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Sodium in PDB 3ifv: Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen

Protein crystallography data

The structure of Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen, PDB code: 3ifv was solved by J.A.Winter, P.Christofi, S.Morroll, K.A.Bunting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.360, 143.760, 78.030, 90.00, 121.56, 90.00
R / Rfree (%) 21.4 / 25.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen (pdb code 3ifv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen, PDB code: 3ifv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 3ifv

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Sodium binding site 1 out of 9 in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen


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 Haloferax Volcanii Proliferating Cell Nuclear Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:13.2
occ:1.00
 OD2 A:ASP150 2.0 20.5 1.0
O A:HOH325 2.1 29.7 1.0
OD1 A:ASP150 2.3 20.1 1.0
O A:HOH324 2.4 24.8 1.0
CG A:ASP150 2.5 20.9 1.0
O A:HOH264 2.7 31.2 1.0
O A:HOH321 2.7 25.4 1.0
O A:HOH294 2.8 19.7 1.0
NA A:NA402 3.8 22.3 1.0
CB A:ASP150 4.1 17.7 1.0
OD1 A:ASP146 4.3 18.8 1.0
O A:HOH257 4.4 26.4 1.0
OD2 A:ASP198 4.4 28.5 1.0
OD1 A:ASP198 4.5 28.2 1.0
CG A:ASP198 5.0 24.0 1.0
CA A:ASP150 5.0 17.4 1.0

Sodium binding site 2 out of 9 in 3ifv

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Sodium binding site 2 out of 9 in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen


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 Haloferax Volcanii Proliferating Cell Nuclear Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:22.3
occ:1.00
 O A:ASP146 2.3 13.8 1.0
OD1 A:ASP150 2.3 20.1 1.0
O A:SER149 2.4 15.1 1.0
OD1 A:ASP146 2.4 18.8 1.0
O A:HOH257 2.5 26.4 1.0
O A:HOH294 2.7 19.7 1.0
C A:SER149 3.2 17.4 1.0
C A:ASP146 3.2 17.1 1.0
CA A:ASP146 3.4 15.7 1.0
CG A:ASP146 3.4 15.1 1.0
CG A:ASP150 3.5 20.9 1.0
NA A:NA401 3.8 13.2 1.0
N A:ASP150 3.8 17.6 1.0
O A:HOH321 3.9 25.4 1.0
CA A:ASP150 3.9 17.4 1.0
CB A:ASP146 4.0 14.8 1.0
O A:HOH264 4.0 31.2 1.0
N A:SER149 4.0 19.6 1.0
CA A:SER149 4.1 18.3 1.0
CB A:ASP150 4.4 17.7 1.0
OD2 A:ASP150 4.4 20.5 1.0
OD2 A:ASP146 4.4 19.3 1.0
N A:MET147 4.4 18.2 1.0
O A:ALA145 4.6 14.6 1.0
N A:ASP146 4.7 16.0 1.0
N A:VAL148 4.8 20.8 1.0
C A:VAL148 4.8 20.2 1.0
CD1 A:LEU197 4.9 10.7 1.0
C A:MET147 5.0 20.2 1.0

Sodium binding site 3 out of 9 in 3ifv

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Sodium binding site 3 out of 9 in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen


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 Haloferax Volcanii Proliferating Cell Nuclear Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:27.1
occ:1.00
 O A:HOH304 1.8 20.9 1.0
O A:HOH261 2.1 31.2 1.0
O A:LEU127 2.6 26.8 1.0
O A:HOH258 2.7 15.7 1.0
C A:LEU127 3.8 26.3 1.0
N A:LEU127 4.0 31.1 1.0
OE1 A:GLU187 4.3 38.4 1.0
C A:ASP126 4.3 33.7 1.0
CA A:ASP126 4.4 34.3 1.0
O A:ALA129 4.4 18.9 1.0
OE2 A:GLU216 4.4 32.9 1.0
CA A:LEU127 4.5 28.8 1.0
C A:ALA128 4.5 22.6 1.0
O A:ALA128 4.6 19.7 1.0
O A:HOH256 4.7 31.4 1.0
N A:ALA129 4.7 20.8 1.0
N A:ALA128 4.8 24.6 1.0
C A:ALA129 4.8 18.6 1.0
CA A:ALA128 4.8 22.1 1.0
CB A:ASP126 4.9 33.3 1.0
CB A:LEU127 5.0 29.1 1.0
CB A:ASN130 5.0 19.9 1.0

