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Sodium 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
Calcium (Ca) 5 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 13 binding sites of Sodium where determined in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes, PDB code: 2iwf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in 2iwf

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Sodium binding site 1 out of 13 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na1609

b:22.8
occ:1.00
 NA A:NA1612 2.7 34.4 1.0
N A:GLY169 2.9 18.5 1.0
OD1 A:ASN167 3.1 20.1 1.0
CB A:MET172 3.3 19.1 1.0
CA A:GLY169 3.4 18.7 1.0
N A:ASP168 3.4 20.9 1.0
CA A:MET172 3.5 19.3 1.0
N A:MET172 3.5 19.4 1.0
CA A:ASN167 3.6 21.6 1.0
C A:ASN167 3.7 21.1 1.0
C A:GLY169 3.7 19.6 1.0
CA B:GLY572 3.9 16.4 1.0
CG A:PRO164 3.9 23.7 1.0
N A:SER170 3.9 19.4 1.0
C A:ASP168 4.0 19.3 1.0
CG A:ASN167 4.1 21.7 1.0
N A:THR171 4.1 18.9 1.0
O A:VAL166 4.2 22.6 1.0
OD1 A:ASP168 4.2 26.0 1.0
N B:VAL573 4.2 16.0 1.0
C A:THR171 4.3 19.0 1.0
CA A:ASP168 4.3 20.6 1.0
CG A:MET172 4.3 19.1 1.0
O A:GLY169 4.4 19.5 1.0
O A:ASN167 4.4 21.5 1.0
CB A:PRO164 4.4 23.3 1.0
CB A:ASN167 4.4 21.1 1.0
C B:GLY572 4.5 17.1 1.0
CD A:PRO164 4.6 23.3 1.0
N A:ASN167 4.7 21.6 1.0
CA A:THR171 4.7 19.0 1.0
OG1 A:THR171 4.8 18.7 1.0
SD A:MET172 4.8 19.8 1.0
C A:VAL166 4.9 22.4 1.0
N B:GLY572 4.9 17.1 1.0
C A:SER170 5.0 19.4 1.0
CA A:SER170 5.0 19.5 1.0
C A:MET172 5.0 20.0 1.0

Sodium binding site 2 out of 13 in 2iwf

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Sodium binding site 2 out of 13 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


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Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na1610

b:19.0
occ:1.00
 O B:HOH2009 2.7 16.7 1.0
OD1 B:ASP18 2.8 23.2 1.0
N A:LEU419 3.0 19.9 1.0
N B:ASP18 3.1 19.1 1.0
CA A:PHE418 3.5 20.5 1.0
CG B:ASP18 3.7 20.8 1.0
C A:PHE418 3.7 19.9 1.0
CB B:ASP18 3.8 20.0 1.0
CG A:LEU419 3.8 18.4 1.0
CA B:LEU17 3.8 21.1 1.0
CB A:PHE418 3.9 20.1 1.0
CB A:LEU419 3.9 19.6 1.0
C B:LEU17 4.0 20.5 1.0
CA A:LEU419 4.0 19.3 1.0
CD2 B:LEU17 4.0 23.2 1.0
CA B:ASP18 4.0 19.3 1.0
NH2 B:ARG41 4.0 18.6 1.0
CD2 A:PHE418 4.1 19.4 1.0
CB B:LEU17 4.2 21.0 1.0
CD2 B:LEU43 4.3 25.3 1.0
CG A:PHE418 4.5 20.2 1.0
O A:ARG417 4.6 20.5 1.0
CD1 A:LEU419 4.6 18.7 1.0
CD1 B:LEU43 4.7 22.3 1.0
CG B:LEU17 4.7 23.0 1.0
N A:PHE418 4.8 19.9 1.0
O B:LYS16 4.8 21.1 1.0
OD2 B:ASP18 4.8 21.1 1.0
O A:PHE418 4.9 20.6 1.0
CD2 A:LEU419 4.9 16.4 1.0
O B:ASP18 5.0 19.0 1.0

