Atomistry » Sodium » PDB 3ogc-3p1l » 3osj
Atomistry »
  Sodium »
    PDB 3ogc-3p1l »
      3osj »

Sodium in PDB 3osj: X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C

Protein crystallography data

The structure of X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C, PDB code: 3osj was solved by A.Kuzin, M.Su, S.Lew, J.Seetharaman, S.Sahdev, R.Xiao, C.Ciccosanti, D.Lee, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.29 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.568, 79.607, 73.705, 90.00, 95.50, 90.00
R / Rfree (%) 16.2 / 22.8

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C (pdb code 3osj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C, PDB code: 3osj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 3osj

Go back to Sodium Binding Sites List in 3osj
Sodium binding site 1 out of 7 in the X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2

b:7.6
occ:1.00
O A:HOH123 3.2 18.8 1.0
O A:HOH128 3.5 19.9 1.0
NH1 A:ARG322 3.5 1.9 1.0
CD2 A:LEU305 3.8 7.3 1.0
CD A:ARG322 3.9 11.6 1.0
CE2 A:TYR304 4.2 4.0 1.0
CZ A:ARG322 4.2 9.8 1.0
NE A:ARG322 4.3 12.0 1.0
CD2 A:TYR304 4.5 5.1 1.0
CG A:LEU305 4.8 12.8 1.0
CG A:ARG322 4.9 14.1 1.0

Sodium binding site 2 out of 7 in 3osj

Go back to Sodium Binding Sites List in 3osj
Sodium binding site 2 out of 7 in the X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4

b:22.7
occ:1.00
CD A:PRO327 3.7 14.7 1.0
OG A:SER299 3.7 29.3 1.0
N A:LEU328 3.8 13.8 1.0
CB A:SER326 3.9 6.8 1.0
O A:HOH407 3.9 33.7 1.0
N A:PRO327 4.0 8.6 1.0
CD1 A:ILE302 4.0 30.2 1.0
CB A:LEU328 4.1 21.0 1.0
CG1 A:ILE302 4.2 21.7 1.0
OG A:SER326 4.2 11.7 1.0
CB A:PRO327 4.2 14.1 1.0
CG A:PRO327 4.2 18.3 1.0
CB A:SER299 4.3 26.6 1.0
CE2 A:TYR298 4.3 44.0 1.0
CD2 A:TYR298 4.5 38.4 1.0
CA A:LEU328 4.5 14.4 1.0
CA A:PRO327 4.6 11.6 1.0
C A:PRO327 4.7 14.9 1.0
C A:SER326 4.7 11.7 1.0
CA A:SER326 4.7 8.8 1.0
O A:HOH403 4.8 26.6 1.0
CB A:SER301 4.9 24.3 1.0

Sodium binding site 3 out of 7 in 3osj

Go back to Sodium Binding Sites List in 3osj
Sodium binding site 3 out of 7 in the X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na7

b:11.8
occ:1.00
NZ A:LYS325 3.1 9.6 1.0
CE A:LYS325 3.7 8.7 1.0
CB A:PRO374 3.8 4.4 1.0
O A:HOH416 4.0 32.0 1.0
CD A:LYS325 4.1 8.0 1.0
OD2 A:ASP378 4.3 12.4 1.0
O A:HOH31 4.6 10.3 1.0
CG A:PRO374 4.7 1.7 1.0
CA A:PRO374 4.8 10.0 1.0

Sodium binding site 4 out of 7 in 3osj

Go back to Sodium Binding Sites List in 3osj
Sodium binding site 4 out of 7 in the X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na6

b:26.4
occ:1.00
O B:HOH471 3.4 43.2 1.0
OG B:SER299 3.6 23.4 1.0
CD B:PRO327 3.7 11.7 1.0
N B:LEU328 3.9 12.8 1.0
CD1 B:ILE302 3.9 42.4 1.0
CB B:SER326 4.0 10.7 1.0
O B:HOH420 4.0 31.8 1.0
CB B:LEU328 4.0 2.4 1.0
CG1 B:ILE302 4.1 35.5 1.0
CG B:PRO327 4.1 13.5 1.0
CB B:SER299 4.2 25.9 1.0
CB B:PRO327 4.2 12.8 1.0
N B:PRO327 4.3 13.3 1.0
CE2 B:TYR298 4.4 74.3 1.0
OG B:SER326 4.4 7.3 1.0
CA B:LEU328 4.6 8.3 1.0
CB B:SER301 4.7 21.2 1.0
CA B:PRO327 4.8 12.6 1.0
CD2 B:TYR298 4.8 70.2 1.0
O B:HOH401 4.8 24.7 1.0
OG B:SER301 4.8 26.0 1.0
C B:PRO327 4.9 11.9 1.0
CA B:SER326 4.9 14.1 1.0
C B:SER326 4.9 15.2 1.0

