Calcium in PDB 8dt6: Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis

Protein crystallography data

The structure of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis, PDB code: 8dt6 was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.26 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.41, 88.01, 100.24, 90, 95.75, 90
R / Rfree (%) 17.6 / 21.8

Other elements in 8dt6:

The structure of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis (pdb code 8dt6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis, PDB code: 8dt6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 8dt6

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Calcium binding site 1 out of 9 in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:93.3
occ:1.00
 O A:HOH546 2.6 63.7 1.0
OE1 A:GLN11 2.8 56.9 1.0
O A:PHE81 2.9 65.2 1.0
CD A:GLN11 3.9 57.3 1.0
C A:PHE81 4.1 63.4 1.0
O A:HOH563 4.2 67.3 1.0
CA A:GLY82 4.2 69.4 1.0
C A:GLY82 4.3 72.6 1.0
O A:LYS79 4.4 49.6 1.0
O A:GLY82 4.5 73.1 1.0
OD1 A:ASP83 4.5 91.2 1.0
NE2 A:GLN11 4.5 58.8 1.0
N A:GLY82 4.6 67.0 1.0
O A:ILE78 4.7 51.9 1.0
N A:ASP83 4.7 82.2 1.0
OG A:SER7 5.0 65.2 1.0

Calcium binding site 2 out of 9 in 8dt6

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Calcium binding site 2 out of 9 in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:93.0
occ:1.00
 O B:HOH600 2.8 75.2 1.0
OE1 B:GLU364 3.3 64.1 1.0
OE2 B:GLU364 3.3 60.7 1.0
CD B:GLU364 3.7 58.2 1.0
O B:HOH561 3.9 59.6 1.0
O B:HOH509 4.0 57.8 1.0
OE2 B:GLU141 4.1 64.1 1.0
CD B:GLU141 4.1 66.4 1.0
O B:GLY359 4.2 63.3 1.0
CG B:GLU141 4.4 55.5 1.0
CG B:GLU361 4.4 73.4 1.0
OE1 B:GLU141 4.6 60.5 1.0
OE2 B:GLU361 4.8 96.1 1.0
CD B:GLU361 5.0 84.7 1.0

Calcium binding site 3 out of 9 in 8dt6

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Calcium binding site 3 out of 9 in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:64.5
occ:1.00
 O B:HOH588 2.4 57.4 1.0
OD2 B:ASP40 2.5 67.5 1.0
O B:SER61 2.5 56.0 1.0
OD1 B:ASP40 2.6 61.8 1.0
CG B:ASP40 2.9 54.2 1.0
O B:HOH631 3.0 62.1 1.0
C B:SER61 3.7 64.8 1.0
OE1 B:GLU62 3.7 82.2 1.0
N B:SER61 4.3 56.9 1.0
CB B:ASP40 4.4 55.8 1.0
OG B:SER61 4.5 58.3 1.0
CA B:SER61 4.6 57.9 1.0
N B:GLU62 4.6 64.4 1.0
CA B:GLU62 4.7 70.3 1.0
CD B:GLU62 4.9 77.5 1.0

Calcium binding site 4 out of 9 in 8dt6

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Calcium binding site 4 out of 9 in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:53.7
occ:1.00
 O C:HOH623 2.5 45.0 1.0
O C:HOH654 2.5 50.2 1.0
OE1 C:GLU141 2.6 49.7 1.0
OE1 C:GLU364 2.7 45.7 1.0
OE2 C:GLU364 2.7 47.0 1.0
OE2 C:GLU141 2.8 44.8 1.0
CD C:GLU364 3.1 47.1 1.0
CD C:GLU141 3.1 47.4 1.0
CG C:GLU361 3.6 67.8 1.0
OE2 C:GLU361 3.8 77.9 1.0
CD C:GLU361 4.0 69.4 1.0
O C:HOH510 4.1 38.7 1.0
O C:GLY359 4.2 60.6 1.0
O C:HOH603 4.4 47.0 1.0
O C:HOH653 4.5 61.1 1.0
N C:GLU361 4.5 50.5 1.0
CG C:GLU364 4.6 40.2 1.0
CG C:GLU141 4.6 42.5 1.0
OH C:TYR184 4.8 43.0 1.0
NH1 C:ARG186 4.8 34.9 1.0
CB C:GLU361 4.9 55.5 1.0

