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Sodium in PDB 1vi6: Crystal Structure of Ribosomal Protein S2P

Protein crystallography data

The structure of Crystal Structure of Ribosomal Protein S2P, PDB code: 1vi6 was solved by Structural Genomix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.48 / 1.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 123.829, 123.829, 131.949, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ribosomal Protein S2P (pdb code 1vi6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Ribosomal Protein S2P, PDB code: 1vi6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 1vi6

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Sodium binding site 1 out of 10 in the Crystal Structure of Ribosomal Protein S2P


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 Ribosomal Protein S2P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:19.8
occ:1.00
 O A:HOH261 2.3 32.2 1.0
O A:ASP152 2.3 18.8 1.0
O A:HOH232 2.4 20.0 1.0
OG1 A:THR134 2.6 17.3 1.0
OD1 A:ASP154 2.6 16.7 1.0
C A:ASP152 3.3 17.4 1.0
CG A:ASP154 3.4 16.2 1.0
CB A:THR134 3.6 20.7 1.0
OD2 A:ASP154 3.6 18.9 1.0
CG2 A:THR134 3.6 19.8 1.0
CG2 A:VAL140 3.7 13.5 1.0
CB A:VAL140 3.9 15.5 1.0
CA A:ASP152 3.9 20.2 1.0
CA A:THR134 4.0 20.1 1.0
O A:ILE138 4.2 15.4 1.0
N A:VAL140 4.2 16.7 1.0
CB A:ASP152 4.3 24.2 1.0
O A:HOH348 4.4 29.3 1.0
N A:VAL153 4.4 16.2 1.0
N A:ASP154 4.5 15.8 1.0
O A:HOH247 4.5 29.1 1.0
N A:THR134 4.7 16.9 1.0
CA A:VAL153 4.7 14.3 1.0
CA A:VAL140 4.7 15.0 1.0
CB A:ASP154 4.8 13.9 1.0
C A:VAL153 4.8 14.7 1.0

Sodium binding site 2 out of 10 in 1vi6

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Sodium binding site 2 out of 10 in the Crystal Structure of Ribosomal Protein S2P


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 Ribosomal Protein S2P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:23.3
occ:1.00
 O A:HOH357 2.4 29.5 1.0
OD2 A:ASP145 2.4 16.6 1.0
O A:ILE22 2.6 19.5 1.0
O A:GLY23 3.2 23.6 1.0
OD1 A:ASN160 3.2 22.9 1.0
CG A:ASP145 3.3 17.4 1.0
C A:GLY23 3.3 20.6 1.0
CG A:ASN160 3.4 19.5 1.0
OD1 A:ASP145 3.4 17.1 1.0
CA A:GLY23 3.5 18.1 1.0
C A:ILE22 3.6 18.1 1.0
CB A:ASN160 3.9 14.4 1.0
CG2 A:THR24 3.9 18.3 1.0
ND2 A:ASN160 3.9 17.0 1.0
N A:GLY23 4.0 16.0 1.0
CA A:ASN160 4.0 13.8 1.0
N A:THR24 4.1 19.3 1.0
O A:HOH314 4.1 32.8 1.0
CD A:LYS162 4.3 19.8 1.0
O A:HOH256 4.5 35.4 1.0
NZ A:LYS162 4.6 15.8 1.0
CB A:ASP145 4.7 13.6 1.0
CG A:LYS162 4.7 16.5 1.0
CB A:LYS162 4.8 17.1 1.0
CA A:THR24 4.8 19.0 1.0
N A:ASN161 4.8 14.2 1.0
C A:ASN160 4.8 14.6 1.0
CG2 A:ILE22 4.8 22.6 1.0
CA A:ILE22 4.9 19.1 1.0
CE A:LYS162 4.9 16.5 1.0
CB A:ILE22 5.0 24.5 1.0
CB A:THR24 5.0 22.1 1.0

Sodium binding site 3 out of 10 in 1vi6

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Sodium binding site 3 out of 10 in the Crystal Structure of Ribosomal Protein S2P


