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Calcium in PDB 7np8: Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution

Enzymatic activity of Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution

All present enzymatic activity of Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution:
1.8.98.3;

Protein crystallography data

The structure of Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution, PDB code: 7np8 was solved by M.Jespersen, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.82 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 167.258, 172.202, 195.888, 90, 90, 90
R / Rfree (%) 18.2 / 20.5

Other elements in 7np8:

The structure of Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Iron (Fe) 101 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution (pdb code 7np8). 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 the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution, PDB code: 7np8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7np8

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Calcium binding site 1 out of 9 in the Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1113

b:77.6
occ:1.00
 O A:HOH1347 2.4 54.8 1.0
OD1 A:ASP228 2.5 55.2 1.0
OD2 A:ASP228 2.5 59.9 1.0
O A:HOH1291 2.6 42.5 1.0
OD1 A:ASP85 2.8 48.5 1.0
CG A:ASP228 2.8 57.0 1.0
SG A:CYS273 3.3 50.6 1.0
CG A:ASP85 3.7 44.0 1.0
OD2 A:ASP85 4.0 42.3 1.0
NE2 A:GLN84 4.2 46.4 1.0
CB A:CYS273 4.2 48.2 1.0
CB A:ASP228 4.3 56.4 1.0
O A:HOH1233 4.5 46.5 1.0
O A:GLN84 4.5 44.7 1.0
CE A:LYS230 4.7 66.5 1.0
CG A:GLN84 4.9 36.6 1.0
O A:ILE229 4.9 70.6 1.0
O A:HOH1277 4.9 24.6 1.0

Calcium binding site 2 out of 9 in 7np8

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Calcium binding site 2 out of 9 in the Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1011

b:68.8
occ:1.00
 OD2 B:ASP511 2.2 55.4 1.0
CG B:ASP511 2.8 53.2 1.0
OD1 B:ASP511 3.0 59.3 1.0
O B:HOH1291 3.2 52.1 1.0
O B:ILE510 4.0 42.0 1.0
CB B:ASP511 4.2 44.4 1.0
CA B:ASP511 4.5 37.9 1.0
C B:ILE510 4.6 35.2 1.0
O B:HOH1243 4.7 27.0 1.0
O B:GLU508 4.8 41.2 1.0
N B:ASP511 4.9 33.8 1.0

Calcium binding site 3 out of 9 in 7np8

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Calcium binding site 3 out of 9 in the Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1012

b:104.7
occ:1.00
 O B:HOH1114 2.4 39.1 1.0
OD2 B:ASP228 2.6 66.0 1.0
OD1 B:ASP228 2.6 60.2 1.0
OD1 B:ASP85 2.7 52.4 1.0
CG B:ASP228 2.9 62.1 1.0
SG B:CYS273 3.2 62.4 1.0
CG B:ASP85 3.7 49.1 1.0
OD2 B:ASP85 4.0 50.5 1.0
CB B:CYS273 4.1 51.0 1.0
NE2 B:GLN84 4.3 47.0 1.0
CB B:ASP228 4.4 58.2 1.0
CG B:LYS230 4.6 84.0 1.0
CE B:LYS230 4.6 88.8 1.0
O B:GLN84 4.6 56.2 1.0
O B:ILE229 4.9 58.6 1.0
O B:HOH1211 5.0 34.9 1.0
NZ B:LYS226 5.0 52.3 1.0

Calcium binding site 4 out of 9 in 7np8

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Calcium binding site 4 out of 9 in the Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1114

b:72.8
occ:1.00
 OD2 C:ASP228 2.7 64.4 1.0
OD1 C:ASP228 2.7 63.7 1.0
OD1 C:ASP85 2.8 47.5 1.0
SG C:CYS273 2.8 56.5 1.0
CG C:ASP228 3.1 63.8 1.0
O C:HOH1237 3.2 38.3 1.0
CE C:LYS230 3.7 108.2 1.0
CB C:CYS273 3.8 52.7 1.0
CG C:ASP85 3.8 46.1 1.0
OD2 C:ASP85 4.1 42.9 1.0
CG C:LYS230 4.2 101.1 1.0
CD C:LYS230 4.5 106.9 1.0
CB C:ASP228 4.6 60.9 1.0
NE2 C:GLN84 4.7 40.3 1.0
O C:ILE229 4.7 73.9 1.0
NZ C:LYS230 4.8 110.0 1.0
O C:HOH1272 5.0 20.9 1.0

