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Calcium in PDB 6oz7: Putative Oxidoreductase From Escherichia Coli Str. K-12

Protein crystallography data

The structure of Putative Oxidoreductase From Escherichia Coli Str. K-12, PDB code: 6oz7 was solved by J.Osipiuk, T.Skarina, N.Mesa, M.Endres, A.Savchenko, A.Joachimiak, Centerfor Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.14 / 1.36
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.819, 72.210, 119.945, 82.59, 87.03, 67.82
R / Rfree (%) 12.3 / 16.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Putative Oxidoreductase From Escherichia Coli Str. K-12 (pdb code 6oz7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Putative Oxidoreductase From Escherichia Coli Str. K-12, PDB code: 6oz7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6oz7

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Calcium binding site 1 out of 8 in the Putative Oxidoreductase From Escherichia Coli Str. K-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Putative Oxidoreductase From Escherichia Coli Str. K-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:18.9
occ:0.80
 OE2 A:GLU46 2.3 25.7 1.0
O A:HOH760 2.3 32.8 1.0
OD1 A:ASP42 2.4 24.4 1.0
O A:HOH776 2.4 20.8 1.0
O A:HOH795 2.4 26.7 1.0
O A:HOH672 2.5 25.2 1.0
O A:HOH679 2.5 20.2 1.0
CG A:ASP42 3.3 26.6 1.0
CD A:GLU46 3.4 21.4 1.0
OD2 A:ASP42 3.7 38.2 1.0
CG A:GLU46 3.8 21.2 1.0
NZ A:LYS16 4.0 30.3 1.0
O A:ASP42 4.3 17.6 1.0
CB A:ASP42 4.5 22.5 1.0
OE1 A:GLU46 4.5 23.2 1.0
C A:ASP42 4.7 17.8 1.0
CA A:ASP42 4.8 19.8 1.0

Calcium binding site 2 out of 8 in 6oz7

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Calcium binding site 2 out of 8 in the Putative Oxidoreductase From Escherichia Coli Str. K-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Putative Oxidoreductase From Escherichia Coli Str. K-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:28.2
occ:0.80
 O B:HOH774 2.2 42.7 1.0
O B:HOH734 2.3 50.5 1.0
O B:HOH747 2.3 39.0 1.0
O B:HOH622 2.5 25.0 1.0
O B:HOH785 2.5 29.4 1.0
O B:GLN131 2.5 23.5 1.0
C B:GLN131 3.7 22.3 1.0
O B:HOH725 4.2 39.1 1.0
CB B:GLN131 4.2 22.4 1.0
OD1 B:ASP82 4.3 18.9 1.0
O B:HOH739 4.4 26.7 1.0
O B:GLY132 4.4 16.5 1.0
C B:GLY132 4.5 16.4 1.0
CA B:GLN131 4.5 21.6 1.0
N B:GLY132 4.6 18.6 1.0
CA B:GLY132 4.7 18.4 1.0
N B:GLY133 4.9 15.6 1.0
OE1 B:GLN3 5.0 38.4 1.0

Calcium binding site 3 out of 8 in 6oz7

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Calcium binding site 3 out of 8 in the Putative Oxidoreductase From Escherichia Coli Str. K-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Putative Oxidoreductase From Escherichia Coli Str. K-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:31.8
occ:0.70
 O C:HOH628 2.3 33.4 1.0
O C:HOH760 2.4 36.8 1.0
O C:GLN131 2.5 21.9 1.0
O C:HOH617 2.5 28.2 1.0
C C:GLN131 3.7 19.6 1.0
OD1 C:ASP82 4.3 19.9 1.0
CB C:GLN131 4.3 20.7 1.0
O C:HOH721 4.4 28.9 1.0
O C:GLY132 4.5 18.2 1.0
CA C:GLN131 4.5 19.4 1.0
C C:GLY132 4.5 16.8 1.0
N C:GLY132 4.7 17.7 1.0
CA C:GLY132 4.7 17.3 1.0
OE1 C:GLN3 5.0 31.8 1.0

Calcium binding site 4 out of 8 in 6oz7

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Calcium binding site 4 out of 8 in the Putative Oxidoreductase From Escherichia Coli Str. K-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Putative Oxidoreductase From Escherichia Coli Str. K-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:17.9
occ:0.85
 O G:LYS128 2.3 20.4 1.0
O G:HOH696 2.3 35.3 1.0
O G:HOH704 2.3 23.7 1.0
O G:HOH750 2.4 25.5 1.0
OE2 D:GLU37 2.4 21.4 1.0
O D:HOH763 2.4 29.5 1.0
OE1 D:GLU37 2.5 19.0 1.0
CD D:GLU37 2.8 19.6 1.0
C G:LYS128 3.5 19.5 1.0
CA G:LYS128 4.1 19.8 1.0
CG D:GLU37 4.3 20.3 1.0
NZ D:LYS41 4.4 36.2 1.0
O D:HOH793 4.4 46.6 1.0
C G:GLN129 4.4 21.0 1.0
O G:GLN129 4.4 23.1 1.0
N G:GLN129 4.5 19.2 1.0
O D:HOH617 4.5 28.6 1.0
O D:HOH692 4.6 23.6 1.0
O D:HOH654 4.6 24.3 1.0
CZ2 D:TRP33 4.6 18.2 1.0
O G:VAL127 4.7 20.1 1.0
CG G:LYS128 4.8 29.6 1.0
CA G:GLN129 4.8 20.3 1.0
O D:HOH794 4.8 34.9 1.0
N G:GLY130 4.8 22.2 1.0
O D:HOH798 4.8 42.4 1.0
O G:HOH774 4.8 42.8 1.0
O G:HOH753 4.9 43.4 1.0

