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Sodium in PDB 5chc: Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps

Protein crystallography data

The structure of Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps, PDB code: 5chc was solved by C.-L.Tsai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.52 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 133.926, 176.022, 193.691, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 22.7

Other elements in 5chc:

The structure of Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps also contains other interesting chemical elements:

Molybdenum (Mo) 3 atoms
Zinc (Zn) 3 atoms
Iron (Fe) 57 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps (pdb code 5chc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps, PDB code: 5chc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5chc

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Sodium binding site 1 out of 8 in the Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1015

b:23.2
occ:1.00
 O A:HOH1335 3.2 24.9 1.0
N A:VAL777 3.3 25.1 1.0
CG2 A:VAL777 3.5 19.1 1.0
CB A:VAL777 3.8 21.5 1.0
O A:HOH1433 3.8 38.5 1.0
O A:HOH1381 3.8 35.2 1.0
CE1 A:HIS88 3.9 28.6 1.0
CD A:PRO87 4.0 24.8 1.0
ND2 A:ASN776 4.1 25.0 1.0
CA A:ASN776 4.1 21.4 1.0
CA A:VAL777 4.2 22.8 1.0
C A:ASN776 4.2 23.4 1.0
ND1 A:HIS88 4.3 27.2 1.0
CG A:ASN776 4.4 26.8 1.0
CG A:PRO87 4.6 26.0 1.0
CB A:ASP82 4.6 26.2 1.0
OD2 A:ASP82 4.7 34.3 1.0
O A:ASP775 4.7 21.1 1.0
CB A:ASN776 4.8 18.6 1.0
CG A:ASP82 4.8 29.9 1.0
OD1 A:ASN776 4.9 27.8 1.0
CA A:GLY86 5.0 26.0 1.0

Sodium binding site 2 out of 8 in 5chc

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Sodium binding site 2 out of 8 in the Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1016

b:46.2
occ:1.00
 NE2 A:HIS128 3.1 37.8 1.0
O A:HOH1412 3.1 38.5 1.0
OE2 A:GLU559 3.1 40.2 1.0
O A:HOH1274 3.6 37.5 1.0
OE1 A:GLU559 3.7 36.0 1.0
CE1 A:HIS128 3.8 38.2 1.0
CD A:GLU559 3.8 39.6 1.0
CD2 A:HIS128 4.2 34.8 1.0
NZ A:LYS531 4.4 42.8 1.0
O A:HOH1402 4.6 40.1 1.0
CE A:LYS531 4.8 39.7 1.0
O D:HOH535 4.9 47.3 1.0

Sodium binding site 3 out of 8 in 5chc

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Sodium binding site 3 out of 8 in the Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:44.7
occ:1.00
 O B:GLY102 3.6 33.6 1.0
O B:ASP91 3.8 28.3 1.0
CB B:ARG95 4.0 34.3 1.0
O B:PRO101 4.0 38.6 1.0
N B:ARG95 4.1 30.2 1.0
OD2 B:ASP91 4.1 34.5 1.0
O B:ARG103 4.2 23.8 1.0
CB B:LYS100 4.3 36.0 1.0
CA B:ARG95 4.4 29.2 1.0
C B:GLY102 4.5 33.4 1.0
C B:GLY94 4.5 33.0 1.0
CG B:ASP91 4.6 32.4 1.0
CG2 B:VAL104 4.7 20.9 1.0
C B:ARG103 4.7 28.3 1.0
O B:LYS100 4.7 33.8 1.0
CA B:GLY94 4.8 33.9 1.0
CD B:LYS100 4.8 44.6 1.0
CB B:ASP91 4.8 26.5 1.0
C B:PRO101 4.8 35.6 1.0
CA B:VAL104 4.9 22.4 1.0
C B:ASP91 4.9 26.2 1.0
O B:HOH562 5.0 30.2 1.0
N B:VAL104 5.0 25.0 1.0

Sodium binding site 4 out of 8 in 5chc

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Sodium binding site 4 out of 8 in the Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1011

b:27.5
occ:1.00
 O C:HOH1328 2.8 37.2 1.0
N C:VAL777 3.3 31.1 1.0
CG2 C:VAL777 3.7 31.4 1.0
CB C:VAL777 3.9 29.5 1.0
CE1 C:HIS88 3.9 33.7 1.0
ND2 C:ASN776 4.0 27.1 1.0
CD C:PRO87 4.0 34.6 1.0
CA C:ASN776 4.1 29.9 1.0
CA C:VAL777 4.2 30.1 1.0
C C:ASN776 4.2 27.0 1.0
CG C:ASN776 4.3 30.8 1.0
OD2 C:ASP82 4.5 33.9 1.0
ND1 C:HIS88 4.5 35.1 1.0
CG C:PRO87 4.5 30.2 1.0
CB C:ASP82 4.6 33.0 1.0
CB C:ASN776 4.7 30.7 1.0
CG C:ASP82 4.7 38.0 1.0
O C:ASP775 4.8 30.9 1.0
OD1 C:ASN776 4.9 29.1 1.0
NE2 C:HIS88 5.0 33.2 1.0
N C:LEU778 5.0 32.1 1.0
O C:ASP82 5.0 35.5 1.0

