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Calcium in PDB 2iwk: Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution

Enzymatic activity of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution

All present enzymatic activity of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution:
1.7.99.6;

Protein crystallography data

The structure of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution, PDB code: 2iwk 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) 50.00 / 1.7
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.114, 120.913, 137.343, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.7

Other elements in 2iwk:

The structure of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution also contains other interesting chemical elements:

Iodine (I) 15 atoms
Copper (Cu) 12 atoms
Chlorine (Cl) 8 atoms
Sodium (Na) 30 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Calcium atom in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution (pdb code 2iwk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 28 binding sites of Calcium where determined in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution, PDB code: 2iwk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 28 in 2iwk

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Calcium binding site 1 out of 28 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1606

b:19.2
occ:1.00
O B:HOH2392 2.3 25.9 1.0
OE1 A:GLU427 2.4 32.0 1.0
O A:LYS412 2.4 25.1 1.0
O A:HOH2310 2.4 20.7 1.0
O A:HOH2325 2.4 25.4 1.0
O A:HOH2308 2.5 21.2 1.0
CD A:GLU427 3.1 30.8 1.0
OE2 A:GLU427 3.1 36.2 1.0
C A:LYS412 3.6 25.6 1.0
OD1 B:ASP540 4.1 28.0 1.0
CD1 B:TRP580 4.3 25.0 1.0
CA A:LYS412 4.4 26.2 1.0
CD2 A:PHE413 4.4 26.4 1.0
CA A:PHE413 4.5 24.2 1.0
N A:PHE413 4.5 23.8 1.0
O B:HOH2393 4.5 20.2 1.0
CG A:GLU427 4.5 26.9 1.0
O B:HOH2391 4.5 20.2 1.0
NE1 B:TRP580 4.5 26.0 1.0
O A:LYS425 4.6 23.0 1.0
OE1 A:GLU450 4.6 34.6 1.0
O A:PRO426 4.7 19.3 1.0
O B:PHE581 4.8 25.0 1.0
CA A:GLU427 4.8 22.8 1.0
O B:ASP540 4.9 26.8 1.0
CE2 A:PHE413 4.9 24.5 1.0
CB A:LYS412 4.9 26.0 1.0
CG B:ASP540 4.9 25.9 1.0
N A:GLU427 4.9 21.9 1.0
C A:PRO426 5.0 21.1 1.0

Calcium binding site 2 out of 28 in 2iwk

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Calcium binding site 2 out of 28 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1607

b:20.0
occ:1.00
O A:MET230 2.3 22.6 1.0
O A:TYR219 2.4 20.1 1.0
O A:HOH2176 2.4 21.4 1.0
OD1 A:ASN283 2.4 19.7 1.0
OE2 A:GLU222 2.4 20.4 1.0
OD1 A:ASP236 2.6 23.8 1.0
OE1 A:GLU222 2.6 21.2 1.0
OD2 A:ASP236 2.6 21.0 1.0
CD A:GLU222 2.8 22.3 1.0
CG A:ASP236 2.9 21.5 1.0
CG A:ASN283 3.4 21.1 1.0
C A:MET230 3.5 23.5 1.0
C A:TYR219 3.5 21.4 1.0
ND2 A:ASN283 3.9 20.8 1.0
CA A:THR231 4.1 24.7 1.0
N A:THR231 4.2 23.5 1.0
CA A:ASN220 4.3 20.8 1.0
N A:ASN220 4.3 21.1 1.0
CG A:GLU222 4.4 22.0 1.0
CB A:ASP236 4.5 20.7 1.0
N A:SER221 4.5 21.5 1.0
CA A:TYR219 4.5 21.0 1.0
N A:ASN283 4.5 21.7 1.0
CA A:MET230 4.6 23.6 1.0
CA A:ASN283 4.6 21.2 1.0
CB A:ASN283 4.6 21.5 1.0
OD1 A:ASN282 4.6 32.6 1.0
OG A:SER221 4.7 21.3 1.0
C A:THR231 4.7 25.2 1.0
O A:SER233 4.8 24.1 1.0
C A:ASN220 4.9 21.7 1.0
CB A:SER233 4.9 25.3 1.0
N A:LYS232 4.9 25.2 1.0
N A:SER233 4.9 25.4 1.0

