Manganese binding site 2 out of 3 in 3upq

Go back to Manganese Binding Sites List in 3upq
Manganese binding site 2 out of 3 in the Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2

b:26.3
occ:1.00
OD2 A:ASP427 2.1 23.4 1.0
OD2 A:ASP490 2.1 20.2 1.0
OD1 A:ASP429 2.2 20.4 1.0
O A:HOH213 2.2 28.6 1.0
O3' P:DC6 2.3 25.4 1.0
O1A A:ZAN0 2.4 19.5 1.0
CG A:ASP427 3.1 21.5 1.0
CG A:ASP490 3.2 25.8 1.0
CG A:ASP429 3.2 23.1 1.0
OD1 A:ASP427 3.4 23.3 1.0
C3' P:DC6 3.4 21.2 1.0
PA A:ZAN0 3.5 23.2 1.0
MN A:MN1 3.6 22.9 1.0
OD2 A:ASP429 3.7 24.0 1.0
C5' A:ZAN0 3.8 26.1 1.0
O2A A:ZAN0 3.8 24.5 1.0
CB A:ASP490 3.9 23.6 1.0
O5' A:ZAN0 3.9 24.5 1.0
O A:HOH211 4.1 25.1 1.0
C4' P:DC6 4.1 19.3 1.0
C5' P:DC6 4.1 19.4 1.0
OD1 A:ASP490 4.2 23.8 1.0
CB A:ASP427 4.5 22.0 1.0
CB A:ASP429 4.5 16.7 1.0
NH2 A:ARG488 4.6 20.1 1.0
C2' P:DC6 4.7 22.2 1.0
O5' P:DC6 4.7 25.6 1.0
O2G A:ZAN0 4.8 18.9 1.0
OP1 P:DC6 4.8 20.9 1.0

Manganese binding site 3 out of 3 in 3upq

Go back to Manganese Binding Sites List in 3upq
Manganese binding site 3 out of 3 in the Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3

b:24.4
occ:1.00
OD2 A:ASP382 2.1 21.0 1.0
O A:HOH197 2.2 27.8 1.0
O A:HOH195 2.2 24.6 1.0
O A:HOH196 2.2 30.0 1.0
O A:HOH198 2.2 23.5 1.0
ND1 A:HIS486 2.3 20.5 1.0
CE1 A:HIS486 3.1 26.3 1.0
CG A:ASP382 3.2 21.0 1.0
CG A:HIS486 3.5 22.3 1.0
OD1 A:ASP382 3.6 18.5 1.0
N A:HIS486 3.7 16.9 1.0
CB A:HIS486 4.0 17.5 1.0
O A:HOH241 4.1 40.1 1.0
ND1 A:HIS379 4.2 18.9 1.0
NE2 A:HIS486 4.3 22.1 1.0
O A:HOH199 4.4 17.6 1.0
CB A:ASP382 4.4 13.1 1.0
CA A:HIS486 4.5 20.4 1.0
CD2 A:HIS486 4.5 21.7 1.0
O A:HOH235 4.6 40.5 1.0
C A:ARG485 4.6 25.6 1.0
CA A:ARG485 4.6 22.1 1.0
CE1 A:HIS379 4.7 23.3 1.0
NH1 A:ARG478 4.8 39.0 1.0
O A:ARG484 5.0 25.9 1.0

Reference:

R.A.Gosavi, A.F.Moon, T.A.Kunkel, L.C.Pedersen, K.Bebenek. The Catalytic Cycle For Ribonucleotide Incorporation By Human Dna Pol Lambda Nucleic Acids Res. V. 40 7518 2012.
ISSN: ISSN 0305-1048
PubMed: 22584622
DOI: 10.1093/NAR/GKS413
Page generated: Sat Oct 5 18:08:34 2024

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