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Calcium in PDB 6is7: Structure of 9N-I Dna Polymerase Incorporation with Da in the Active Site

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

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

Protein crystallography data

The structure of Structure of 9N-I Dna Polymerase Incorporation with Da in the Active Site, PDB code: 6is7 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) 46.29 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.951, 106.767, 255.903, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 27.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of 9N-I Dna Polymerase Incorporation with Da in the Active Site (pdb code 6is7). 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 Da in the Active Site, PDB code: 6is7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 6is7

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

b:1.0
occ:1.00
 O A:LEU575 3.0 82.5 1.0
O A:ASN568 3.1 85.9 1.0
O A:LEU571 3.1 85.3 1.0
O A:GLY573 3.3 81.9 1.0
O A:HOH932 3.7 71.9 1.0
C A:ASN568 4.0 87.7 1.0
C A:LEU575 4.0 79.7 1.0
C A:LEU571 4.1 84.5 1.0
CB A:LEU571 4.4 82.5 1.0
O A:PRO572 4.5 81.6 1.0
C A:GLY573 4.5 81.7 1.0
N A:LEU575 4.6 78.5 1.0
CA A:ASN568 4.7 86.1 1.0
C A:PRO572 4.7 82.5 1.0
CA A:LEU571 4.7 84.2 1.0
N A:GLU576 4.8 77.4 1.0
CB A:ASN568 4.8 85.9 1.0
CA A:GLU576 4.8 77.2 1.0
N A:PRO569 4.8 90.9 1.0
CA A:LEU575 4.9 79.0 1.0

Calcium binding site 2 out of 7 in 6is7

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

b:0.8
occ:1.00
 OH A:TYR583 3.5 78.2 1.0
CE1 A:HIS545 3.9 73.2 1.0
CD2 A:TYR402 4.0 81.7 1.0
CG A:TYR402 4.1 81.5 1.0
CZ A:TYR583 4.1 78.8 1.0
OH A:TYR594 4.3 65.6 1.0
CE2 A:TYR402 4.3 80.6 1.0
CE2 A:TYR583 4.3 78.4 1.0
NE2 A:HIS545 4.4 71.6 1.0
CD1 A:TYR402 4.5 81.4 1.0
CB A:TYR402 4.5 82.2 1.0
CZ A:TYR402 4.7 80.5 1.0
CE1 A:TYR402 4.8 80.8 1.0
O A:HOH954 4.8 81.7 1.0
CG2 A:VAL596 4.8 82.0 1.0
NH1 A:ARG606 4.8 91.8 1.0
CE2 A:TYR594 4.8 69.6 1.0
CG2 A:THR604 4.8 76.2 1.0

Calcium binding site 3 out of 7 in 6is7

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

b:0.9
occ:1.00
 NH1 B:ARG606 3.7 81.5 1.0
OH B:TYR594 4.2 70.7 1.0
OH B:TYR583 4.3 89.3 1.0
CE2 B:TYR402 4.5 77.9 1.0
CD2 B:TYR402 4.5 79.0 1.0
CG2 B:THR604 4.6 82.6 1.0
CZ B:TYR402 4.8 77.4 1.0
CZ B:ARG606 4.8 80.1 1.0
CG B:TYR402 4.8 78.7 1.0
CE1 B:HIS545 4.9 72.6 1.0

Calcium binding site 4 out of 7 in 6is7

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

b:0.7
occ:1.00
 OD2 B:ASP343 3.0 75.1 1.0
OD2 B:ASP4 3.2 87.4 1.0
OE2 B:GLU251 3.3 0.4 1.0
OD1 B:ASP4 3.4 84.7 1.0
OD1 B:ASP343 3.6 73.7 1.0
CG B:ASP4 3.7 83.8 1.0
CG B:ASP343 3.7 73.2 1.0
OG B:SER340 4.0 69.4 1.0
CE3 B:TRP342 4.2 74.8 1.0
O B:HOH926 4.4 60.4 1.0
CE B:LYS118 4.5 75.0 1.0
CD B:GLU251 4.5 0.1 1.0
O B:THR5 4.5 68.6 1.0
CZ3 B:TRP342 4.6 75.1 1.0
CB B:SER340 4.7 69.5 1.0
OE1 B:GLU251 5.0 1.0 1.0

