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Sodium in PDB 6b0d: An E. Coli Dps Protein From Ferritin Superfamily

Protein crystallography data

The structure of An E. Coli Dps Protein From Ferritin Superfamily, PDB code: 6b0d was solved by W.Rui, S.Ruslan, K.Ronan, J.S.Adam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.25 / 1.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 117.625, 133.969, 139.112, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.8

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the An E. Coli Dps Protein From Ferritin Superfamily (pdb code 6b0d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the An E. Coli Dps Protein From Ferritin Superfamily, PDB code: 6b0d:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 6b0d

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Sodium binding site 1 out of 12 in the An E. Coli Dps Protein From Ferritin Superfamily


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of An E. Coli Dps Protein From Ferritin Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:24.2
occ:1.00
 O D:HOH404 2.5 26.9 1.0
O A:HOH415 2.6 23.9 1.0
O D:HOH329 2.7 11.4 1.0
NE A:ARG153 3.1 11.7 1.0
CD1 D:ILE147 3.5 11.7 1.0
CB A:ARG153 3.6 9.1 1.0
CG A:ARG153 3.7 9.5 1.0
NH2 A:ARG153 3.8 11.1 1.0
O D:HOH321 3.8 18.3 1.0
CZ A:ARG153 3.9 10.8 1.0
CD A:ARG153 3.9 10.2 1.0
CG1 D:ILE147 4.1 10.7 1.0
O A:ARG153 4.2 9.1 1.0
CA A:ARG153 4.3 9.0 1.0
CG2 D:THR79 4.3 11.7 1.0
C A:ARG153 4.5 9.2 1.0
O A:HOH384 4.5 25.9 1.0
OE1 D:GLN86 4.5 12.8 1.0
CD D:ARG83 4.7 11.1 1.0
NE2 D:GLN86 4.9 13.7 1.0
O D:THR79 4.9 10.1 1.0
CB D:ARG83 4.9 10.9 1.0

Sodium binding site 2 out of 12 in 6b0d

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Sodium binding site 2 out of 12 in the An E. Coli Dps Protein From Ferritin Superfamily


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of An E. Coli Dps Protein From Ferritin Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:26.0
occ:1.00
 O A:ALA150 2.7 10.2 1.0
O A:HOH451 2.7 28.2 1.0
O A:HOH384 2.8 25.9 1.0
O A:HOH459 2.8 30.9 1.0
C A:ALA150 3.5 8.5 1.0
CA A:ALA150 3.6 10.2 1.0
CG A:ASP154 3.8 12.9 1.0
CB A:ALA150 3.8 8.6 1.0
OD2 A:ASP154 3.9 14.1 1.0
OD1 A:ASP154 4.0 13.0 1.0
CB A:ARG153 4.0 9.1 1.0
N A:ASP154 4.1 8.0 1.0
O E:HOH474 4.2 35.4 1.0
CE1 A:HIS76 4.3 11.6 1.0
O A:HOH452 4.4 27.1 1.0
CB A:ASP154 4.5 11.4 1.0
NE2 A:HIS76 4.5 11.6 1.0
O D:HOH324 4.6 24.4 1.0
N A:ALA151 4.7 9.3 1.0
C A:ARG153 4.7 9.2 1.0
CA A:ASP154 4.8 9.6 1.0
NE A:ARG153 4.8 11.7 1.0
CD A:ARG153 4.8 10.2 1.0
CA A:ARG153 4.8 9.0 1.0
CG A:ARG153 4.9 9.5 1.0
N A:ALA150 5.0 9.9 1.0

Sodium binding site 3 out of 12 in 6b0d

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Sodium binding site 3 out of 12 in the An E. Coli Dps Protein From Ferritin Superfamily