Sodium binding site 3 out of 13 in 2iwf

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Sodium binding site 3 out of 13 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na1611

b:21.3
occ:1.00
 O A:HOH2303 2.5 35.0 1.0
N A:LEU441 3.3 21.1 1.0
CA A:VAL440 3.9 20.5 1.0
CB A:LEU441 4.0 22.0 1.0
CD1 A:LEU383 4.1 22.4 1.0
C A:VAL440 4.1 20.6 1.0
CA A:LEU441 4.1 21.9 1.0
O A:LEU441 4.3 23.2 1.0
O A:HOH2262 4.4 35.6 1.0
O A:MET439 4.4 20.7 1.0
CG1 A:VAL440 4.5 20.7 1.0
CB A:VAL440 4.8 20.1 1.0
C A:LEU441 4.8 22.7 1.0
N A:VAL440 4.9 20.5 1.0

Sodium binding site 4 out of 13 in 2iwf

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Sodium binding site 4 out of 13 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
A:Na1612

b:34.4
occ:1.00
 O A:VAL166 2.5 22.6 1.0
NA A:NA1609 2.7 22.8 1.0
OD1 A:ASP168 3.0 26.0 1.0
OG1 A:THR171 3.2 18.7 1.0
OG A:SER170 3.3 21.2 1.0
N A:THR171 3.3 18.9 1.0
C A:VAL166 3.7 22.4 1.0
N A:ASP168 3.7 20.9 1.0
O A:HOH2122 3.7 21.7 1.0
CB A:PRO164 3.8 23.3 1.0
N A:SER170 3.8 19.4 1.0
CA A:THR171 4.0 19.0 1.0
CA A:ASN167 4.0 21.6 1.0
CB A:THR171 4.0 19.3 1.0
CG A:PRO164 4.1 23.7 1.0
N A:GLY169 4.1 18.5 1.0
CG A:ASP168 4.2 21.1 1.0
C A:SER170 4.2 19.4 1.0
C A:THR171 4.3 19.0 1.0
N A:ASN167 4.3 21.6 1.0
CA A:SER170 4.3 19.5 1.0
O A:HOH2121 4.3 47.5 1.0
N A:MET172 4.3 19.4 1.0
CB A:SER170 4.3 19.5 1.0
C A:ASN167 4.4 21.1 1.0
CG2 A:THR171 4.4 19.4 1.0
C A:GLY169 4.5 19.6 1.0
CA A:ASP168 4.7 20.6 1.0
O A:HOH2117 4.7 27.9 1.0
C A:ASP168 4.8 19.3 1.0
CA A:GLY169 4.8 18.7 1.0
CA A:VAL166 4.9 22.5 1.0
CA A:MET172 5.0 19.3 1.0
O A:THR171 5.0 18.9 1.0

Sodium binding site 5 out of 13 in 2iwf

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Sodium binding site 5 out of 13 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
A:Na1613

b:26.9
occ:1.00
 CG2 A:ILE250 3.6 22.5 1.0
CB A:ILE250 3.9 21.9 1.0
CD1 A:TRP194 4.0 19.2 1.0
CG A:GLU247 4.0 21.8 1.0
CA A:GLU247 4.1 19.7 1.0
OH A:TYR154 4.2 18.6 1.0
CB A:GLU247 4.2 19.9 1.0
NE1 A:TRP194 4.2 19.3 1.0
CG A:LYS251 4.3 26.7 1.0
O A:GLU247 4.3 19.1 1.0
CE A:LYS251 4.5 29.4 1.0
CG1 A:ILE250 4.6 21.5 1.0
C A:GLU247 4.7 19.6 1.0
N A:LYS251 4.9 23.6 1.0
CD A:GLU247 4.9 22.5 1.0