Calcium binding site 3 out of 28 in 2iwk

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Calcium binding site 3 out of 28 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1608

b:22.7
occ:1.00
OD2 A:ASP320 1.7 38.9 1.0
CG A:ASP320 2.9 32.5 1.0
OD1 A:ASP320 3.4 41.1 1.0
N A:ALA316 4.0 21.7 1.0
CA A:ALA316 4.0 21.5 1.0
CB A:ASP315 4.0 21.9 1.0
C A:ASP315 4.0 20.8 1.0
CB A:TYR319 4.1 24.0 1.0
O A:ASP315 4.1 19.8 1.0
CB A:ASP320 4.2 29.7 1.0
CB A:ALA316 4.6 21.9 1.0
CA A:ASP315 4.7 20.9 1.0
C A:TYR319 4.8 25.6 1.0
N A:ASP320 4.8 27.2 1.0
O A:HOH2234 4.8 27.6 1.0
CD1 A:TYR319 4.9 23.1 1.0
CA A:TYR319 5.0 24.1 1.0
CG A:TYR319 5.0 24.0 1.0

Calcium binding site 4 out of 28 in 2iwk

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Calcium binding site 4 out of 28 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1609

b:26.8
occ:0.75
O A:HOH2104 3.3 28.1 1.0
O A:ALA367 3.4 22.4 1.0
N A:PRO332 3.5 23.2 1.0
N A:GLU331 3.6 21.7 1.0
CA A:PRO332 3.7 23.7 1.0
C A:GLU331 3.7 23.2 1.0
CB A:TYR371 3.9 27.1 1.0
N A:TYR371 4.0 25.8 1.0
CD A:PRO332 4.0 23.3 1.0
O A:GLU331 4.1 22.9 1.0
CB A:PRO332 4.1 24.0 1.0
CA A:TYR371 4.1 26.0 1.0
CD1 A:TYR371 4.2 27.1 1.0
CA A:GLU331 4.3 22.2 1.0
CB A:ALA370 4.3 23.6 1.0
C A:ALA367 4.3 21.0 1.0
CB A:ALA330 4.4 20.6 1.0
CA A:ALA330 4.4 20.6 1.0
C A:ALA330 4.5 21.3 1.0
CA A:ALA367 4.5 20.6 1.0
CB A:ALA367 4.5 20.7 1.0
CG A:TYR371 4.6 27.0 1.0
O A:HOH2254 4.6 36.2 1.0
C A:ALA370 4.6 24.7 1.0
CG A:PRO332 4.7 23.5 1.0

Calcium binding site 5 out of 28 in 2iwk

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Calcium binding site 5 out of 28 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1610

b:21.1
occ:0.50
O A:PHE49 2.6 19.8 1.0
O A:HIS87 2.9 21.5 1.0
NH1 A:ARG118 3.0 21.1 1.0
NH2 A:ARG118 3.1 20.5 1.0
C A:HIS87 3.2 19.9 1.0
C A:PHE49 3.4 18.6 1.0
CB A:HIS87 3.4 20.5 1.0
CE1 A:HIS67 3.4 25.0 1.0
CZ A:ARG118 3.5 19.6 1.0
O A:ASN89 3.6 19.9 1.0
CA A:PHE49 3.6 17.6 1.0
CA A:HIS87 3.9 19.7 1.0
CB A:PHE49 3.9 17.8 1.0
N A:ASP88 3.9 21.6 1.0
N A:ASN89 3.9 21.6 1.0
ND1 A:HIS67 4.0 24.1 1.0
O A:HOH2067 4.2 24.1 1.0
CA A:ASP88 4.2 22.4 1.0
C A:ASN89 4.2 21.3 1.0
N A:HIS87 4.4 19.2 1.0
C A:ASP88 4.4 22.4 1.0
O A:HOH2069 4.4 20.0 1.0
CD1 A:PHE49 4.5 19.1 1.0
NE2 A:HIS67 4.5 24.3 1.0
O A:HOH2031 4.6 23.2 1.0
N A:ASN50 4.6 19.5 1.0
CA A:ASN89 4.7 20.6 1.0
CG A:PHE49 4.7 18.2 1.0
CG A:HIS87 4.8 17.9 1.0
NE A:ARG118 4.8 18.8 1.0
N A:PHE49 4.9 17.1 1.0
O A:VAL48 5.0 16.8 1.0