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of An E. Coli Dps Protein From Ferritin Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:24.8
occ:1.00
 O A:HOH433 2.3 28.8 1.0
O E:HOH388 2.5 19.3 1.0
O A:HOH323 2.7 11.7 1.0
NE E:ARG153 3.0 10.2 1.0
CD1 A:ILE147 3.4 9.6 1.0
CG E:ARG153 3.7 9.5 1.0
NH2 E:ARG153 3.7 11.4 1.0
CB E:ARG153 3.7 8.5 1.0
CZ E:ARG153 3.8 11.6 1.0
O A:HOH349 3.8 17.6 1.0
CD E:ARG153 3.9 9.9 1.0
CG1 A:ILE147 4.0 9.2 1.0
O E:ARG153 4.3 9.5 1.0
CA E:ARG153 4.3 8.6 1.0
CG2 A:THR79 4.3 12.5 1.0
OE1 A:GLN86 4.5 12.2 1.0
C E:ARG153 4.6 7.8 1.0
O E:HOH340 4.6 25.1 1.0
CD A:ARG83 4.6 10.7 1.0
O A:THR79 4.9 11.0 1.0
NE2 A:GLN86 4.9 11.5 1.0
CB A:ARG83 4.9 8.9 1.0

Sodium binding site 4 out of 12 in 6b0d

Go back to Sodium Binding Sites List in 6b0d
Sodium binding site 4 out of 12 in the An E. Coli Dps Protein From Ferritin Superfamily


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of An E. Coli Dps Protein From Ferritin Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:23.7
occ:1.00
 O B:HOH456 2.7 25.0 1.0
O B:ALA150 2.8 8.7 1.0
O B:HOH356 2.8 26.3 1.0
O B:HOH464 2.8 28.0 1.0
C B:ALA150 3.5 8.4 1.0
CA B:ALA150 3.7 8.7 1.0
CG B:ASP154 3.8 12.5 1.0
CB B:ARG153 3.9 9.8 1.0
OD1 B:ASP154 3.9 14.3 1.0
CB B:ALA150 3.9 9.7 1.0
OD2 B:ASP154 3.9 12.9 1.0
N B:ASP154 4.2 8.6 1.0
O B:HOH457 4.4 29.9 1.0
CE1 B:HIS76 4.5 9.8 1.0
CB B:ASP154 4.5 10.7 1.0
O C:HOH316 4.7 23.9 1.0
NE2 B:HIS76 4.7 10.3 1.0
NE B:ARG153 4.7 11.1 1.0
C B:ARG153 4.7 8.7 1.0
CD B:ARG153 4.7 9.9 1.0
CA B:ARG153 4.8 8.9 1.0
N B:ALA151 4.8 8.7 1.0
CA B:ASP154 4.8 8.9 1.0
O B:HOH428 4.9 25.9 1.0
CG B:ARG153 4.9 9.9 1.0

Sodium binding site 5 out of 12 in 6b0d

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Sodium binding site 5 out of 12 in the An E. Coli Dps Protein From Ferritin Superfamily


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of An E. Coli Dps Protein From Ferritin Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:24.7
occ:1.00
 O C:HOH396 2.6 24.7 1.0
O B:HOH428 2.6 25.9 1.0
O C:HOH329 2.7 12.3 1.0
NE B:ARG153 3.0 11.1 1.0
CD1 C:ILE147 3.5 10.7 1.0
CG B:ARG153 3.7 9.9 1.0
CB B:ARG153 3.7 9.8 1.0
NH2 B:ARG153 3.8 11.8 1.0
CZ B:ARG153 3.9 11.8 1.0
CD B:ARG153 3.9 9.9 1.0
O C:HOH310 3.9 17.7 1.0
CG1 C:ILE147 4.1 10.6 1.0
O B:ARG153 4.2 9.2 1.0
CA B:ARG153 4.3 8.9 1.0
CG2 C:THR79 4.3 10.9 1.0
OE1 C:GLN86 4.5 14.1 1.0
C B:ARG153 4.5 8.7 1.0
O B:HOH356 4.5 26.3 1.0
CD C:ARG83 4.6 8.9 1.0
NE2 C:GLN86 4.9 13.2 1.0
O C:THR79 4.9 10.4 1.0
CB C:ARG83 5.0 10.0 1.0

