Calcium in PDB 5cwr: Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp

Enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp, PDB code: 5cwr 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) 28.12 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.003, 148.712, 86.414, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp (pdb code 5cwr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp, PDB code: 5cwr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5cwr

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Calcium binding site 1 out of 4 in the Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:34.3
occ:1.00
 OD2 A:ASP427 2.5 30.5 1.0
OD1 A:ASP429 2.5 25.2 1.0
OD1 A:ASP490 2.5 31.3 1.0
O A:HOH733 2.6 32.3 1.0
O1A A:DCP601 2.7 16.7 1.0
O3' P:DC6 2.9 27.9 1.0
OD1 A:ASP427 3.0 28.8 1.0
CG A:ASP427 3.1 27.3 1.0
CG A:ASP429 3.4 26.5 1.0
C3' P:DC6 3.5 23.4 1.0
PA A:DCP601 3.5 18.5 1.0
CG A:ASP490 3.6 33.4 1.0
O2A A:DCP601 3.6 25.1 1.0
OD2 A:ASP429 3.7 25.7 1.0
O5' A:DCP601 3.7 24.2 1.0
C5' A:DCP601 4.0 20.4 1.0
CA A:CA603 4.0 25.6 1.0
C5' P:DC6 4.2 25.0 1.0
CB A:ASP490 4.2 25.0 1.0
C4' P:DC6 4.3 24.5 1.0
O5' P:DC6 4.5 27.1 1.0
CB A:ASP427 4.6 27.3 1.0
OD2 A:ASP490 4.6 30.7 1.0
OP1 P:DC6 4.7 23.9 1.0
C2' P:DC6 4.8 20.4 1.0
NH2 A:ARG488 4.8 23.2 1.0
CB A:ASP429 4.8 24.2 1.0
O A:HOH790 4.9 31.7 1.0
O3A A:DCP601 5.0 26.6 1.0

Calcium binding site 2 out of 4 in 5cwr

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Calcium binding site 2 out of 4 in the Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:25.6
occ:1.00
 OD1 A:ASP427 2.2 28.8 1.0
OD2 A:ASP429 2.4 25.7 1.0
O1A A:DCP601 2.4 16.7 1.0
O2B A:DCP601 2.4 20.9 1.0
O2G A:DCP601 2.5 20.9 1.0
O A:HOH716 2.5 25.7 1.0
O A:ASP427 2.8 33.1 1.0
CG A:ASP427 3.4 27.3 1.0
CG A:ASP429 3.4 26.5 1.0
PB A:DCP601 3.6 21.2 1.0
PG A:DCP601 3.6 21.5 1.0
C A:ASP427 3.7 26.2 1.0
PA A:DCP601 3.7 18.5 1.0
N A:ASP427 3.7 27.1 1.0
O1G A:DCP601 3.8 24.1 1.0
OD1 A:ASP429 3.9 25.2 1.0
O3B A:DCP601 4.0 26.4 1.0
O3A A:DCP601 4.0 26.6 1.0
CA A:CA602 4.0 34.3 1.0
CA A:ASP427 4.1 30.3 1.0
OG A:SER417 4.1 23.6 1.0
OD2 A:ASP427 4.3 30.5 1.0
O A:HOH714 4.3 27.3 1.0
CB A:ASP427 4.3 27.3 1.0
N A:SER417 4.4 25.7 1.0
C5' A:DCP601 4.6 20.4 1.0
O A:HOH790 4.6 31.7 1.0
CA A:GLY416 4.6 22.8 1.0
CB A:ASP429 4.7 24.2 1.0
N A:GLY426 4.7 28.4 1.0
O5' A:DCP601 4.7 24.2 1.0
N A:VAL428 4.7 26.6 1.0
O2A A:DCP601 4.7 25.1 1.0
C A:GLY426 4.8 26.7 1.0
O1B A:DCP601 4.8 23.2 1.0
N A:ASP429 4.8 25.6 1.0
O3G A:DCP601 4.9 30.6 1.0
O A:HOH733 4.9 32.3 1.0
CB A:SER417 5.0 20.4 1.0
CA A:GLY426 5.0 30.5 1.0

