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Calcium in PDB 5dkw: Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active

Enzymatic activity of Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active

All present enzymatic activity of Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active, PDB code: 5dkw was solved by M.S.Liu, M.D.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.47 / 2.69
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.466, 151.310, 83.606, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active (pdb code 5dkw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active, PDB code: 5dkw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5dkw

Go back to Calcium Binding Sites List in 5dkw
Calcium binding site 1 out of 5 in the Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:63.4
occ:1.00
 O1B A:DTP601 2.3 46.3 1.0
O A:HOH744 2.3 40.9 1.0
OD1 A:ASP427 2.5 58.5 1.0
O1A A:DTP601 2.7 59.1 1.0
O A:HOH747 2.8 32.5 1.0
O A:ASP427 3.0 37.4 1.0
O3G A:DTP601 3.1 38.5 1.0
CG A:ASP427 3.1 51.7 1.0
OD2 A:ASP427 3.5 55.5 1.0
C A:ASP427 3.6 36.3 1.0
PB A:DTP601 3.6 63.4 1.0
PA A:DTP601 3.6 72.8 1.0
OD2 A:ASP429 3.8 55.3 1.0
O3A A:DTP601 3.9 70.1 1.0
N A:ASP427 4.0 34.2 1.0
O5' A:DTP601 4.0 61.6 1.0
CA A:ASP427 4.1 34.6 1.0
CB A:ASP427 4.1 37.5 1.0
O A:HOH707 4.2 28.3 1.0
CG A:ASP429 4.2 46.9 1.0
OD1 A:ASP429 4.2 49.4 1.0
PG A:DTP601 4.2 57.6 1.0
N A:VAL428 4.3 34.0 1.0
O3B A:DTP601 4.4 48.1 1.0
CA A:GLY416 4.5 22.3 1.0
O2G A:DTP601 4.5 60.6 1.0
N A:SER417 4.6 25.1 1.0
CA A:VAL428 4.6 28.2 1.0
OG A:SER417 4.7 26.8 1.0
O A:HOH724 4.7 43.8 1.0
N A:ASP429 4.7 23.8 1.0
O2B A:DTP601 4.7 49.5 1.0
O A:HOH705 4.8 30.6 1.0
C A:VAL428 4.9 23.1 1.0
C5' A:DTP601 4.9 59.6 1.0
O2A A:DTP601 5.0 62.2 1.0

Calcium binding site 2 out of 5 in 5dkw

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Calcium binding site 2 out of 5 in the Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:46.4
occ:1.00
 O A:CYS300 2.5 38.0 1.0
O A:ILE305 2.5 30.5 1.0
O A:ILE302 2.7 37.9 1.0
O A:HOH786 2.8 40.9 1.0
O D:HOH101 2.8 36.5 1.0
OP1 D:DC3 2.9 34.6 1.0
C A:ILE305 3.5 29.5 1.0
OP2 D:DC3 3.5 27.4 1.0
C A:ILE302 3.5 36.5 1.0
C A:CYS300 3.6 31.0 1.0
P D:DC3 3.7 41.1 1.0
N A:ILE305 4.0 32.8 1.0
CA A:PRO303 4.0 38.1 1.0
N A:PRO303 4.1 40.2 1.0
N A:GLY304 4.2 29.3 1.0
C A:SER301 4.3 35.9 1.0
CA A:ILE305 4.3 31.3 1.0
O D:HOH102 4.3 37.8 1.0
N A:ILE302 4.3 35.9 1.0
CA A:CYS300 4.3 31.8 1.0
O A:SER301 4.4 42.0 1.0
N A:GLY306 4.4 28.3 1.0
C A:PRO303 4.5 32.2 1.0
CA A:ILE302 4.6 34.7 1.0
N A:SER301 4.6 31.4 1.0
CA A:GLY306 4.7 27.8 1.0
CA A:SER301 4.7 31.0 1.0
O3' D:DC2 4.7 37.3 1.0
CB A:ILE305 4.8 31.7 1.0
O5' D:DC3 4.9 40.1 1.0
O A:ALA299 4.9 36.2 1.0
C A:GLY304 5.0 34.5 1.0

Calcium binding site 3 out of 5 in 5dkw

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Calcium binding site 3 out of 5 in the Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:47.8
occ:1.00
 O B:CYS300 2.4 40.9 1.0
O B:ILE305 2.7 40.2 1.0
O B:ILE302 2.8 31.6 1.0
OP1 C:DC3 3.2 38.9 1.0
OP2 C:DC3 3.5 25.9 1.0
C B:CYS300 3.6 36.5 1.0
C B:ILE305 3.6 33.0 1.0
C B:ILE302 3.7 35.6 1.0
P C:DC3 3.8 35.9 1.0
N B:ILE305 4.1 32.5 1.0
CA B:CYS300 4.2 34.2 1.0
CA B:PRO303 4.3 40.5 1.0
N B:ILE302 4.3 36.2 1.0
N B:GLY304 4.4 29.6 1.0
N B:PRO303 4.4 40.1 1.0
CA B:ILE305 4.4 28.8 1.0
N B:GLY306 4.4 32.3 1.0
CA B:GLY306 4.5 29.0 1.0
C B:SER301 4.6 38.3 1.0
N B:SER301 4.6 30.4 1.0
CA B:ILE302 4.7 38.7 1.0
C B:PRO303 4.7 37.2 1.0
O3' C:DC2 4.8 38.2 1.0
CA B:SER301 4.9 30.7 1.0
CB B:CYS300 4.9 33.8 1.0
CB B:ILE305 4.9 28.1 1.0
O B:ALA299 5.0 32.6 1.0