Calcium binding site 5 out of 9 in 7np8

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Calcium binding site 5 out of 9 in the Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1115

b:99.7
occ:1.00
 OD2 C:ASP220 2.4 95.0 1.0
OD1 C:ASP220 2.7 95.6 1.0
CG C:ASP220 2.8 90.4 1.0
O C:HOH1354 3.6 39.7 1.0
NZ C:LYS223 4.1 55.2 1.0
CB C:ASP220 4.2 78.4 1.0
CE C:LYS223 4.5 51.1 1.0

Calcium binding site 6 out of 9 in 7np8

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Calcium binding site 6 out of 9 in the Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1116

b:94.7
occ:1.00
 OD1 C:ASP40 2.7 62.9 1.0
CG C:ASP40 3.7 58.0 1.0
OD2 C:ASP40 4.1 61.9 1.0
CB C:GLU41 4.2 55.6 1.0
N C:GLU41 4.2 48.8 1.0
OE1 C:GLU41 4.5 78.3 1.0
CA C:GLU41 4.8 46.2 1.0

Calcium binding site 7 out of 9 in 7np8

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Calcium binding site 7 out of 9 in the Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution


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 the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1114

b:73.5
occ:1.00
 O D:HOH1219 2.4 60.8 1.0
SG D:CYS273 2.6 61.0 1.0
OD2 D:ASP228 2.8 57.0 1.0
OD1 D:ASP228 3.0 48.2 1.0
OD1 D:ASP85 3.2 55.1 1.0
CG D:ASP228 3.3 49.7 1.0
CE D:LYS230 3.4 83.8 1.0
CB D:CYS273 3.7 48.1 1.0
CG D:LYS230 3.9 76.9 1.0
CD D:LYS230 4.1 82.0 1.0
CG D:ASP85 4.2 51.4 1.0
OD2 D:ASP85 4.4 48.6 1.0
O D:ILE229 4.5 60.1 1.0
NZ D:LYS230 4.6 84.9 1.0
CB D:ASP228 4.8 45.3 1.0
O D:HOH1309 4.8 21.8 1.0

Calcium binding site 8 out of 9 in 7np8

Go back to Calcium Binding Sites List in 7np8
Calcium binding site 8 out of 9 in the Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution


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 the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1115

b:70.3
occ:1.00
 OD1 D:ASP511 2.4 51.1 1.0
O D:HOH1374 2.8 46.3 1.0
CG D:ASP511 3.1 48.4 1.0
OD2 D:ASP511 3.3 49.7 1.0
O D:HOH1362 3.4 44.2 1.0
O D:ILE510 3.9 28.0 1.0
O D:HOH1298 4.0 50.9 1.0
CB D:ASP511 4.4 41.2 1.0
O D:GLU508 4.4 33.5 1.0
C D:ILE510 4.5 26.1 1.0
CA D:ASP511 4.7 35.2 1.0
N D:ASP511 4.9 32.3 1.0
O D:HOH1339 4.9 24.8 1.0

Calcium binding site 9 out of 9 in 7np8

Go back to Calcium Binding Sites List in 7np8
Calcium binding site 9 out of 9 in the Crystal Structure of the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution


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 the Coenzyme F420-Dependent Sulfite Reductase From Methanocaldococcus Jannaschii at 2.3-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1116

b:84.3
occ:1.00
 O D:GLU618 2.4 63.2 1.0
O D:HOH1363 2.5 51.9 1.0
O D:CYS620 2.5 69.5 1.0
O D:HOH1387 2.8 58.3 1.0
C D:CYS620 3.4 65.7 1.0
C D:GLU618 3.4 51.9 1.0
O D:LYS617 4.0 58.6 1.0
OXT D:CYS620 4.0 63.1 1.0
N D:CYS620 4.1 59.6 1.0
CA D:GLU618 4.1 50.0 1.0
C D:ILE619 4.2 59.4 1.0
CA D:CYS620 4.4 63.6 1.0
N D:ILE619 4.4 49.2 1.0
O D:ILE619 4.4 60.7 1.0
CA D:ILE619 4.7 56.7 1.0
OE2 D:GLU618 4.8 58.6 1.0
C D:LYS617 4.9 52.3 1.0

Reference:

M.Jespersen, T.Wagner. The Structure of the F420-Dependent Sulfite-Detoxifying Enzyme From Methanococcales Reveals A Prototypical Sulfite-Reductase with Assimilatory Traits. To Be Published.
Page generated: Fri Jul 19 02:19:37 2024

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