Calcium binding site 3 out of 4 in 5cwr

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Calcium binding site 3 out of 4 in the Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:35.2
occ:1.00
 OD2 B:ASP427 2.5 30.1 1.0
OD2 B:ASP490 2.5 25.1 1.0
OD1 B:ASP429 2.5 27.5 1.0
O3' E:DC6 2.7 23.8 1.0
O2A B:DCP601 2.8 17.5 1.0
CG B:ASP427 3.2 27.1 1.0
OD1 B:ASP427 3.2 29.3 1.0
CG B:ASP429 3.4 24.5 1.0
O5' B:DCP601 3.5 23.5 1.0
C3' E:DC6 3.6 21.8 1.0
OD2 B:ASP429 3.6 26.0 1.0
PA B:DCP601 3.6 24.8 1.0
CG B:ASP490 3.6 30.0 1.0
C5' B:DCP601 3.8 17.1 1.0
CA B:CA603 4.0 28.7 1.0
O1A B:DCP601 4.0 25.0 1.0
CB B:ASP490 4.3 23.9 1.0
C5' E:DC6 4.3 21.7 1.0
C4' E:DC6 4.3 23.4 1.0
O B:HOH778 4.5 26.5 1.0
OD1 B:ASP490 4.6 31.4 1.0
O5' E:DC6 4.6 23.1 1.0
CB B:ASP427 4.7 28.1 1.0
OP1 E:DC6 4.8 22.0 1.0
CB B:ASP429 4.8 22.7 1.0
NH2 B:ARG488 4.8 22.8 1.0
C2' E:DC6 4.9 22.2 1.0

Calcium binding site 4 out of 4 in 5cwr

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Calcium binding site 4 out of 4 in the Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Dna Polymerase Lambda L431A Mutant in Complex with A One Nucleotide Dna Gap and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:28.7
occ:1.00
 OD1 B:ASP427 2.2 29.3 1.0
OD2 B:ASP429 2.3 26.0 1.0
O2A B:DCP601 2.4 17.5 1.0
O1B B:DCP601 2.4 17.7 1.0
O2G B:DCP601 2.5 22.3 1.0
O B:HOH717 2.6 25.5 1.0
O B:ASP427 3.0 27.4 1.0
CG B:ASP429 3.4 24.5 1.0
CG B:ASP427 3.4 27.1 1.0
PB B:DCP601 3.6 19.4 1.0
PG B:DCP601 3.6 24.5 1.0
PA B:DCP601 3.7 24.8 1.0
C B:ASP427 3.8 24.2 1.0
OD1 B:ASP429 3.8 27.5 1.0
CA B:CA602 4.0 35.2 1.0
O3G B:DCP601 4.0 24.6 1.0
N B:ASP427 4.0 26.3 1.0
O3B B:DCP601 4.0 25.0 1.0
O3A B:DCP601 4.1 26.5 1.0
O B:HOH727 4.1 22.7 1.0
OD2 B:ASP427 4.1 30.1 1.0
OG B:SER417 4.2 23.5 1.0
CA B:ASP427 4.3 27.4 1.0
N B:SER417 4.3 24.8 1.0
O B:HOH778 4.4 26.5 1.0
C5' B:DCP601 4.4 17.1 1.0
CB B:ASP427 4.5 28.1 1.0
CA B:GLY416 4.5 19.6 1.0
O5' B:DCP601 4.6 23.5 1.0
CB B:ASP429 4.6 22.7 1.0
N B:VAL428 4.7 26.9 1.0
O1A B:DCP601 4.7 25.0 1.0
O2B B:DCP601 4.8 19.9 1.0
N B:ASP429 4.9 23.1 1.0
O1G B:DCP601 4.9 29.2 1.0
N B:GLY426 4.9 25.6 1.0
C B:GLY416 5.0 23.2 1.0
C B:VAL428 5.0 27.2 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: Sat Dec 12 05:20:31 2020

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