Sodium binding site 6 out of 13 in 2iwf

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Sodium binding site 6 out of 13 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1614

b:25.4
occ:1.00
 O A:VAL95 2.5 23.0 1.0
N A:VAL95 2.9 22.4 1.0
C A:VAL95 3.2 22.5 1.0
OD2 A:ASP453 3.3 24.6 1.0
CB A:ASP453 3.3 20.6 1.0
N A:ALA454 3.3 20.3 1.0
CA A:VAL95 3.4 22.0 1.0
CG A:ASP453 3.5 20.2 1.0
C A:ASP453 3.6 20.5 1.0
NE2 A:HIS96 3.7 24.4 1.0
CE1 A:HIS96 3.7 25.5 1.0
CA A:ALA454 3.7 20.0 1.0
C A:ALA454 3.8 20.7 1.0
C A:HIS94 3.9 23.1 1.0
CB A:VAL95 3.9 21.9 1.0
CA A:ASP453 4.1 20.8 1.0
O A:ASP453 4.1 21.7 1.0
CA A:HIS94 4.1 22.9 1.0
ND1 A:HIS96 4.1 26.1 1.0
O A:ALA454 4.1 20.7 1.0
CD2 A:HIS96 4.1 25.9 1.0
CG2 A:ILE455 4.1 22.0 1.0
NZ A:LYS393 4.2 21.1 1.0
O A:HOH2070 4.3 30.6 1.0
CG A:HIS96 4.4 23.0 1.0
N A:ILE455 4.4 20.5 1.0
OD1 A:ASP453 4.4 17.6 1.0
N A:HIS96 4.4 22.3 1.0
CG2 A:VAL95 4.8 21.9 1.0
CB A:HIS94 4.8 23.4 1.0
O A:HIS93 4.9 21.4 1.0
CG1 A:ILE455 5.0 20.5 1.0
O A:PHE23 5.0 22.2 1.0
CA A:HIS96 5.0 22.0 1.0

Sodium binding site 7 out of 13 in 2iwf

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Sodium binding site 7 out of 13 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1608

b:15.8
occ:1.00
 O B:HOH2088 2.3 18.1 1.0
O B:HOH2095 3.2 17.1 1.0
O B:THR129 3.5 22.2 1.0
CB B:ASP130 3.8 20.7 1.0
NH1 B:ARG123 3.9 18.4 1.0
CD1 B:LEU475 4.0 22.6 1.0
CB B:LYS128 4.0 21.0 1.0
CD B:ARG123 4.0 23.4 1.0
CA B:ASP130 4.1 19.7 1.0
O B:LYS128 4.2 19.7 1.0
CG2 B:VAL126 4.2 21.4 1.0
C B:THR129 4.2 21.2 1.0
CD2 B:LEU475 4.3 21.4 1.0
CB B:LEU475 4.3 22.3 1.0
CH2 B:TRP469 4.3 21.2 1.0
CG B:LEU475 4.4 22.8 1.0
CZ B:ARG123 4.4 21.5 1.0
NE B:ARG123 4.4 23.2 1.0
C B:LYS128 4.5 20.6 1.0
N B:ASP130 4.5 20.1 1.0
CZ3 B:TRP469 4.5 18.7 1.0
OD1 B:ASP473 4.8 25.1 1.0
O B:HOH2087 4.8 31.0 1.0
CG B:ARG123 4.8 24.4 1.0
CA B:LYS128 4.8 20.6 1.0
N B:THR129 5.0 21.3 1.0
CB B:ARG123 5.0 21.9 1.0

