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Calcium in PDB 1g8k: Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis

Protein crystallography data

The structure of Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis, PDB code: 1g8k was solved by P.J.Ellis, T.Conrads, R.Hille, P.Kuhn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.80 / 1.64
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 90.740, 109.520, 117.640, 97.71, 90.00, 96.43
R / Rfree (%) 15.4 / 17.9

Other elements in 1g8k:

The structure of Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms
Mercury (Hg) 12 atoms
Iron (Fe) 20 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis (pdb code 1g8k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis, PDB code: 1g8k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1g8k

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Calcium binding site 1 out of 8 in the Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis


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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 Analysis of Arsenite Oxidase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5007

b:18.2
occ:1.00
 O A:HOH7807 2.2 39.0 1.0
O B:HOH6164 2.4 18.5 1.0
O A:HOH7806 2.4 20.1 1.0
O B:HOH6165 2.4 16.4 1.0
O B:HOH6166 2.5 19.5 1.0
O A:GLY825 2.5 21.6 1.0
O A:HOH7805 2.6 18.7 1.0
C A:GLY825 3.6 22.2 1.0
O A:HOH7486 4.1 33.3 1.0
N A:GLY825 4.2 18.4 1.0
CA A:GLY825 4.3 20.9 1.0
O A:ARG823 4.4 14.5 1.0
O B:HOH6083 4.4 28.3 1.0
O A:HOH7365 4.5 25.9 1.0
OXT A:GLY825 4.5 24.2 1.0
OD1 B:ASP70 4.5 18.9 1.0
OE1 B:GLU84 4.5 14.9 1.0
O A:HOH7746 4.7 36.4 1.0
O A:HOH7101 4.7 14.1 1.0
CB A:SER821 4.7 11.7 1.0
OE2 B:GLU84 4.8 15.7 1.0
OG B:SER73 4.8 13.5 1.0
O A:HOH7318 4.9 27.1 1.0
CB B:SER73 4.9 13.4 1.0

Calcium binding site 2 out of 8 in 1g8k

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Calcium binding site 2 out of 8 in the Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis


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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 Analysis of Arsenite Oxidase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5008

b:12.9
occ:1.00
 OD1 A:ASP783 2.4 14.1 1.0
O A:SER754 2.4 12.8 1.0
OE1 A:GLN467 2.4 14.2 1.0
O A:HOH7808 2.5 15.8 1.0
OD2 C:ASP129 2.5 13.8 1.0
O C:HOH7910 2.5 13.1 1.0
OD1 C:ASP129 2.5 12.4 1.0
CG C:ASP129 2.8 13.4 1.0
CD A:GLN467 3.3 15.4 1.0
CG A:ASP783 3.5 13.9 1.0
C A:SER754 3.6 13.5 1.0
NH2 A:ARG470 3.9 14.2 1.0
OE2 C:GLU130 4.0 14.4 1.0
N A:SER754 4.0 13.6 1.0
CB A:ASP783 4.0 13.5 1.0
CG A:GLN467 4.1 15.9 1.0
NE2 A:GLN467 4.1 16.6 1.0
O A:HOH7116 4.2 15.1 1.0
CA A:SER754 4.3 13.9 1.0
CB C:ASP129 4.3 13.5 1.0
O C:ALA127 4.4 16.1 1.0
CB A:GLN467 4.4 15.6 1.0
CB A:SER754 4.5 14.6 1.0
OD2 A:ASP783 4.5 14.0 1.0
N A:THR755 4.6 12.6 1.0
O C:HOH7343 4.7 23.3 1.0
CA A:THR755 4.8 12.8 1.0
CD C:GLU130 4.8 13.4 1.0
CG C:GLU130 4.9 12.8 1.0
N C:ASP129 5.0 14.2 1.0

Calcium binding site 3 out of 8 in 1g8k

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Calcium binding site 3 out of 8 in the Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis


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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 Analysis of Arsenite Oxidase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca5107

b:19.3
occ:1.00
 O C:GLY825 2.2 21.6 1.0
O D:HOH6157 2.3 18.8 1.0
O C:HOH7912 2.4 21.1 1.0
O C:HOH7913 2.4 38.3 1.0
O D:HOH6159 2.4 19.7 1.0
O D:HOH6158 2.4 17.5 1.0
O C:HOH7911 2.6 19.7 1.0
C C:GLY825 3.4 22.0 1.0
N C:GLY825 4.1 18.1 1.0
O D:HOH6089 4.1 28.4 1.0
CA C:GLY825 4.2 21.3 1.0
OXT C:GLY825 4.2 23.8 1.0
O C:ARG823 4.4 15.1 1.0
O D:HOH6106 4.5 30.6 1.0
OD1 D:ASP70 4.5 18.7 1.0
O C:HOH7422 4.5 25.7 1.0
OE1 D:GLU84 4.5 15.7 1.0
O D:HOH6029 4.7 16.6 1.0
OE2 D:GLU84 4.8 15.1 1.0
CB C:SER821 4.8 12.1 1.0
OG D:SER73 4.9 15.3 1.0

