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

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

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

Protein crystallography data

The structure of Structure of 9N-I Dna Polymerase Incorporation with Dt in the Active Site, PDB code: 6isf 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) 46.38 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.088, 107.361, 255.665, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 27.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of 9N-I Dna Polymerase Incorporation with Dt in the Active Site (pdb code 6isf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Structure of 9N-I Dna Polymerase Incorporation with Dt in the Active Site, PDB code: 6isf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 6isf

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Calcium binding site 1 out of 7 in the Structure of 9N-I Dna Polymerase Incorporation with Dt 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 Dt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:81.0
occ:1.00
 O A:LEU575 2.7 56.7 1.0
O A:LEU571 2.9 57.4 1.0
O A:GLY573 3.0 51.0 1.0
O A:ASN568 3.0 54.5 1.0
C A:LEU575 3.8 53.1 1.0
C A:LEU571 3.8 55.8 1.0
C A:ASN568 4.1 55.7 1.0
C A:GLY573 4.1 52.4 1.0
CB A:LEU571 4.1 55.3 1.0
O A:LEU574 4.2 55.4 1.0
O A:PRO572 4.2 52.0 1.0
C A:LEU574 4.4 53.9 1.0
C A:PRO572 4.4 52.9 1.0
CA A:LEU571 4.5 57.1 1.0
N A:LEU575 4.6 52.3 1.0
N A:GLY573 4.6 53.9 1.0
N A:GLU576 4.7 52.5 1.0
CA A:LEU575 4.7 53.1 1.0
N A:PRO572 4.7 53.5 1.0
CA A:GLU576 4.7 51.7 1.0
CA A:ASN568 4.8 53.9 1.0
CB A:GLU576 4.8 54.0 1.0
CA A:GLY573 4.9 53.0 1.0
N A:LEU571 4.9 58.9 1.0
CA A:PRO572 5.0 52.3 1.0
CB A:ASN568 5.0 53.4 1.0
N A:PRO569 5.0 59.3 1.0

Calcium binding site 2 out of 7 in 6isf

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Calcium binding site 2 out of 7 in the Structure of 9N-I Dna Polymerase Incorporation with Dt 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 Dt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:0.4
occ:1.00
 CE1 A:HIS545 3.7 49.2 1.0
OH A:TYR594 3.7 48.0 1.0
CD2 A:TYR402 3.9 65.2 1.0
OH A:TYR583 3.9 66.2 1.0
NE2 A:HIS545 4.1 50.4 1.0
CE2 A:TYR402 4.1 65.7 1.0
CG A:TYR402 4.2 62.8 1.0
CE2 A:TYR594 4.4 47.9 1.0
CZ A:TYR583 4.4 62.8 1.0
CZ A:TYR594 4.5 47.6 1.0
CZ A:TYR402 4.6 66.6 1.0
CD1 A:TYR402 4.7 63.4 1.0
CB A:TYR402 4.7 59.0 1.0
CG2 A:THR604 4.7 54.4 1.0
CE2 A:TYR583 4.8 62.5 1.0
CE1 A:TYR402 4.9 64.7 1.0
CG2 A:VAL596 4.9 53.3 1.0
ND1 A:HIS545 5.0 48.3 1.0

Calcium binding site 3 out of 7 in 6isf

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Calcium binding site 3 out of 7 in the Structure of 9N-I Dna Polymerase Incorporation with Dt 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 Dt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:85.6
occ:1.00
 NH1 B:ARG606 3.5 59.4 1.0
OH B:TYR583 4.0 64.8 1.0
OH B:TYR594 4.0 45.6 1.0
CG2 B:THR604 4.5 54.1 1.0
CE1 B:HIS545 4.5 47.1 1.0
CD2 B:TYR402 4.5 51.7 1.0
CZ B:TYR583 4.6 64.9 1.0
CE2 B:TYR402 4.7 50.0 1.0
CZ B:ARG606 4.7 55.0 1.0
CG B:TYR402 4.8 52.3 1.0
CE2 B:TYR583 4.8 63.5 1.0