Sodium binding site 6 out of 12 in 6b0d

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Sodium binding site 6 out of 12 in the An E. Coli Dps Protein From Ferritin Superfamily


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of An E. Coli Dps Protein From Ferritin Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:22.7
occ:1.00
 O C:HOH314 2.7 26.2 1.0
O C:HOH446 2.7 28.2 1.0
O C:ALA150 2.8 9.0 1.0
O C:HOH454 2.9 28.4 1.0
C C:ALA150 3.6 9.4 1.0
CA C:ALA150 3.7 9.2 1.0
CB C:ARG153 3.8 8.4 1.0
CG C:ASP154 3.9 12.5 1.0
OD1 C:ASP154 3.9 13.4 1.0
CB C:ALA150 4.0 9.4 1.0
OD2 C:ASP154 4.0 13.8 1.0
N C:ASP154 4.2 8.8 1.0
O B:HOH475 4.3 36.4 1.0
O C:HOH450 4.3 28.6 1.0
CE1 C:HIS76 4.5 10.0 1.0
CB C:ASP154 4.6 11.1 1.0
NE C:ARG153 4.6 9.8 1.0
NE2 C:HIS76 4.7 10.8 1.0
CD C:ARG153 4.7 9.5 1.0
C C:ARG153 4.7 8.8 1.0
CA C:ARG153 4.7 8.4 1.0
O C:HOH406 4.8 20.9 1.0
N C:ALA151 4.8 8.5 1.0
CA C:ASP154 4.9 9.1 1.0
CG C:ARG153 4.9 8.9 1.0
CZ C:ARG153 4.9 10.8 1.0

Sodium binding site 7 out of 12 in 6b0d

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Sodium binding site 7 out of 12 in the An E. Coli Dps Protein From Ferritin Superfamily


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of An E. Coli Dps Protein From Ferritin Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:25.8
occ:1.00
 O C:HOH406 2.5 20.9 1.0
NE C:ARG153 3.1 9.8 1.0
CB C:ARG153 3.7 8.4 1.0
CG C:ARG153 3.8 8.9 1.0
NH2 C:ARG153 3.8 10.8 1.0
CZ C:ARG153 3.9 10.8 1.0
CD C:ARG153 4.0 9.5 1.0
O C:ARG153 4.2 9.0 1.0
CA C:ARG153 4.3 8.4 1.0
C C:ARG153 4.6 8.8 1.0
O C:HOH314 4.7 26.2 1.0

Sodium binding site 8 out of 12 in 6b0d

Go back to Sodium Binding Sites List in 6b0d
Sodium binding site 8 out of 12 in the An E. Coli Dps Protein From Ferritin Superfamily


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of An E. Coli Dps Protein From Ferritin Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:23.3
occ:1.00
 O D:HOH360 2.7 26.4 1.0
O D:HOH441 2.7 26.5 1.0
O D:ALA150 2.8 9.3 1.0
O D:HOH445 2.8 31.1 1.0
C D:ALA150 3.6 9.2 1.0
CA D:ALA150 3.7 9.2 1.0
CG D:ASP154 3.9 14.2 1.0
CB D:ARG153 3.9 10.0 1.0
OD1 D:ASP154 3.9 15.7 1.0
CB D:ALA150 3.9 9.4 1.0
OD2 D:ASP154 4.0 15.2 1.0
N D:ASP154 4.2 9.3 1.0
O D:HOH473 4.2 31.2 1.0
O D:HOH442 4.4 31.6 1.0
CE1 D:HIS76 4.5 10.8 1.0
O E:HOH332 4.6 25.9 1.0
CB D:ASP154 4.6 10.3 1.0
NE2 D:HIS76 4.7 10.3 1.0
NE D:ARG153 4.7 11.3 1.0
C D:ARG153 4.7 9.6 1.0
CD D:ARG153 4.8 10.7 1.0
CA D:ARG153 4.8 9.0 1.0
CA D:ASP154 4.8 9.9 1.0
N D:ALA151 4.8 9.2 1.0
O D:HOH307 4.9 34.6 1.0
CG D:ARG153 4.9 9.8 1.0
CZ D:ARG153 5.0 12.3 1.0

