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Calcium in PDB 6isg: Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site

Enzymatic activity of Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site

All present enzymatic activity of Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site, PDB code: 6isg was solved by S.W.Linwu, M.Maestre-Reyna, M.D.Tsai, Y.H.Tu, W.H.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.81 / 3.40
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 208.078, 208.078, 208.078, 90.00, 90.00, 90.00
R / Rfree (%) 25.2 / 30.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site (pdb code 6isg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site, PDB code: 6isg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6isg

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Calcium binding site 1 out of 5 in the Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:0.3
occ:1.00
 OH A:TYR594 3.5 88.8 1.0
OH A:TYR583 3.8 0.4 1.0
NH1 A:ARG606 4.0 0.8 1.0
CE1 A:HIS545 4.0 90.9 1.0
NE2 A:HIS545 4.3 90.6 1.0
CD2 A:TYR402 4.4 83.0 1.0
CE2 A:TYR402 4.4 83.2 1.0
CG A:TYR402 4.5 83.4 1.0
CZ A:TYR402 4.5 83.7 1.0
CD1 A:TYR402 4.6 83.4 1.0
CE1 A:TYR402 4.6 83.6 1.0
CZ A:TYR594 4.6 89.4 1.0
CZ A:TYR583 4.7 0.3 1.0
CE2 A:TYR594 4.8 90.7 1.0

Calcium binding site 2 out of 5 in 6isg

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Calcium binding site 2 out of 5 in the Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:0.6
occ:1.00
 O21 A:PPV801 3.3 0.1 1.0
O22 A:PPV801 3.5 0.1 1.0
P1 A:PPV801 4.3 0.4 1.0
OPP A:PPV801 4.4 0.4 1.0
P2 A:PPV801 4.4 0.7 1.0
O31 A:PPV801 4.5 0.2 1.0
O12 A:PPV801 4.6 0.8 1.0

Calcium binding site 3 out of 5 in 6isg

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Calcium binding site 3 out of 5 in the Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:0.8
occ:1.00
 O A:VAL106 3.4 0.9 1.0
O A:HIS103 3.9 0.8 1.0
O A:ARG101 4.0 0.3 1.0
O A:VAL107 4.1 0.5 1.0
C A:VAL106 4.6 0.2 1.0
O A:ALA102 4.6 0.9 1.0
CA A:PRO104 4.7 0.1 1.0
C A:VAL107 4.8 0.4 1.0
C A:HIS103 4.8 0.9 1.0
CA A:VAL107 5.0 0.8 1.0

Calcium binding site 4 out of 5 in 6isg

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Calcium binding site 4 out of 5 in the Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca805

b:0.2
occ:1.00
 O A:LYS632 3.6 0.5 1.0
C A:LYS632 4.7 0.6 1.0
NH2 A:ARG585 4.7 0.6 1.0

Calcium binding site 5 out of 5 in 6isg

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Calcium binding site 5 out of 5 in the Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of 9N-I Dna Polymerase Incorporation with Dg in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:1.0
occ:1.00
 OP2 D:DG4 3.0 0.3 1.0
O D:HOH202 3.3 0.9 1.0
O D:HOH201 3.4 0.8 1.0
OP2 D:DC3 3.7 0.9 1.0
N7 D:DG4 4.3 0.3 1.0
C8 D:DG4 4.3 0.8 1.0
P D:DG4 4.5 0.1 1.0
O5' D:DG4 5.0 0.3 1.0

Reference:

S.W.Linwu, Y.H.Tu, T.Y.Tsai, M.Maestre-Reyna, M.S.Liu, W.J.Wu, J.Y.Huang, H.W.Chi, W.H.Chang, C.F.Chiou, A.H.Wang, J.Lee, M.D.Tsai. Thermococcus Sp. 9°N Dna Polymerase Exhibits 3'-Esterase Activity That Can Be Harnessed For Dna Sequencing. Commun Biol V. 2 224 2019.
ISSN: ESSN 2399-3642
PubMed: 31240262
DOI: 10.1038/S42003-019-0458-7
Page generated: Tue Jul 16 09:34:10 2024

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