Calcium binding site 6 out of 28 in 2iwk

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Calcium binding site 6 out of 28 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1611

b:32.0
occ:0.75
OH A:TYR209 2.7 19.8 1.0
O A:GLY397 2.8 21.3 1.0
O A:MET289 2.8 18.9 1.0
N A:PRO291 3.1 20.2 1.0
CD A:PRO291 3.4 20.6 1.0
CA A:PRO291 3.4 20.1 1.0
C A:ALA290 3.4 19.8 1.0
C A:GLU398 3.6 19.7 1.0
CZ A:TYR209 3.6 18.9 1.0
CA A:GLU398 3.6 21.3 1.0
N A:THR399 3.7 20.1 1.0
CB A:PRO291 3.7 20.1 1.0
CE1 A:TYR209 3.7 18.6 1.0
C A:GLY397 3.8 19.8 1.0
C A:MET289 3.8 18.4 1.0
O A:ALA290 3.9 19.5 1.0
O A:HOH2157 4.0 34.6 1.0
CA A:ALA290 4.0 19.6 1.0
O A:GLU398 4.1 19.6 1.0
CG A:PRO291 4.1 18.9 1.0
O A:THR399 4.1 18.9 1.0
N A:GLU398 4.2 20.6 1.0
N A:ALA290 4.3 19.3 1.0
C A:THR399 4.5 20.0 1.0
CA A:THR399 4.5 19.9 1.0
CD1 A:PHE343 4.5 22.4 1.0
C A:PRO291 4.9 20.8 1.0
CB A:GLU398 4.9 22.9 1.0
CE2 A:TYR209 4.9 19.5 1.0
CE A:LYS148 4.9 16.6 1.0
NZ A:LYS148 4.9 17.5 1.0

Calcium binding site 7 out of 28 in 2iwk

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Calcium binding site 7 out of 28 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1612

b:42.1
occ:0.80
O A:HOH2159 2.9 22.8 1.0
OE2 A:GLU210 3.1 40.9 1.0
NZ A:LYS212 3.3 33.8 1.0
NE1 A:TRP213 3.3 18.0 1.0
O A:HOH2237 3.4 30.8 1.0
O A:VAL311 3.6 18.2 1.0
CE A:LYS212 3.7 28.8 1.0
CD A:LYS212 3.8 24.9 1.0
CA A:THR312 3.9 21.5 1.0
C A:VAL311 4.0 19.9 1.0
CD1 A:TRP213 4.1 16.6 1.0
N A:THR312 4.2 20.8 1.0
CD A:GLU210 4.2 34.6 1.0
CE2 A:TRP213 4.3 16.4 1.0
CG2 A:VAL311 4.3 22.8 1.0
CG2 A:THR312 4.3 24.2 1.0
O A:HOH2235 4.5 40.2 1.0
CB A:THR312 4.6 22.7 1.0
CZ2 A:TRP213 4.7 17.2 1.0
OD2 A:ASP315 4.7 31.0 1.0
OE1 A:GLU210 4.7 40.4 1.0
CB A:VAL311 4.8 20.3 1.0
C A:THR312 4.9 20.7 1.0
CG A:LYS212 4.9 19.9 1.0
CB A:LYS212 5.0 17.1 1.0

Calcium binding site 8 out of 28 in 2iwk

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Calcium binding site 8 out of 28 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1613