Sodium binding site 8 out of 13 in 2iwf

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Sodium binding site 8 out of 13 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1609

b:19.2
occ:1.00
 O B:LYS248 2.8 15.2 1.0
O B:HOH2170 2.9 12.9 1.0
C B:LYS248 3.6 15.8 1.0
CA B:LYS248 3.6 15.1 1.0
N B:ALA252 3.7 14.5 1.0
CG B:LYS248 3.8 13.9 1.0
CB B:LYS251 3.8 14.7 1.0
CB B:ALA252 3.8 14.7 1.0
C B:LYS251 4.1 14.6 1.0
CB B:LYS248 4.2 14.7 1.0
CA B:ALA252 4.2 14.7 1.0
CA B:LYS251 4.5 14.6 1.0
O B:LYS251 4.6 15.4 1.0
O B:GLU247 4.7 15.6 1.0
CD B:LYS251 4.7 17.0 1.0
CD B:LYS248 4.8 13.7 1.0
N B:ALA249 4.8 15.8 1.0
N B:LYS248 4.8 15.3 1.0
CG B:LYS251 4.9 16.4 1.0
N B:LYS251 4.9 14.3 1.0

Sodium binding site 9 out of 13 in 2iwf

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Sodium binding site 9 out of 13 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1610

b:23.6
occ:1.00
 O B:HOH2047 2.7 30.9 1.0
O B:HOH2040 2.8 14.9 1.0
O B:ASP130 2.8 20.4 1.0
O B:HOH2096 3.5 16.3 1.0
CA B:ALA131 3.7 18.9 1.0
NE B:ARG69 3.7 16.2 1.0
CG1 B:ILE66 3.8 18.1 1.0
CB B:ALA131 3.8 18.9 1.0
C B:ASP130 3.9 19.2 1.0
CD B:ARG69 3.9 19.5 1.0
N B:ALA131 4.2 19.0 1.0
CA B:ILE66 4.3 20.9 1.0
O B:HOH2039 4.3 30.7 1.0
CG2 B:ILE66 4.4 20.4 1.0
CB B:ILE66 4.4 19.7 1.0
CZ B:ARG69 4.5 14.8 1.0
O B:HOH2036 4.6 28.1 1.0
NH2 B:ARG69 4.8 14.1 1.0
CD1 B:ILE66 4.8 13.9 1.0
C B:ALA131 4.9 19.3 1.0
O B:ILE66 4.9 21.9 1.0
N B:ILE132 4.9 19.2 1.0
CB B:ARG69 4.9 20.9 1.0

Sodium binding site 10 out of 13 in 2iwf

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Sodium binding site 10 out of 13 in the Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Resting Form of Pink Nitrous Oxide Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1611

b:18.6
occ:1.00
 O B:HOH2059 2.4 26.4 1.0
O B:HOH2028 2.7 19.8 1.0
O B:HIS87 2.9 18.1 1.0
CA B:ASP88 3.5 22.4 1.0
CD1 B:ILE86 3.6 18.5 1.0
CA B:GLY58 3.7 18.9 1.0
C B:HIS87 3.8 19.1 1.0
CA B:ARG51 3.9 17.3 1.0
CB B:ARG51 3.9 18.7 1.0
O B:ASN50 3.9 18.0 1.0
CB B:ASP88 4.0 22.5 1.0
N B:ARG51 4.0 17.7 1.0
CG1 B:ILE86 4.0 18.3 1.0
C B:ASN50 4.1 18.4 1.0
CD B:ARG51 4.1 20.2 1.0
N B:ASP88 4.1 21.6 1.0
NA B:NA1613 4.3 19.2 1.0
O B:GLY58 4.4 19.4 1.0
C B:ASP88 4.5 22.2 1.0
CG B:ARG51 4.5 17.7 1.0
O B:PHE49 4.6 17.2 1.0
C B:GLY58 4.6 19.5 1.0
CE1 B:HIS67 4.6 24.7 1.0
O B:TRP57 4.7 18.8 1.0
NZ B:LYS85 4.7 23.6 1.0
NE2 B:HIS67 4.7 26.5 1.0
O B:ASP88 4.8 21.3 1.0
N B:GLY58 4.8 18.8 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: Mon Oct 7 02:55:14 2024

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