Calcium binding site 4 out of 8 in 1g8k

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Calcium binding site 4 out of 8 in the Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis


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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 Analysis of Arsenite Oxidase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca5108

b:14.1
occ:1.00
 OD1 C:ASP783 2.3 14.8 1.0
OE1 C:GLN467 2.4 15.5 1.0
O C:SER754 2.4 14.2 1.0
O C:HOH7914 2.5 16.3 1.0
OD1 A:ASP129 2.5 13.6 1.0
OD2 A:ASP129 2.5 15.4 1.0
O A:HOH7809 2.6 13.5 1.0
CG A:ASP129 2.8 13.9 1.0
CD C:GLN467 3.3 15.8 1.0
CG C:ASP783 3.5 14.5 1.0
C C:SER754 3.6 14.9 1.0
OE2 A:GLU130 4.0 16.5 1.0
NH2 C:ARG470 4.0 13.4 1.0
N C:SER754 4.0 13.9 1.0
CB C:ASP783 4.1 13.5 1.0
CG C:GLN467 4.1 16.1 1.0
O C:HOH7132 4.1 16.9 1.0
NE2 C:GLN467 4.1 17.4 1.0
O A:ALA127 4.3 17.7 1.0
CA C:SER754 4.3 14.3 1.0
CB C:GLN467 4.4 15.3 1.0
CB A:ASP129 4.4 15.2 1.0
OD2 C:ASP783 4.5 14.0 1.0
CB C:SER754 4.6 15.1 1.0
N C:THR755 4.6 14.5 1.0
O A:HOH7270 4.7 23.4 1.0
CA C:THR755 4.8 13.7 1.0
CD A:GLU130 4.8 16.0 1.0
CG A:GLU130 4.9 14.1 1.0
N A:ASP129 5.0 15.6 1.0
CB C:THR755 5.0 14.1 1.0

Calcium binding site 5 out of 8 in 1g8k

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Calcium binding site 5 out of 8 in the Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis


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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 Analysis of Arsenite Oxidase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca5207

b:18.2
occ:1.00
 O F:HOH6164 2.3 17.6 1.0
O F:HOH6165 2.4 18.5 1.0
O E:HOH7885 2.4 29.8 1.0
O E:HOH7884 2.4 19.6 1.0
O E:GLY825 2.5 20.5 1.0
O E:HOH7882 2.5 17.6 1.0
O E:HOH7883 2.6 18.4 1.0
C E:GLY825 3.5 21.1 1.0
N E:GLY825 4.1 16.3 1.0
O F:HOH6086 4.1 29.9 1.0
CA E:GLY825 4.3 19.6 1.0
O E:ARG823 4.4 13.5 1.0
OXT E:GLY825 4.4 21.9 1.0
OD1 F:ASP70 4.5 18.7 1.0
O F:HOH6110 4.5 35.2 1.0
O E:HOH7304 4.5 21.8 1.0
OE1 F:GLU84 4.5 14.4 1.0
O E:HOH7113 4.7 14.2 1.0
CB E:SER821 4.7 10.5 1.0
OG F:SER73 4.8 14.7 1.0
OE2 F:GLU84 4.8 14.0 1.0
O E:HOH7648 4.9 30.2 1.0
CB F:SER73 5.0 15.0 1.0

Calcium binding site 6 out of 8 in 1g8k

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Calcium binding site 6 out of 8 in the Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis


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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 Analysis of Arsenite Oxidase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca5208

b:12.3
occ:1.00
 OE1 E:GLN467 2.4 13.0 1.0
OD1 E:ASP783 2.4 13.3 1.0
O E:SER754 2.4 11.6 1.0
O E:HOH7886 2.5 14.2 1.0
OD1 G:ASP129 2.5 11.2 1.0
OD2 G:ASP129 2.5 13.7 1.0
O G:HOH7853 2.5 13.4 1.0
CG G:ASP129 2.8 12.1 1.0
CD E:GLN467 3.3 12.0 1.0
CG E:ASP783 3.5 13.3 1.0
C E:SER754 3.6 12.4 1.0
NH2 E:ARG470 4.0 13.0 1.0
OE2 G:GLU130 4.0 16.3 1.0
CG E:GLN467 4.0 14.5 1.0
CB E:ASP783 4.0 12.3 1.0
N E:SER754 4.1 12.2 1.0
O E:HOH7146 4.1 16.7 1.0
NE2 E:GLN467 4.1 14.8 1.0
O G:ALA127 4.3 16.9 1.0
CA E:SER754 4.3 11.9 1.0
CB G:ASP129 4.3 12.7 1.0
CB E:GLN467 4.4 14.5 1.0
OD2 E:ASP783 4.5 14.0 1.0
CB E:SER754 4.6 12.5 1.0
N E:THR755 4.6 11.6 1.0
O G:HOH7349 4.7 26.3 1.0
CD G:GLU130 4.8 15.0 1.0
CA E:THR755 4.8 11.5 1.0
N G:ASP129 4.9 14.2 1.0
CG G:GLU130 4.9 13.2 1.0

Calcium binding site 7 out of 8 in 1g8k

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Calcium binding site 7 out of 8 in the Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca5307

b:18.5
occ:1.00
 O G:GLY825 2.3 21.4 1.0
O H:HOH6166 2.4 17.9 1.0
O G:HOH7856 2.4 31.1 1.0
O H:HOH6168 2.4 18.7 1.0
O G:HOH7855 2.4 19.8 1.0
O H:HOH6167 2.5 17.8 1.0
O G:HOH7854 2.5 19.1 1.0
C G:GLY825 3.4 22.3 1.0
O G:HOH7495 4.0 31.1 1.0
N G:GLY825 4.1 17.4 1.0
OXT G:GLY825 4.2 24.0 1.0
CA G:GLY825 4.3 20.7 1.0
O G:ARG823 4.4 13.9 1.0
O H:HOH6086 4.4 29.5 1.0
OD1 H:ASP70 4.5 19.3 1.0
O G:HOH7371 4.5 23.8 1.0
OE1 H:GLU84 4.6 14.4 1.0
O G:HOH7115 4.7 14.7 1.0
OE2 H:GLU84 4.8 15.8 1.0
CB G:SER821 4.8 11.4 1.0
OG H:SER73 4.9 14.6 1.0
O G:HOH7390 4.9 25.5 1.0
O G:HOH7734 4.9 35.5 1.0
CB H:SER73 4.9 14.6 1.0

Calcium binding site 8 out of 8 in 1g8k

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Calcium binding site 8 out of 8 in the Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure Analysis of Arsenite Oxidase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca5308

b:13.0
occ:1.00
 OD1 G:ASP783 2.3 13.5 1.0
OE1 G:GLN467 2.4 14.3 1.0
O G:SER754 2.4 12.5 1.0
OD1 E:ASP129 2.4 12.1 1.0
OD2 E:ASP129 2.5 14.2 1.0
O G:HOH7857 2.5 14.2 1.0
O E:HOH7887 2.6 11.8 1.0
CG E:ASP129 2.8 13.2 1.0
CD G:GLN467 3.3 14.5 1.0
CG G:ASP783 3.5 12.8 1.0
C G:SER754 3.6 13.1 1.0
NH2 G:ARG470 3.9 13.8 1.0
OE2 E:GLU130 4.0 16.2 1.0
CB G:ASP783 4.0 12.4 1.0
N G:SER754 4.0 12.4 1.0
CG G:GLN467 4.1 15.0 1.0
NE2 G:GLN467 4.1 15.6 1.0
O G:HOH7092 4.2 15.7 1.0
CB E:ASP129 4.3 13.6 1.0
CB G:GLN467 4.3 14.8 1.0
O E:ALA127 4.3 15.8 1.0
CA G:SER754 4.3 12.5 1.0
OD2 G:ASP783 4.4 12.5 1.0
N G:THR755 4.6 11.8 1.0
CB G:SER754 4.6 14.0 1.0
CA G:THR755 4.8 11.5 1.0
O E:HOH7362 4.8 26.9 1.0
CD E:GLU130 4.8 13.5 1.0
N E:ASP129 4.9 13.7 1.0
CG E:GLU130 5.0 13.1 1.0
CB G:THR755 5.0 11.5 1.0

Reference:

P.J.Ellis, T.Conrads, R.Hille, P.Kuhn. Crystal Structure of the 100 kDa Arsenite Oxidase From Alcaligenes Faecalis in Two Crystal Forms at 1.64 A and 2.03 A. Structure V. 9 125 2001.
ISSN: ISSN 0969-2126
PubMed: 11250197
DOI: 10.1016/S0969-2126(01)00566-4
Page generated: Thu Jul 11 08:35:37 2024

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