b:33.9
occ:1.00
O A:ALA553 2.7 21.0 1.0
O A:SER53 2.9 19.4 1.0
NH2 A:ARG51 3.0 24.2 1.0
NH1 A:ARG51 3.2 22.1 1.0
OE1 A:GLN59 3.4 24.9 1.0
C A:SER53 3.5 19.9 1.0
CA A:GLY56 3.5 17.9 1.0
CZ A:ARG51 3.5 19.7 1.0
O A:CYS52 3.5 19.0 1.0
CB A:ALA553 3.6 19.9 1.0
C A:ALA553 3.6 18.4 1.0
CA A:SER53 3.6 19.4 1.0
N A:GLY56 3.7 17.8 1.0
N A:ALA553 3.9 18.3 1.0
CA A:ALA553 3.9 18.0 1.0
CB B:ASN89 4.0 19.8 1.0
CD A:GLN59 4.0 24.8 1.0
C A:CYS52 4.4 19.5 1.0
CG A:GLN59 4.4 24.1 1.0
N A:SER53 4.5 19.8 1.0
O B:HOH2061 4.5 15.7 1.0
N A:ALA54 4.6 19.5 1.0
C A:GLY56 4.6 18.0 1.0
CG B:ASN89 4.7 19.1 1.0
NE2 A:GLN59 4.8 24.2 1.0
OG A:SER53 4.8 19.0 1.0
CB A:SER53 4.8 20.6 1.0
C A:THR55 4.8 19.3 1.0
N A:MET554 4.8 18.7 1.0
NE A:ARG51 4.8 20.9 1.0
OD1 B:ASN89 4.9 21.9 1.0
C A:ALA54 4.9 21.2 1.0
N A:THR55 5.0 21.3 1.0
C A:VAL552 5.0 19.0 1.0

Calcium binding site 9 out of 28 in 2iwk

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Calcium binding site 9 out of 28 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1614

b:37.2
occ:1.00
O A:HOH2378 2.7 20.5 1.0
OG A:SER514 2.7 26.5 1.0
O B:HOH2146 2.9 28.4 1.0
O A:HOH2375 3.0 24.7 1.0
O A:GLU588 3.0 19.7 1.0
O A:PRO513 3.4 24.7 1.0
CB A:SER514 3.4 24.4 1.0
CA A:SER514 3.7 23.3 1.0
CB B:LEU227 3.8 22.5 1.0
CA A:MET589 3.9 18.5 1.0
C A:GLU588 3.9 19.4 1.0
C A:PRO513 4.3 23.8 1.0
N A:MET589 4.3 18.8 1.0
N A:ARG590 4.3 19.4 1.0
N B:LEU227 4.5 21.2 1.0
N A:SER514 4.5 22.9 1.0
CD2 B:LEU227 4.5 26.7 1.0
CA B:LEU227 4.6 22.0 1.0
CG B:LEU227 4.6 23.9 1.0
O A:ARG590 4.6 20.5 1.0
C A:MET589 4.7 18.9 1.0
N A:PHE515 4.7 21.3 1.0
CB A:MET589 4.7 18.0 1.0
CD1 B:LEU227 4.8 25.4 1.0
C A:SER514 4.8 22.0 1.0
O A:HOH2427 4.8 38.9 1.0
CG A:MET589 5.0 18.3 1.0
O A:HOH2426 5.0 28.2 1.0

Calcium binding site 10 out of 28 in 2iwk

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Calcium binding site 10 out of 28 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1615

b:39.2
occ:1.00
O A:HOH2288 2.6 28.5 1.0
N A:TYR104 2.9 18.6 1.0
OG1 A:THR399 3.0 20.4 1.0
CB A:THR399 3.3 19.8 1.0
CG2 A:THR399 3.5 20.5 1.0
CA A:LYS103 3.6 18.5 1.0
CB A:LYS103 3.6 19.3 1.0
CB A:TYR104 3.7 19.6 1.0
C A:LYS103 3.7 18.9 1.0
CG A:TYR104 3.8 21.7 1.0
SD A:MET396 3.9 27.2 1.0
CA A:TYR104 3.9 19.7 1.0
CD2 A:TYR104 4.0 20.9 1.0
CB A:ASP401 4.1 24.2 1.0
CD1 A:ILE461 4.1 29.1 1.0
CG A:LYS103 4.1 22.1 1.0
CB A:MET396 4.3 20.6 1.0
CG A:MET396 4.3 23.7 1.0
OD2 A:ASP401 4.4 33.0 1.0
O A:TYR104 4.5 19.0 1.0
CD1 A:TYR104 4.7 19.0 1.0
CG A:ASP401 4.7 27.1 1.0
C A:TYR104 4.7 20.2 1.0
N A:ASP401 4.7 22.3 1.0
CE2 A:TYR104 4.8 19.3 1.0
O A:LYS103 4.9 18.4 1.0
CA A:THR399 4.9 19.9 1.0
N A:LYS103 4.9 18.4 1.0
O A:HOH2090 4.9 34.2 1.0
CD A:LYS103 5.0 26.6 1.0
CA A:ASP401 5.0 23.3 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: Sat Dec 12 03:40:42 2020

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