Sodium binding site 9 out of 12 in 6b0d

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Sodium binding site 9 out of 12 in the An E. Coli Dps Protein From Ferritin Superfamily


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of An E. Coli Dps Protein From Ferritin Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na203

b:26.0
occ:1.00
 O D:HOH413 2.5 27.5 1.0
O E:HOH416 2.7 22.3 1.0
O E:HOH326 2.7 12.0 1.0
NE D:ARG153 2.9 11.3 1.0
CD1 E:ILE147 3.4 10.1 1.0
CB D:ARG153 3.5 10.0 1.0
CG D:ARG153 3.6 9.8 1.0
NH2 D:ARG153 3.7 11.8 1.0
CZ D:ARG153 3.8 12.3 1.0
CD D:ARG153 3.8 10.7 1.0
O E:HOH329 3.9 19.4 1.0
CG1 E:ILE147 4.0 9.2 1.0
O D:ARG153 4.2 9.6 1.0
CA D:ARG153 4.2 9.0 1.0
CG2 E:THR79 4.3 10.9 1.0
C D:ARG153 4.4 9.6 1.0
O D:HOH360 4.4 26.4 1.0
OE1 E:GLN86 4.6 13.1 1.0
CD E:ARG83 4.8 10.5 1.0

Sodium binding site 10 out of 12 in 6b0d

Go back to Sodium Binding Sites List in 6b0d
Sodium binding site 10 out of 12 in the An E. Coli Dps Protein From Ferritin Superfamily


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of An E. Coli Dps Protein From Ferritin Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:24.5
occ:1.00
 O E:HOH444 2.5 28.4 1.0
O E:HOH447 2.7 24.8 1.0
O E:HOH340 2.8 25.1 1.0
O E:ALA150 2.8 10.4 1.0
C E:ALA150 3.6 10.2 1.0
CA E:ALA150 3.7 9.7 1.0
CG E:ASP154 3.9 11.5 1.0
CB E:ARG153 3.9 8.5 1.0
CB E:ALA150 3.9 11.4 1.0
OD1 E:ASP154 3.9 13.8 1.0
OD2 E:ASP154 4.0 14.7 1.0
N E:ASP154 4.2 8.9 1.0
O E:HOH445 4.3 29.1 1.0
CE1 E:HIS76 4.5 10.1 1.0
O A:HOH317 4.5 22.6 1.0
CB E:ASP154 4.6 9.8 1.0
NE E:ARG153 4.6 10.2 1.0
NE2 E:HIS76 4.7 9.9 1.0
C E:ARG153 4.8 7.8 1.0
CA E:ARG153 4.8 8.6 1.0
CD E:ARG153 4.8 9.9 1.0
N E:ALA151 4.8 8.4 1.0
CA E:ASP154 4.9 8.1 1.0
CG E:ARG153 4.9 9.5 1.0
O E:HOH312 5.0 35.7 1.0
O E:HOH388 5.0 19.3 1.0
CZ E:ARG153 5.0 11.6 1.0

Reference:

A.J.Simpkin, F.Simkovic, J.M.H.Thomas, M.Savko, A.Lebedev, V.Uski, C.Ballard, M.Wojdyr, R.Wu, R.Sanishvili, Y.Xu, M.N.Lisa, A.Buschiazzo, W.Shepard, D.J.Rigden, R.M.Keegan. Simbad: A Sequence-Independent Molecular-Replacement Pipeline. Acta Crystallogr D Struct V. 74 595 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29968670
DOI: 10.1107/S2059798318005752
Page generated: Tue Oct 8 01:57:30 2024

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