Calcium binding site 5 out of 9 in 8dt6

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Calcium binding site 5 out of 9 in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:80.3
occ:1.00
 O C:HOH586 2.3 61.6 1.0
O C:SER61 2.5 75.8 1.0
OD2 C:ASP40 2.8 64.8 1.0
OD1 C:ASP40 2.8 65.4 1.0
CG C:ASP40 3.1 58.7 1.0
C C:SER61 3.7 73.1 1.0
N C:SER61 4.1 55.9 1.0
CA C:SER61 4.5 58.6 1.0
CB C:ASP40 4.6 52.3 1.0
N C:GLU62 4.6 87.5 1.0
CA C:GLU62 4.8 88.4 1.0
OG C:SER61 5.0 64.4 1.0

Calcium binding site 6 out of 9 in 8dt6

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Calcium binding site 6 out of 9 in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca404

b:36.8
occ:1.00
 OD1 C:ASN194 2.3 42.4 1.0
O C:HOH620 2.4 36.0 1.0
OE2 C:GLU168 2.5 39.7 1.0
O C:HOH633 2.5 38.0 1.0
OE1 C:GLU168 2.5 40.5 1.0
CD C:GLU168 2.8 43.6 1.0
CG C:ASN194 3.3 37.0 1.0
ND2 C:ASN194 3.7 38.6 1.0
CG C:GLU168 4.3 41.1 1.0
O C:HOH551 4.6 35.0 1.0
CB C:ASN167 4.7 36.7 1.0
CB C:ASN194 4.7 40.4 1.0
O C:HOH643 4.7 42.5 1.0

Calcium binding site 7 out of 9 in 8dt6

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Calcium binding site 7 out of 9 in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:88.5
occ:1.00
 O D:HOH567 2.9 60.5 1.0
OE1 D:GLN11 3.0 52.5 1.0
O D:HOH622 3.1 61.8 1.0
O D:PHE81 3.4 59.7 1.0
CD D:GLN11 4.0 49.7 1.0
OD1 D:ASP83 4.1 88.3 1.0
C D:GLY82 4.3 70.7 1.0
O D:GLY82 4.4 73.7 1.0
C D:PHE81 4.4 57.7 1.0
CA D:GLY82 4.5 68.3 1.0
NE2 D:GLN11 4.5 55.3 1.0
N D:ASP83 4.8 80.1 1.0
CA D:GLY8 4.8 54.0 1.0
O D:LYS79 4.8 53.0 1.0
N D:GLY82 4.9 58.7 1.0
CG D:ASP83 4.9 92.3 1.0
OG D:SER7 5.0 58.9 1.0

Calcium binding site 8 out of 9 in 8dt6

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Calcium binding site 8 out of 9 in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:74.6
occ:1.00
 O D:HOH582 2.5 74.7 1.0
OD2 D:ASP40 2.5 78.9 1.0
O D:HOH601 2.5 59.3 1.0
O D:SER61 2.6 71.6 1.0
OD1 D:ASP40 2.6 73.2 1.0
CG D:ASP40 2.9 70.5 1.0
C D:SER61 3.7 65.9 1.0
OE1 D:GLU62 4.2 81.0 1.0
N D:SER61 4.2 63.1 1.0
CB D:ASP40 4.3 60.6 1.0
CA D:SER61 4.6 60.5 1.0
OG D:SER61 4.6 60.8 1.0
N D:GLU62 4.6 64.2 1.0
CA D:GLU62 4.7 67.9 1.0
CD D:GLU62 5.0 82.5 1.0

Calcium binding site 9 out of 9 in 8dt6

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Calcium binding site 9 out of 9 in the Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:55.6
occ:1.00
 OD1 D:ASN194 2.4 57.3 1.0
OE1 D:GLU168 2.5 59.4 1.0
OE2 D:GLU168 2.5 70.6 1.0
CD D:GLU168 2.8 66.7 1.0
CG D:ASN194 3.4 55.0 1.0
ND2 D:ASN194 3.9 49.1 1.0
CG D:GLU168 4.3 68.5 1.0
CB D:ASN167 4.5 49.9 1.0
O D:HOH523 4.6 47.8 1.0
CB D:ASN194 4.8 45.5 1.0
N D:GLU168 4.9 45.6 1.0

Reference:

N.D.Debouver, J.Abendroth, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Dna Polymerase III Beta Subunit From Elizabethkingia Anophelis To Be Published.
Page generated: Tue Apr 4 19:35:44 2023

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