Sodium binding site 5 out of 7 in 3osj

Go back to Sodium Binding Sites List in 3osj
Sodium binding site 5 out of 7 in the X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3

b:19.2
occ:1.00
OH C:TYR329 2.8 10.9 1.0
O C:PHE333 2.8 10.2 1.0
O C:ALA342 2.8 15.5 1.0
N C:ALA346 3.4 9.6 1.0
CE2 C:TYR329 3.4 12.0 1.0
CZ C:TYR329 3.5 12.3 1.0
CB C:ALA346 3.6 7.7 1.0
C C:ALA342 3.7 10.1 1.0
C C:PHE333 3.7 10.4 1.0
CA C:ALA346 3.7 8.9 1.0
CB C:PHE333 3.8 9.1 1.0
CB C:LEU345 3.8 9.3 1.0
C C:LEU345 3.9 8.9 1.0
CA C:ALA342 3.9 11.7 1.0
CB C:ALA342 4.2 5.6 1.0
CA C:PHE333 4.4 13.1 1.0
CA C:LEU345 4.4 7.5 1.0
O C:LEU345 4.5 7.0 1.0
CD2 C:TYR329 4.6 7.2 1.0
N C:PHE334 4.7 12.8 1.0
CE1 C:TYR329 4.8 7.5 1.0
CD2 C:HIS349 4.8 6.3 1.0
N C:LEU345 4.8 8.6 1.0
CA C:PHE334 4.9 12.7 1.0
CG C:PHE333 4.9 4.3 1.0
N C:LEU343 4.9 9.2 1.0
CD1 C:LEU373 5.0 10.0 1.0

Sodium binding site 6 out of 7 in 3osj

Go back to Sodium Binding Sites List in 3osj
Sodium binding site 6 out of 7 in the X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na5

b:23.9
occ:1.00
N C:LEU328 3.6 13.1 1.0
CD C:PRO327 3.7 14.1 1.0
CB C:LEU328 3.7 8.7 1.0
CD1 C:ILE302 3.8 27.2 1.0
O C:HOH469 3.8 41.0 1.0
CB C:SER326 3.9 8.1 1.0
OG C:SER299 4.0 35.4 1.0
N C:PRO327 4.0 13.2 1.0
CG1 C:ILE302 4.1 26.5 1.0
CG C:PRO327 4.1 13.0 1.0
CB C:PRO327 4.1 9.0 1.0
OG C:SER326 4.2 8.4 1.0
O C:HOH231 4.3 25.2 1.0
CA C:LEU328 4.3 8.3 1.0
C C:PRO327 4.5 13.9 1.0
CA C:PRO327 4.5 6.2 1.0
O C:HOH415 4.6 28.9 1.0
C C:SER326 4.7 15.4 1.0
CB C:SER299 4.7 33.6 1.0
CA C:SER326 4.7 11.8 1.0
CB C:SER301 4.8 21.7 1.0
OG C:SER301 5.0 24.1 1.0

Sodium binding site 7 out of 7 in 3osj

Go back to Sodium Binding Sites List in 3osj
Sodium binding site 7 out of 7 in the X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of X-Ray Structure of Phycobilisome Lcm Core-Membrane Linker Polypeptide (Fragment 254-400) From Synechocystis Sp. Pcc 6803, Northeast Structural Genomics Consortium Target SGR209C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1

b:10.4
occ:1.00
NZ D:LYS325 3.4 4.1 1.0
CB D:PRO374 3.8 13.8 1.0
CE D:LYS325 4.0 9.7 1.0
CD D:LYS325 4.4 6.4 1.0
OD2 D:ASP378 4.4 10.9 1.0
CG D:PRO374 4.6 9.2 1.0
O D:HOH9 4.6 8.7 1.0
O D:HOH445 4.9 30.8 1.0
CA D:PRO374 4.9 11.9 1.0
O D:HOH180 5.0 20.2 1.0

Reference:

A.Kuzin, M.Su, S.Lew, J.Seetharaman, S.Sahdev, R.Xiao, C.Ciccosanti, D.Lee, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelione, L.Tong, J.F.Hunt. Northeast Structural Genomics Consortium Target SGR209C To Be Published.
Page generated: Tue Dec 15 06:20:24 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy