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Calcium in PDB 2iwf: Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes

Enzymatic activity of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes

All present enzymatic activity of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes:
1.7.99.6;

Protein crystallography data

The structure of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes, PDB code: 2iwf was solved by K.Paraskevopoulos, S.V.Antonyuk, R.G.Sawers, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.292, 118.180, 131.135, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 27.1

Other elements in 2iwf:

The structure of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes also contains other interesting chemical elements:

Copper (Cu) 12 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 13 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes (pdb code 2iwf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes, PDB code: 2iwf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2iwf

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Calcium binding site 1 out of 5 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1605

b:13.7
occ:1.00
 O B:HOH2349 1.9 15.6 1.0
O A:LYS412 2.2 21.3 1.0
O A:HOH2292 2.3 9.9 1.0
O B:HOH2347 2.4 14.6 1.0
OE1 A:GLU427 2.4 29.2 1.0
O A:HOH2309 2.5 21.4 1.0
OE2 A:GLU427 2.6 27.0 1.0
CD A:GLU427 2.8 25.9 1.0
C A:LYS412 3.4 21.6 1.0
CA A:LYS412 4.2 21.5 1.0
CD1 B:TRP580 4.3 19.4 1.0
OD1 B:ASP540 4.3 22.8 1.0
CG A:GLU427 4.3 23.1 1.0
N A:PHE413 4.4 21.3 1.0
CD1 A:PHE413 4.4 22.0 1.0
CA A:PHE413 4.4 21.5 1.0
NE1 B:TRP580 4.5 17.4 1.0
O A:LYS425 4.6 19.1 1.0
O B:HOH2351 4.6 18.6 1.0
OE1 A:GLU450 4.7 23.7 1.0
CB A:LYS412 4.7 21.1 1.0
O B:PHE581 4.7 20.6 1.0
O A:PRO426 4.8 21.6 1.0
CA A:GLU427 4.8 21.2 1.0
O B:HOH2348 4.8 12.0 1.0
O A:HOH2291 4.8 15.2 1.0
N A:GLU427 4.9 21.6 1.0
CE1 A:PHE413 4.9 22.6 1.0
CB A:GLU427 5.0 22.4 1.0
C A:PRO426 5.0 21.6 1.0

Calcium binding site 2 out of 5 in 2iwf

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Calcium binding site 2 out of 5 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1606

b:28.2
occ:1.00
 O B:ARG51 2.7 19.0 1.0
N A:ARG51 2.8 21.3 1.0
O A:ASP88 2.8 20.1 1.0
N B:SER53 3.5 19.7 1.0
CA A:ASN50 3.5 21.1 1.0
CB A:ASN50 3.5 20.8 1.0
C A:ASN50 3.6 21.9 1.0
CB B:SER53 3.7 21.0 1.0
C B:ARG51 3.7 17.6 1.0
CB A:ARG51 3.7 21.6 1.0
CG B:ARG51 3.7 17.7 1.0
CA A:ARG51 3.8 21.1 1.0
O B:HOH2030 3.8 14.0 1.0
CA B:SER53 3.9 20.9 1.0
O A:ARG51 3.9 19.4 1.0
C A:ASP88 3.9 19.8 1.0
O A:HOH2027 4.0 21.5 1.0
CB B:ARG51 4.2 18.7 1.0
C A:ARG51 4.2 20.1 1.0
C B:CYS52 4.2 18.7 1.0
N B:CYS52 4.4 16.6 1.0
CA B:CYS52 4.5 17.2 1.0
CA B:ARG51 4.6 17.3 1.0
CB A:ASP88 4.7 20.6 1.0
CA A:ASP88 4.7 20.4 1.0
OG B:SER53 4.8 22.1 1.0
O A:ASN50 4.8 23.8 1.0
NH1 B:ARG51 4.8 25.0 1.0
N A:ASN89 4.8 19.6 1.0
N A:ASN50 4.9 21.1 1.0
CG A:ASN50 4.9 20.6 1.0
CZ B:ARG51 4.9 21.9 1.0
CA A:ASN89 4.9 18.7 1.0
CD B:ARG51 5.0 20.2 1.0
NE B:ARG51 5.0 21.4 1.0

Calcium binding site 3 out of 5 in 2iwf

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Calcium binding site 3 out of 5 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1607