Sodium binding site 4 out of 9 in 3ifv

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Sodium binding site 4 out of 9 in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen


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 Haloferax Volcanii Proliferating Cell Nuclear Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:18.7
occ:1.00
 O B:HOH269 2.1 33.5 1.0
O B:HOH248 2.1 24.7 1.0
O B:HOH253 2.2 21.6 1.0
OD2 B:ASP150 2.5 30.7 1.0
O B:HOH265 2.5 23.6 1.0
OD1 B:ASP150 2.6 27.9 1.0
O B:HOH249 2.6 25.6 1.0
CG B:ASP150 2.9 25.6 1.0
NA B:NA405 3.5 28.7 1.0
OD2 B:ASP198 4.2 36.7 1.0
OD1 B:ASP146 4.4 24.1 1.0
CB B:ASP150 4.4 25.5 1.0
O B:HOH291 4.4 31.3 1.0
O B:HOH282 4.5 33.5 1.0
OD1 B:ASP198 4.7 34.1 1.0
CG B:ASP198 4.9 30.9 1.0

Sodium binding site 5 out of 9 in 3ifv

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Sodium binding site 5 out of 9 in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen


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 Haloferax Volcanii Proliferating Cell Nuclear Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:28.7
occ:1.00
 OD1 B:ASP150 2.1 27.9 1.0
O B:HOH291 2.4 31.3 1.0
O B:SER149 2.4 26.9 1.0
OD1 B:ASP146 2.5 24.1 1.0
O B:ASP146 2.6 26.4 1.0
O B:HOH253 2.7 21.6 1.0
C B:SER149 3.1 26.6 1.0
CG B:ASP150 3.3 25.6 1.0
C B:ASP146 3.5 26.6 1.0
O B:HOH269 3.5 33.5 1.0
NA B:NA404 3.5 18.7 1.0
CG B:ASP146 3.5 28.0 1.0
CA B:ASP146 3.6 25.4 1.0
N B:ASP150 3.7 24.0 1.0
O B:HOH265 3.8 23.6 1.0
CA B:ASP150 3.9 23.1 1.0
N B:SER149 4.0 27.3 1.0
CA B:SER149 4.0 26.9 1.0
OD2 B:ASP150 4.2 30.7 1.0
CB B:ASP146 4.2 24.4 1.0
CB B:ASP150 4.2 25.5 1.0
OD2 B:ASP146 4.5 27.2 1.0
N B:MET147 4.7 27.7 1.0
O B:ALA145 4.9 24.3 1.0
N B:ASP146 5.0 24.4 1.0
CD2 B:LEU197 5.0 20.8 1.0

Sodium binding site 6 out of 9 in 3ifv

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Sodium binding site 6 out of 9 in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen


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 Haloferax Volcanii Proliferating Cell Nuclear Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:24.2
occ:1.00
 O B:HOH260 2.0 31.7 1.0
O B:LEU127 2.6 29.0 1.0
O B:HOH259 2.6 22.5 1.0
C B:LEU127 3.8 25.9 1.0
OE1 B:GLU216 4.2 34.7 1.0
N B:LEU127 4.2 25.2 1.0
OE1 B:GLU187 4.3 33.6 1.0
O B:ALA128 4.4 18.9 1.0
O B:ALA129 4.5 21.3 1.0
CA B:LEU127 4.6 25.3 1.0
C B:ALA128 4.6 22.0 1.0
N B:ALA128 4.7 24.9 1.0
CB B:ASN130 4.8 22.5 1.0
CA B:ALA128 4.8 22.8 1.0

Sodium binding site 7 out of 9 in 3ifv

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Sodium binding site 7 out of 9 in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen


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 Haloferax Volcanii Proliferating Cell Nuclear Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na407

b:14.5
occ:1.00
 O C:HOH252 2.1 26.3 1.0
O C:HOH357 2.2 24.3 1.0
OD2 C:ASP150 2.2 31.6 1.0
OD1 C:ASP150 2.4 23.3 1.0
O C:HOH266 2.5 28.9 1.0
O C:HOH287 2.5 30.8 1.0
O C:HOH286 2.5 32.0 1.0
CG C:ASP150 2.7 23.8 1.0
NA C:NA408 3.7 26.5 1.0
CB C:ASP150 4.2 20.3 1.0
OD1 C:ASP146 4.4 20.3 1.0
OD2 C:ASP198 4.5 30.3 1.0
O C:HOH276 4.6 41.7 1.0
OD1 C:ASP198 4.6 28.5 1.0
CG C:ASP198 5.0 24.3 1.0

Sodium binding site 8 out of 9 in 3ifv

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Sodium binding site 8 out of 9 in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen


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 Haloferax Volcanii Proliferating Cell Nuclear Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na408

b:26.5
occ:1.00
 OD1 C:ASP150 2.3 23.3 1.0
OD1 C:ASP146 2.3 20.3 1.0
O C:ASP146 2.4 18.0 1.0
O C:SER149 2.5 16.2 1.0
O C:HOH286 2.5 32.0 1.0
C C:SER149 3.2 17.3 1.0
C C:ASP146 3.3 19.5 1.0
CG C:ASP146 3.4 19.6 1.0
CG C:ASP150 3.5 23.8 1.0
O C:HOH252 3.5 26.3 1.0
CA C:ASP146 3.5 18.7 1.0
O C:HOH266 3.7 28.9 1.0
NA C:NA407 3.7 14.5 1.0
N C:ASP150 3.8 16.0 1.0
CA C:ASP150 4.0 17.4 1.0
N C:SER149 4.0 17.9 1.0
CB C:ASP146 4.0 18.5 1.0
CA C:SER149 4.1 18.1 1.0
O C:HOH276 4.3 41.7 1.0
OD2 C:ASP146 4.3 18.8 1.0
CB C:ASP150 4.3 20.3 1.0
OD2 C:ASP150 4.4 31.6 1.0
N C:MET147 4.5 20.1 1.0
O C:ALA145 4.8 16.3 1.0
N C:ASP146 4.8 18.0 1.0
C C:MET147 4.9 20.2 1.0

Sodium binding site 9 out of 9 in 3ifv

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Sodium binding site 9 out of 9 in the Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Haloferax Volcanii Proliferating Cell Nuclear Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na409

b:22.9
occ:1.00
 O C:HOH256 2.1 24.4 1.0
O C:LEU127 2.4 23.0 1.0
O C:HOH325 2.5 34.1 1.0
O C:HOH257 2.5 18.4 1.0
O C:HOH282 2.7 29.6 1.0
C C:LEU127 3.6 21.9 1.0
N C:LEU127 4.0 26.8 1.0
C C:ASP126 4.1 29.7 1.0
OE1 C:GLU216 4.3 30.9 1.0
OE1 C:GLU187 4.4 34.4 1.0
O C:ASP126 4.4 31.0 1.0
O C:ALA128 4.4 15.9 1.0
CA C:LEU127 4.4 24.6 1.0
O C:ALA129 4.4 16.2 1.0
C C:ALA128 4.5 16.9 1.0
N C:ALA128 4.6 19.4 1.0
CA C:ASP126 4.6 29.1 1.0
CB C:ASN130 4.8 16.4 1.0
C C:ALA129 4.8 16.0 1.0
N C:ALA129 4.8 14.7 1.0
CA C:ALA128 4.8 17.8 1.0

Reference:

J.A.Winter, P.Christofi, S.Morroll, K.A.Bunting. The Crystal Structure of Haloferax Volcanii Proliferating Cell Nuclear Antigen Reveals Unique Surface Charge Characteristics Due to Halophilic Adaptation Bmc Struct.Biol. V. 9 55 2009.
ISSN: ESSN 1472-6807
PubMed: 19698123
DOI: 10.1186/1472-6807-9-55
Page generated: Tue Dec 15 06:14:49 2020

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