Calcium binding site 5 out of 8 in 6oz7

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Calcium binding site 5 out of 8 in the Putative Oxidoreductase From Escherichia Coli Str. K-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Putative Oxidoreductase From Escherichia Coli Str. K-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca501

b:31.6
occ:0.70
 O E:HOH758 2.1 45.2 1.0
O E:GLN131 2.5 24.6 1.0
O E:HOH767 2.5 38.3 1.0
O E:HOH624 2.5 27.2 1.0
C E:GLN131 3.7 19.9 1.0
O E:HOH604 3.8 22.7 1.0
O E:HOH738 3.8 35.5 1.0
O E:HOH682 4.3 37.0 1.0
CB E:GLN131 4.3 24.7 1.0
OD1 E:ASP82 4.3 26.4 1.0
O E:GLY132 4.4 19.8 1.0
C E:GLY132 4.4 19.2 1.0
CA E:GLN131 4.5 21.9 1.0
N E:GLY132 4.6 19.9 1.0
CA E:GLY132 4.6 18.4 1.0
N E:GLY133 4.8 16.7 1.0
OE1 E:GLN3 5.0 39.2 1.0

Calcium binding site 6 out of 8 in 6oz7

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Calcium binding site 6 out of 8 in the Putative Oxidoreductase From Escherichia Coli Str. K-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Putative Oxidoreductase From Escherichia Coli Str. K-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca501

b:24.2
occ:0.70
 O F:HOH790 2.0 39.7 1.0
O F:HOH753 2.3 41.8 1.0
O F:HOH716 2.3 32.5 1.0
O F:GLN131 2.4 22.6 1.0
O F:HOH774 2.4 28.8 1.0
O F:HOH651 2.5 25.9 1.0
C F:GLN131 3.6 19.1 1.0
CB F:GLN131 4.2 22.6 1.0
O F:HOH768 4.2 38.0 1.0
O F:HOH712 4.3 24.2 1.0
OD1 F:ASP82 4.4 20.8 1.0
O F:GLY132 4.4 18.4 1.0
C F:GLY132 4.4 16.5 1.0
CA F:GLN131 4.5 21.1 1.0
N F:GLY132 4.5 17.7 1.0
CA F:GLY132 4.6 18.5 1.0
N F:GLY133 4.8 15.8 1.0
OE1 F:GLN3 4.9 32.2 1.0

Calcium binding site 7 out of 8 in 6oz7

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Calcium binding site 7 out of 8 in the Putative Oxidoreductase From Escherichia Coli Str. K-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Putative Oxidoreductase From Escherichia Coli Str. K-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca501

b:32.7
occ:0.70
 O G:HOH686 2.0 38.1 1.0
O G:HOH758 2.4 42.4 1.0
O G:GLN131 2.5 23.7 1.0
O G:HOH641 2.5 25.2 1.0
C G:GLN131 3.7 19.2 1.0
O G:HOH726 4.2 33.4 1.0
CB G:GLN131 4.3 24.0 1.0
OD1 G:ASP82 4.3 20.4 1.0
O G:GLY132 4.5 18.9 1.0
C G:GLY132 4.6 18.0 1.0
CA G:GLN131 4.6 22.0 1.0
N G:GLY132 4.7 19.0 1.0
CA G:GLY132 4.8 20.8 1.0
OE1 G:GLN3 4.9 29.1 1.0

Calcium binding site 8 out of 8 in 6oz7

Go back to Calcium Binding Sites List in 6oz7
Calcium binding site 8 out of 8 in the Putative Oxidoreductase From Escherichia Coli Str. K-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Putative Oxidoreductase From Escherichia Coli Str. K-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca302

b:17.9
occ:0.90
 O H:HOH600 2.3 22.9 1.0
O H:HOH542 2.4 34.8 1.0
O H:HOH588 2.4 24.0 1.0
OE2 H:GLU37 2.4 18.6 1.0
OE1 H:GLU37 2.5 18.6 1.0
O H:HOH599 2.5 21.3 1.0
CD H:GLU37 2.8 18.2 1.0
NZ H:LYS41 4.2 30.2 1.0
CG H:GLU37 4.3 18.2 1.0
O H:HOH423 4.5 28.2 1.0
O H:HOH481 4.6 22.1 1.0
O H:HOH440 4.6 24.3 1.0
O H:HOH624 4.6 31.7 1.0
CZ2 H:TRP33 4.7 16.9 1.0
O H:HOH636 4.9 42.5 1.0

Reference:

J.Osipiuk, T.Skarina, N.Mesa, M.Endres, A.Savchenko, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Putative Oxidoreductase From Escherichia Coli Str. K-12 To Be Published.
Page generated: Tue Jul 16 12:39:27 2024

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