b:21.0
occ:1.00
 OD2 A:ASP236 2.4 20.8 1.0
OD1 A:ASN283 2.4 19.2 1.0
O A:HOH2197 2.4 23.7 1.0
O A:TYR219 2.5 20.9 1.0
OD1 A:ASP236 2.5 19.7 1.0
OE2 A:GLU222 2.6 19.8 1.0
O A:MET230 2.6 20.6 1.0
OE1 A:GLU222 2.7 22.7 1.0
CG A:ASP236 2.8 19.5 1.0
CD A:GLU222 3.0 18.6 1.0
CG A:ASN283 3.4 21.8 1.0
C A:TYR219 3.6 19.7 1.0
C A:MET230 3.7 19.9 1.0
ND2 A:ASN283 3.9 23.4 1.0
CA A:THR231 4.2 19.2 1.0
CB A:ASP236 4.3 19.9 1.0
N A:THR231 4.3 19.2 1.0
N A:ASN283 4.4 20.8 1.0
CA A:ASN283 4.5 20.3 1.0
CA A:ASN220 4.5 20.1 1.0
N A:SER221 4.5 19.4 1.0
N A:ASN220 4.5 20.1 1.0
CB A:ASN283 4.5 20.3 1.0
CG A:GLU222 4.5 19.9 1.0
CA A:TYR219 4.6 18.8 1.0
OD1 A:ASN282 4.6 24.0 1.0
CA A:MET230 4.7 19.7 1.0
C A:THR231 4.7 19.4 1.0
OG A:SER221 4.7 18.5 1.0
O A:SER233 4.7 21.3 1.0
N A:LYS232 4.9 20.6 1.0
N A:SER233 4.9 21.9 1.0

Calcium binding site 4 out of 5 in 2iwf

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Calcium binding site 4 out of 5 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1605

b:21.9
occ:1.00
 O B:HOH2275 2.3 9.6 1.0
O B:HOH2266 2.4 15.8 1.0
OE1 B:GLU427 2.5 27.6 1.0
O B:HOH2265 2.5 24.2 1.0
O B:LYS412 2.6 20.2 1.0
O A:HOH2366 2.7 21.0 1.0
OE2 B:GLU427 2.7 27.6 1.0
CD B:GLU427 2.9 25.2 1.0
C B:LYS412 3.7 19.8 1.0
OD1 A:ASP540 4.2 27.6 1.0
CD1 A:TRP580 4.3 19.9 1.0
O A:HOH2381 4.4 18.2 1.0
CD2 B:PHE413 4.4 20.8 1.0
CG B:GLU427 4.4 25.2 1.0
CA B:LYS412 4.5 20.1 1.0
O B:LYS425 4.5 21.0 1.0
OE1 B:GLU450 4.6 27.9 1.0
N B:PHE413 4.7 19.8 1.0
NE1 A:TRP580 4.7 19.7 1.0
O A:HOH2365 4.7 29.6 1.0
O B:PRO426 4.7 21.5 1.0
O A:PHE581 4.7 22.6 1.0
CE2 B:PHE413 4.7 21.1 1.0
CA B:PHE413 4.8 21.2 1.0
CA B:GLU427 4.8 22.9 1.0
N B:GLU427 4.9 21.9 1.0
CG B:GLU450 4.9 24.2 1.0
CB B:LYS412 5.0 19.2 1.0
C B:PRO426 5.0 21.1 1.0

Calcium binding site 5 out of 5 in 2iwf

Go back to Calcium Binding Sites List in 2iwf
Calcium binding site 5 out of 5 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1606

b:30.4
occ:1.00
 O B:MET230 2.1 27.0 1.0
OD1 B:ASN283 2.3 11.0 1.0
O B:HOH2162 2.4 23.7 1.0
O B:TYR219 2.6 21.6 1.0
OE1 B:GLU222 2.7 22.1 1.0
OD2 B:ASP236 2.7 23.2 1.0
OD1 B:ASP236 2.7 23.0 1.0
OE2 B:GLU222 2.8 25.6 1.0
CG B:ASP236 3.0 23.9 1.0
CD B:GLU222 3.1 24.4 1.0
C B:MET230 3.3 27.2 1.0
CG B:ASN283 3.3 20.9 1.0
C B:TYR219 3.7 20.9 1.0
CA B:THR231 3.9 27.1 1.0
ND2 B:ASN283 3.9 19.4 1.0
N B:THR231 4.0 27.0 1.0
C B:THR231 4.3 27.6 1.0
CA B:MET230 4.3 27.4 1.0
CA B:ASN220 4.5 21.8 1.0
N B:ASN220 4.5 21.7 1.0
OD1 B:ASN282 4.5 29.6 1.0
CB B:ASP236 4.5 23.2 1.0
CB B:ASN283 4.6 22.0 1.0
N B:ASN283 4.6 23.9 1.0
N B:SER221 4.6 22.6 1.0
CG B:GLU222 4.6 23.6 1.0
N B:LYS232 4.6 27.9 1.0
CA B:ASN283 4.6 23.0 1.0
OG B:SER221 4.6 21.6 1.0
CA B:TYR219 4.7 20.9 1.0
N B:SER233 4.7 27.8 1.0
CB B:SER233 4.7 27.9 1.0
O B:SER233 4.8 27.5 1.0
O B:THR231 4.9 28.1 1.0
CB B:MET230 5.0 27.4 1.0

Reference:

K.Paraskevopoulos, S.V.Antonyuk, R.G.Sawers, R.R.Eady, S.S.Hasnain. Insight Into Catalysis of Nitrous Oxide Reductase From High-Resolution Structures of Resting and Inhibitor-Bound Enzyme From Achromobacter Cycloclastes. J.Mol.Biol. V. 362 55 2006.
ISSN: ISSN 0022-2836
PubMed: 16904686
DOI: 10.1016/J.JMB.2006.06.064
Page generated: Fri Jul 12 13:10:55 2024

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