Sodium binding site 5 out of 8 in 5chc

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Sodium binding site 5 out of 8 in the Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1012

b:43.0
occ:1.00
 NE2 C:HIS128 3.0 30.5 1.0
OE2 C:GLU559 3.0 32.5 1.0
O C:HOH1152 3.4 28.0 1.0
O C:HOH1239 3.5 35.6 1.0
CE1 C:HIS128 3.8 28.9 1.0
CD C:GLU559 3.8 35.7 1.0
OE1 C:GLU559 3.8 34.3 1.0
CD2 C:HIS128 4.0 28.6 1.0
O C:HOH1155 4.1 37.6 1.0
NZ C:LYS531 4.3 35.3 1.0
CE C:LYS531 4.7 32.9 1.0
ND1 C:HIS128 5.0 29.4 1.0

Sodium binding site 6 out of 8 in 5chc

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Sodium binding site 6 out of 8 in the Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1010

b:19.3
occ:1.00
 O E:HOH1349 3.2 24.2 1.0
N E:VAL777 3.2 22.2 1.0
CG2 E:VAL777 3.8 20.7 1.0
CE1 E:HIS88 3.8 27.0 1.0
ND2 E:ASN776 3.8 23.6 1.0
CB E:VAL777 3.9 20.9 1.0
CA E:ASN776 3.9 20.9 1.0
C E:ASN776 4.0 23.0 1.0
CD E:PRO87 4.1 24.5 1.0
CA E:VAL777 4.1 22.7 1.0
CG E:ASN776 4.2 23.2 1.0
ND1 E:HIS88 4.3 26.0 1.0
CB E:ASN776 4.5 19.1 1.0
CB E:ASP82 4.6 21.1 1.0
O E:ASP775 4.7 23.6 1.0
OD1 E:ASN776 4.7 23.6 1.0
CG E:PRO87 4.8 22.9 1.0
NE2 E:HIS88 4.9 27.6 1.0
CG E:ASP82 5.0 26.8 1.0
OD2 E:ASP82 5.0 28.6 1.0
N E:ASN776 5.0 24.3 1.0

Sodium binding site 7 out of 8 in 5chc

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Sodium binding site 7 out of 8 in the Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1011

b:25.2
occ:1.00
 OD2 E:ASP563 2.4 19.9 1.0
OD2 E:ASP569 2.7 17.6 1.0
O E:GLY538 3.1 23.6 1.0
CG E:ASP563 3.3 23.2 1.0
OD1 E:ASP569 3.3 18.9 1.0
ND2 E:ASN565 3.3 18.9 1.0
CG E:ASP569 3.4 21.2 1.0
OD1 E:ASP563 3.4 18.3 1.0
O E:HOH1202 3.4 19.4 1.0
CA E:ASN539 3.7 22.3 1.0
CB E:THR571 3.8 23.7 1.0
C E:GLY538 3.8 23.8 1.0
CG1 E:VAL535 3.8 18.6 1.0
O3' E:MD11004 4.0 19.9 1.0
N E:ASN539 4.1 21.9 1.0
CG2 E:THR571 4.2 20.9 1.0
OG1 E:THR571 4.2 23.7 1.0
O E:VAL535 4.5 22.7 1.0
OD1 E:ASN539 4.5 24.6 1.0
CG E:ASN565 4.5 20.0 1.0
CB E:ASN539 4.5 21.6 1.0
N E:TRP540 4.7 22.3 1.0
C E:ASN539 4.7 24.4 1.0
CG E:ASN539 4.7 21.7 1.0
C4' E:MD11004 4.7 26.0 1.0
N E:ALA572 4.7 20.5 1.0
CB E:ASP563 4.7 20.8 1.0
C E:VAL535 4.8 21.8 1.0
CB E:VAL535 4.8 22.5 1.0
N E:GLY538 4.8 22.4 1.0
CB E:ASP569 4.8 19.8 1.0
CA E:TYR536 4.9 21.4 1.0
C3' E:MD11004 4.9 23.4 1.0
CA E:THR571 5.0 20.7 1.0
CA E:GLY538 5.0 25.2 1.0

Sodium binding site 8 out of 8 in 5chc

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Sodium binding site 8 out of 8 in the Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Perchlorate Reductase Pcrab - Substrate Analog SEO3 Bound - From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1012

b:49.0
occ:1.00
 OE2 E:GLU559 3.0 43.2 1.0
NE2 E:HIS128 3.2 35.0 1.0
O E:HOH1378 3.2 36.4 1.0
CD E:GLU559 3.8 35.2 1.0
OE1 E:GLU559 3.8 34.2 1.0
CE1 E:HIS128 3.8 35.0 1.0
O E:HOH1195 3.9 27.2 1.0
CD2 E:HIS128 4.3 32.0 1.0
NZ E:LYS531 4.5 29.1 1.0
OE1 B:GLU89 4.6 46.3 1.0
O E:HOH1357 4.8 34.7 1.0
CE E:LYS531 4.9 31.4 1.0

Reference:

M.D.Youngblut, C.L.Tsai, I.C.Clark, H.K.Carlson, A.P.Maglaqui, P.S.Gau-Pan, S.A.Redford, A.Wong, J.A.Tainer, J.D.Coates. Perchlorate Reductase Is Distinguished By Active Site Aromatic Gate Residues. J.Biol.Chem. V. 291 9190 2016.
ISSN: ESSN 1083-351X
PubMed: 26940877
DOI: 10.1074/JBC.M116.714618
Page generated: Mon Oct 7 20:20:30 2024

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