Calcium binding site 5 out of 7 in 6is7

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

b:77.8
occ:1.00
 O B:ARG101 2.5 76.0 1.0
O B:VAL106 2.5 74.5 1.0
O B:HIS103 2.6 76.0 1.0
O B:ALA102 3.5 81.3 1.0
C B:HIS103 3.5 78.4 1.0
C B:ARG101 3.7 76.4 1.0
C B:VAL106 3.7 73.4 1.0
C B:ALA102 3.8 79.6 1.0
CA B:PRO104 4.1 82.2 1.0
O B:PRO104 4.1 80.9 1.0
N B:HIS103 4.2 77.8 1.0
N B:PRO104 4.2 81.4 1.0
C B:PRO104 4.3 80.7 1.0
CA B:ALA102 4.3 79.4 1.0
N B:VAL106 4.3 75.7 1.0
CA B:VAL106 4.4 73.5 1.0
CB B:VAL106 4.4 73.0 1.0
N B:ALA102 4.4 77.5 1.0
CA B:HIS103 4.5 78.3 1.0
CA B:ARG101 4.8 74.7 1.0
N B:VAL107 4.8 73.0 1.0
O B:VAL107 4.8 72.9 1.0
CG1 B:VAL106 4.8 71.4 1.0

Calcium binding site 6 out of 7 in 6is7

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Calcium binding site 6 out of 7 in the Structure of 9N-I Dna Polymerase Incorporation with Da 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 Da in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:0.0
occ:1.00
 O B:LEU575 2.6 82.8 1.0
O B:LEU571 3.1 88.2 1.0
O B:ASN568 3.1 96.1 1.0
O B:GLY573 3.5 81.2 1.0
C B:LEU575 3.6 80.0 1.0
C B:LEU571 4.0 88.2 1.0
C B:ASN568 4.0 96.7 1.0
CB B:LEU571 4.1 88.6 1.0
N B:LEU575 4.3 79.0 1.0
N B:GLU576 4.3 79.3 1.0
O B:PRO572 4.4 82.5 1.0
CA B:GLU576 4.4 80.2 1.0
CA B:LEU575 4.5 79.0 1.0
CA B:ASN568 4.6 93.9 1.0
C B:GLY573 4.6 80.8 1.0
CA B:LEU571 4.6 90.1 1.0
CB B:GLU576 4.7 81.5 1.0
C B:PRO572 4.7 83.5 1.0
CB B:ASN568 4.7 93.6 1.0
CD B:GLU576 4.8 85.6 1.0
C B:LEU574 4.9 77.6 1.0
N B:LEU571 5.0 94.8 1.0
N B:PRO572 5.0 86.3 1.0
N B:PRO569 5.0 0.6 1.0

Calcium binding site 7 out of 7 in 6is7

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Calcium binding site 7 out of 7 in the Structure of 9N-I Dna Polymerase Incorporation with Da 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 Da in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:0.1
occ:1.00
 CB B:ALA490 4.0 65.8 1.0
CB B:LEU457 4.1 79.1 1.0
CA B:LEU457 4.1 78.5 1.0
N B:LEU457 4.4 75.3 1.0
CD1 B:LEU457 4.5 81.6 1.0
OG B:SER407 4.8 80.3 1.0
CB B:PRO410 4.9 59.5 1.0
CG B:LEU457 4.9 81.6 1.0
NH1 B:ARG460 4.9 80.1 1.0
O B:LEU453 4.9 68.0 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: Wed Jul 9 14:59:13 2025

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