Calcium binding site 4 out of 5 in 5dkw

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Calcium binding site 4 out of 5 in the Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:42.2
occ:1.00
 OP1 E:DA5 2.5 23.5 1.0
O B:SER339 2.6 26.7 1.0
O B:ALA344 2.6 23.1 1.0
O B:ILE341 2.7 20.6 1.0
O E:HOH103 2.9 19.1 1.0
C B:ILE341 3.5 20.5 1.0
C B:SER339 3.5 21.1 1.0
P E:DA5 3.5 23.3 1.0
OP2 E:DA5 3.7 21.6 1.0
C B:ALA344 3.7 21.9 1.0
O B:HOH739 3.7 19.1 1.0
N B:ALA344 4.1 24.5 1.0
N B:ILE341 4.1 24.2 1.0
CA B:TRP342 4.1 22.4 1.0
N B:TRP342 4.2 25.1 1.0
N B:GLY343 4.2 20.8 1.0
CA B:SER339 4.2 20.1 1.0
C B:ASN340 4.4 20.4 1.0
N B:ASN340 4.4 19.0 1.0
CA B:ALA344 4.4 20.6 1.0
CA B:ILE341 4.5 16.5 1.0
O3' E:DT4 4.5 22.0 1.0
CA B:ASN340 4.5 16.6 1.0
C B:TRP342 4.6 21.4 1.0
N B:GLY345 4.7 21.2 1.0
O5' E:DA5 4.8 25.5 1.0
CB B:SER339 4.8 19.5 1.0
CA B:GLY345 4.8 22.0 1.0
CB B:ALA344 4.9 19.7 1.0

Calcium binding site 5 out of 5 in 5dkw

Go back to Calcium Binding Sites List in 5dkw
Calcium binding site 5 out of 5 in the Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ternary Crystal Structure of Polymerase Lambda with A Ga Mispair at the Primer Terminus with CA2+ in the Active within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:59.1
occ:1.00
 OD1 B:ASP427 2.4 54.5 1.0
O1A B:DTP603 2.4 52.9 1.0
O B:HOH745 2.5 42.0 1.0
O1G B:DTP603 2.6 41.9 1.0
OD2 B:ASP429 2.7 47.6 1.0
O1B B:DTP603 2.9 44.2 1.0
CG B:ASP427 3.6 46.7 1.0
O B:ASP427 3.6 37.9 1.0
PA B:DTP603 3.7 62.6 1.0
CG B:ASP429 3.8 49.5 1.0
CA B:GLY416 3.9 23.5 1.0
PB B:DTP603 3.9 69.5 1.0
O B:HOH704 4.0 29.3 1.0
O3A B:DTP603 4.0 71.2 1.0
PG B:DTP603 4.0 56.9 1.0
N B:SER417 4.0 23.1 1.0
C B:ASP427 4.1 37.1 1.0
OG B:SER417 4.1 34.1 1.0
OD1 B:ASP429 4.2 48.3 1.0
OD2 B:ASP427 4.3 55.4 1.0
O3B B:DTP603 4.3 50.9 1.0
N B:ASP427 4.4 36.2 1.0
C B:GLY416 4.5 22.8 1.0
O B:HOH713 4.5 39.0 1.0
CA B:ASP427 4.6 35.1 1.0
O5' B:DTP603 4.6 67.6 1.0
O B:CYS415 4.6 26.8 1.0
CB B:ASP427 4.6 31.1 1.0
N B:VAL428 4.6 33.2 1.0
O2A B:DTP603 4.7 62.8 1.0
C5' B:DTP603 4.8 59.7 1.0
O2G B:DTP603 4.8 51.1 1.0
N B:ASP429 4.9 24.9 1.0
CA B:VAL428 4.9 29.8 1.0
N B:GLY416 4.9 23.9 1.0
O3G B:DTP603 5.0 60.8 1.0

Reference:

M.S.Liu, H.Y.Tsai, X.X.Liu, M.C.Ho, W.J.Wu, M.D.Tsai. Structural Mechanism For the Fidelity Modulation of Dna Polymerase Lambda J.Am.Chem.Soc. V. 138 2389 2016.
ISSN: ESSN 1520-5126
PubMed: 26836966
DOI: 10.1021/JACS.5B13368
Page generated: Wed Jul 9 05:10:02 2025

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