Calcium binding site 4 out of 7 in 6isf

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Calcium binding site 4 out of 7 in the Structure of 9N-I Dna Polymerase Incorporation with Dt 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 Dt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:0.9
occ:1.00
 OD2 B:ASP343 3.1 52.3 1.0
OD1 B:ASP4 3.2 61.2 1.0
OE2 B:GLU251 3.5 89.6 1.0
OD2 B:ASP4 3.7 65.8 1.0
CG B:ASP343 3.8 50.8 1.0
CG B:ASP4 3.9 61.0 1.0
OD1 B:ASP343 3.9 52.4 1.0
OG B:SER340 4.0 45.5 1.0
O B:THR5 4.3 49.2 1.0
CE B:LYS118 4.6 54.6 1.0
O B:HOH908 4.6 30.4 1.0
CE3 B:TRP342 4.6 47.9 1.0
CB B:SER340 4.7 44.9 1.0
CD B:GLU251 4.8 85.5 1.0

Calcium binding site 5 out of 7 in 6isf

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Calcium binding site 5 out of 7 in the Structure of 9N-I Dna Polymerase Incorporation with Dt 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 Dt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:65.4
occ:1.00
 O B:ARG101 2.6 54.6 1.0
O B:VAL106 2.7 51.4 1.0
O B:HIS103 2.8 53.1 1.0
O B:ALA102 3.5 56.3 1.0
C B:HIS103 3.7 53.5 1.0
C B:ARG101 3.8 55.2 1.0
C B:ALA102 3.8 55.6 1.0
C B:VAL106 3.9 51.9 1.0
CA B:PRO104 4.2 54.0 1.0
O B:PRO104 4.2 55.6 1.0
N B:HIS103 4.3 53.3 1.0
CA B:ALA102 4.4 56.3 1.0
N B:PRO104 4.4 54.7 1.0
C B:PRO104 4.4 53.2 1.0
N B:ALA102 4.5 55.7 1.0
N B:VAL106 4.6 54.5 1.0
CA B:VAL106 4.6 53.8 1.0
CB B:VAL106 4.6 55.0 1.0
CA B:HIS103 4.7 52.0 1.0
O B:VAL107 4.8 47.0 1.0
CA B:ARG101 4.9 53.9 1.0
N B:VAL107 4.9 50.2 1.0

Calcium binding site 6 out of 7 in 6isf

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Calcium binding site 6 out of 7 in the Structure of 9N-I Dna Polymerase Incorporation with Dt in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of 9N-I Dna Polymerase Incorporation with Dt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:90.5
occ:1.00
 O B:LEU575 2.8 63.3 1.0
O B:ASN568 2.9 72.4 1.0
O B:LEU571 3.1 65.2 1.0
OE1 B:GLU576 3.3 76.9 1.0
O B:GLY573 3.6 59.0 1.0
C B:ASN568 3.9 72.6 1.0
C B:LEU575 3.9 61.4 1.0
C B:LEU571 4.0 65.9 1.0
CB B:LEU571 4.1 68.3 1.0
CD B:GLU576 4.4 73.5 1.0
CA B:LEU571 4.5 68.3 1.0
CA B:ASN568 4.5 69.0 1.0
CB B:GLU576 4.6 65.3 1.0
CA B:GLU576 4.6 62.3 1.0
N B:GLU576 4.7 61.4 1.0
C B:GLY573 4.7 61.9 1.0
N B:LEU571 4.8 70.7 1.0
CB B:ASN568 4.8 67.6 1.0
N B:PRO569 4.8 77.3 1.0
N B:LEU575 4.9 63.4 1.0
O B:PRO572 4.9 65.5 1.0
N B:PRO572 5.0 65.2 1.0
C B:PRO572 5.0 63.2 1.0

Calcium binding site 7 out of 7 in 6isf

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Calcium binding site 7 out of 7 in the Structure of 9N-I Dna Polymerase Incorporation with Dt in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of 9N-I Dna Polymerase Incorporation with Dt in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:75.1
occ:1.00
 CD1 B:LEU457 4.0 56.4 1.0
CB B:LEU457 4.1 56.5 1.0
CA B:LEU457 4.3 56.2 1.0
CB B:ALA490 4.5 47.1 1.0
NH1 B:ARG460 4.5 64.0 1.0
OG B:SER407 4.6 65.8 1.0
CG B:LEU457 4.6 56.2 1.0
N B:LEU457 4.7 51.7 1.0
CB B:PRO410 4.8 45.3 1.0
CB B:SER407 4.9 64.6 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 09:33:59 2024

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