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 Ribosomal Protein S2P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na210

b:42.2
occ:1.00
 O A:PHE186 2.2 22.8 1.0
O A:HOH366 2.3 46.2 1.0
O A:HOH351 2.4 39.6 1.0
O A:HOH365 2.4 36.1 1.0
O A:HOH274 2.6 30.3 1.0
C A:PHE186 3.3 20.1 1.0
N A:PHE186 3.9 22.6 1.0
CA A:PHE186 4.1 19.2 1.0
CB A:PHE186 4.3 19.7 1.0
N A:THR187 4.4 18.3 1.0
O A:HOH267 4.4 29.1 1.0
OD1 A:ASP185 4.4 27.1 1.0
CA A:THR187 4.6 21.0 1.0
O A:HOH352 4.6 34.7 1.0
CD1 A:PHE186 4.7 19.5 1.0
CG2 A:THR187 4.7 25.8 1.0
O A:HOH284 4.9 34.1 1.0

Sodium binding site 4 out of 10 in 1vi6

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Sodium binding site 4 out of 10 in the Crystal Structure of Ribosomal Protein S2P


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 Ribosomal Protein S2P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na208

b:19.4
occ:1.00
 O B:HOH233 2.2 22.0 1.0
O B:ASP152 2.2 17.8 1.0
O B:HOH221 2.3 18.4 1.0
OD1 B:ASP154 2.6 14.8 1.0
OG1 B:THR134 2.7 17.9 1.0
C B:ASP152 3.2 17.8 1.0
CG B:ASP154 3.4 13.1 1.0
OD2 B:ASP154 3.5 14.8 1.0
CG2 B:VAL140 3.6 14.1 1.0
CB B:THR134 3.7 15.7 1.0
CG2 B:THR134 3.8 19.4 1.0
CA B:ASP152 3.8 19.8 1.0
CB B:VAL140 3.8 15.1 1.0
CA B:THR134 4.1 16.2 1.0
CB B:ASP152 4.2 21.9 1.0
N B:VAL140 4.2 13.5 1.0
N B:VAL153 4.3 14.2 1.0
O B:ILE138 4.4 12.5 1.0
O B:HOH331 4.4 28.8 1.0
N B:ASP154 4.5 12.8 1.0
O B:HOH242 4.6 24.0 1.0
N B:THR134 4.6 15.6 1.0
CA B:VAL153 4.6 13.4 1.0
CB B:ASP154 4.7 13.4 1.0
CA B:VAL140 4.7 13.7 1.0
C B:VAL153 4.7 15.6 1.0
CG1 B:VAL140 5.0 15.0 1.0

Sodium binding site 5 out of 10 in 1vi6

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Sodium binding site 5 out of 10 in the Crystal Structure of Ribosomal Protein S2P


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 Ribosomal Protein S2P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na209

b:29.1
occ:1.00
 O B:HOH336 2.4 33.6 1.0
OD2 B:ASP145 2.5 22.6 1.0
O B:ILE22 2.7 26.2 1.0
CG B:ASP145 3.3 23.1 1.0
C B:GLY23 3.3 25.1 1.0
O B:GLY23 3.3 28.6 1.0
OD1 B:ASP145 3.4 20.3 1.0
CA B:GLY23 3.4 24.2 1.0
CG B:ASN160 3.5 24.5 1.0
OD1 B:ASN160 3.5 21.3 1.0
C B:ILE22 3.7 25.1 1.0
CG2 B:THR24 3.7 23.5 1.0
ND2 B:ASN160 3.8 24.6 1.0
N B:THR24 4.0 22.6 1.0
CB B:ASN160 4.0 17.8 1.0
N B:GLY23 4.0 24.9 1.0
CA B:ASN160 4.1 19.0 1.0
CD B:LYS162 4.2 23.2 1.0
CA B:THR24 4.6 24.6 1.0
NZ B:LYS162 4.7 20.9 1.0
CG B:LYS162 4.8 24.6 1.0
CB B:ASP145 4.8 18.2 1.0
CE B:LYS162 4.8 24.6 1.0
CB B:THR24 4.8 26.6 1.0
N B:ASN161 4.9 15.8 1.0
CB B:LYS162 4.9 22.4 1.0
C B:ASN160 4.9 17.2 1.0

Sodium binding site 6 out of 10 in 1vi6

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Sodium binding site 6 out of 10 in the Crystal Structure of Ribosomal Protein S2P


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 Ribosomal Protein S2P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na208

b:22.8
occ:1.00
 O C:HOH356 2.2 31.6 1.0
OD2 C:ASP145 2.3 20.6 1.0
O C:ILE22 2.4 22.1 1.0
O C:GLY23 2.6 25.8 1.0
OD1 C:ASN160 2.6 18.7 1.0
CG C:ASN160 3.1 18.0 1.0
C C:GLY23 3.2 22.2 1.0
CG C:ASP145 3.2 21.3 1.0
OD1 C:ASP145 3.4 20.6 1.0
C C:ILE22 3.4 21.6 1.0
CA C:GLY23 3.5 21.0 1.0
CB C:ASN160 3.6 18.0 1.0
CA C:ASN160 3.8 19.6 1.0
CG2 C:THR24 3.9 22.7 1.0
N C:GLY23 3.9 19.3 1.0
ND2 C:ASN160 4.0 19.0 1.0
N C:THR24 4.2 19.8 1.0
CD C:LYS162 4.2 23.0 1.0
O C:HOH247 4.4 34.1 1.0
O C:HOH275 4.4 36.6 1.0
CG2 C:ILE22 4.6 25.3 1.0
C C:ASN160 4.6 19.3 1.0
NZ C:LYS162 4.6 19.9 1.0
N C:ASN161 4.6 18.6 1.0
CB C:LYS162 4.6 21.4 1.0
CB C:ASP145 4.6 19.3 1.0
CG C:LYS162 4.7 22.5 1.0
CA C:ILE22 4.7 22.1 1.0
CB C:ILE22 4.8 25.2 1.0
CA C:THR24 4.8 23.0 1.0
CE C:LYS162 4.9 22.4 1.0
N C:LYS162 4.9 18.5 1.0
CB C:THR24 5.0 21.7 1.0

Sodium binding site 7 out of 10 in 1vi6

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Sodium binding site 7 out of 10 in the Crystal Structure of Ribosomal Protein S2P


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 Ribosomal Protein S2P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na209

b:24.1
occ:1.00
 O C:ASP152 2.2 24.4 1.0
O C:HOH226 2.3 21.0 1.0
O C:HOH234 2.5 28.3 1.0
OG1 C:THR134 2.5 17.9 1.0
OD1 C:ASP154 2.6 16.7 1.0
C C:ASP152 3.3 20.8 1.0
CG C:ASP154 3.4 18.9 1.0
CB C:THR134 3.5 19.2 1.0
CG2 C:VAL140 3.6 16.4 1.0
OD2 C:ASP154 3.7 20.0 1.0
CG2 C:THR134 3.7 20.1 1.0
CA C:ASP152 3.8 22.2 1.0
CB C:VAL140 3.9 15.4 1.0
CA C:THR134 4.0 21.6 1.0
CB C:ASP152 4.2 23.6 1.0
O C:ILE138 4.2 18.0 1.0
N C:VAL140 4.3 15.9 1.0
N C:VAL153 4.4 17.0 1.0
N C:ASP154 4.5 18.9 1.0
N C:THR134 4.6 20.8 1.0
O C:HOH294 4.7 30.8 1.0
CA C:VAL153 4.7 17.7 1.0
CB C:ASP154 4.7 20.5 1.0
CA C:VAL140 4.7 15.6 1.0
C C:VAL153 4.8 20.5 1.0
O C:VAL130 4.9 20.4 1.0

Sodium binding site 8 out of 10 in 1vi6

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Sodium binding site 8 out of 10 in the Crystal Structure of Ribosomal Protein S2P


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 Ribosomal Protein S2P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na210

b:42.9
occ:1.00
 O C:PHE186 2.2 23.2 1.0
O C:HOH282 2.5 25.5 1.0
O C:HOH261 2.6 29.9 1.0
O C:HOH357 2.7 41.0 1.0
C C:PHE186 3.3 20.3 1.0
N C:PHE186 3.9 24.6 1.0
CA C:PHE186 4.0 21.2 1.0
CB C:PHE186 4.2 19.3 1.0
N C:THR187 4.4 20.5 1.0
O C:HOH262 4.5 42.1 1.0
O C:HOH299 4.6 31.3 1.0
CD1 C:PHE186 4.6 20.9 1.0
CA C:THR187 4.6 23.2 1.0
OD1 C:ASP185 4.7 28.5 1.0
O C:HOH263 4.7 34.0 1.0
CG2 C:THR187 4.8 26.1 1.0
CG C:PHE186 4.9 19.2 1.0

Sodium binding site 9 out of 10 in 1vi6

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Sodium binding site 9 out of 10 in the Crystal Structure of Ribosomal Protein S2P


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 Ribosomal Protein S2P within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na208

b:21.1
occ:1.00
 O D:ASP152 2.3 21.2 1.0
O D:HOH224 2.3 15.8 1.0
O D:HOH226 2.4 20.5 1.0
OG1 D:THR134 2.4 16.3 1.0
OD1 D:ASP154 2.7 18.6 1.0
C D:ASP152 3.3 20.1 1.0
CG D:ASP154 3.5 18.6 1.0
CB D:THR134 3.5 18.1 1.0
CG2 D:VAL140 3.6 16.8 1.0
OD2 D:ASP154 3.6 19.7 1.0
CG2 D:THR134 3.8 19.8 1.0
CA D:ASP152 3.8 22.4 1.0
CA D:THR134 3.9 18.5 1.0
CB D:VAL140 3.9 17.1 1.0
O D:HOH243 4.0 36.2 1.0
CB D:ASP152 4.2 19.8 1.0
O D:ILE138 4.3 20.3 1.0
N D:VAL140 4.4 16.4 1.0
N D:VAL153 4.4 19.1 1.0
N D:THR134 4.5 16.5 1.0
N D:ASP154 4.6 17.9 1.0
O D:HOH236 4.7 26.7 1.0
CA D:VAL153 4.8 17.8 1.0
CA D:VAL140 4.8 17.1 1.0
O D:VAL130 4.8 17.5 1.0
CB D:ASP154 4.8 18.9 1.0
C D:VAL153 4.9 20.6 1.0

Sodium binding site 10 out of 10 in 1vi6

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Sodium binding site 10 out of 10 in the Crystal Structure of Ribosomal Protein S2P


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Ribosomal Protein S2P within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na209

b:24.4
occ:1.00
 OD2 D:ASP145 2.3 20.1 1.0
O D:ILE22 2.4 21.1 1.0
O D:HOH332 2.6 40.1 1.0
OD1 D:ASN160 2.7 21.8 1.0
O D:GLY23 2.8 25.8 1.0
CG D:ASP145 3.1 18.7 1.0
CG D:ASN160 3.3 15.7 1.0
OD1 D:ASP145 3.3 20.7 1.0
C D:GLY23 3.3 21.7 1.0
C D:ILE22 3.5 22.3 1.0
CA D:GLY23 3.6 19.3 1.0
CG2 D:THR24 3.7 19.8 1.0
CB D:ASN160 3.7 12.4 1.0
CA D:ASN160 3.9 15.7 1.0
N D:GLY23 4.0 19.3 1.0
ND2 D:ASN160 4.1 14.6 1.0
CD D:LYS162 4.2 23.0 1.0
O D:HOH237 4.2 25.0 1.0
N D:THR24 4.2 18.0 1.0
CB D:ASP145 4.6 15.6 1.0
NZ D:LYS162 4.6 19.7 1.0
CG2 D:ILE22 4.6 25.5 1.0
CG D:LYS162 4.6 21.9 1.0
N D:ASN161 4.7 15.6 1.0
C D:ASN160 4.7 16.0 1.0
CB D:LYS162 4.7 20.0 1.0
CA D:ILE22 4.7 21.4 1.0
CA D:THR24 4.7 18.0 1.0
O D:HOH256 4.8 33.7 1.0
CE D:LYS162 4.8 25.3 1.0
CB D:ILE22 4.8 25.5 1.0
CB D:THR24 4.9 20.0 1.0

Reference:

J.Badger, J.M.Sauder, J.M.Adams, S.Antonysamy, K.Bain, M.G.Bergseid, S.G.Buchanan, M.D.Buchanan, Y.Batiyenko, J.A.Christopher, S.Emtage, A.Eroshkina, I.Feil, E.B.Furlong, K.S.Gajiwala, X.Gao, D.He, J.Hendle, A.Huber, K.Hoda, P.Kearins, C.Kissinger, B.Laubert, H.A.Lewis, J.Lin, K.Loomis, D.Lorimer, G.Louie, M.Maletic, C.D.Marsh, I.Miller, J.Molinari, H.J.Muller-Dieckmann, J.M.Newman, B.W.Noland, B.Pagarigan, F.Park, T.S.Peat, K.W.Post, S.Radojicic, A.Ramos, R.Romero, M.E.Rutter, W.E.Sanderson, K.D.Schwinn, J.Tresser, J.Winhoven, T.A.Wright, L.Wu, J.Xu, T.J.Harris. Structural Analysis of A Set of Proteins Resulting From A Bacterial Genomics Project Proteins V. 60 787 2005.
ISSN: ISSN 0887-3585
PubMed: 16021622
DOI: 10.1002/PROT.20541
Page generated: Sun Oct 6 22:53:00 2024

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