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Sodium in PDB 1x0g: Crystal Structure of Isca with the [2FE-2S] Cluster

Protein crystallography data

The structure of Crystal Structure of Isca with the [2FE-2S] Cluster, PDB code: 1x0g was solved by K.Morimoto, E.Yamashita, Y.Kondou, S.J.Lee, T.Tsukihara, M.Nakai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 77.472, 102.788, 137.032, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.1

Other elements in 1x0g:

The structure of Crystal Structure of Isca with the [2FE-2S] Cluster also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Isca with the [2FE-2S] Cluster (pdb code 1x0g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Isca with the [2FE-2S] Cluster, PDB code: 1x0g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1x0g

Go back to Sodium Binding Sites List in 1x0g
Sodium binding site 1 out of 2 in the Crystal Structure of Isca with the [2FE-2S] Cluster


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 Isca with the [2FE-2S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:54.7
occ:1.00
O D:GLU36 2.3 62.0 1.0
O A:GLU36 2.3 61.3 1.0
O A:GLY38 2.5 59.1 1.0
O D:HOH120 2.6 54.7 1.0
O A:SER35 2.7 61.6 1.0
C A:GLU36 3.1 60.6 1.0
CA A:GLU36 3.4 60.5 1.0
C D:GLU36 3.4 61.8 1.0
C A:SER35 3.7 60.8 1.0
OG D:SER35 3.7 58.3 1.0
C A:GLY38 3.7 59.5 1.0
CB D:CYS37 3.9 57.8 1.0
CA D:CYS37 3.9 57.7 1.0
N A:GLU36 4.0 60.5 1.0
NH1 B:ARG41 4.0 96.0 1.0
N D:CYS37 4.1 60.9 1.0
N A:GLY38 4.1 57.4 1.0
C A:CYS37 4.2 59.6 1.0
O A:CYS37 4.2 60.5 1.0
N A:CYS37 4.2 61.7 1.0
NH2 A:ARG108 4.4 85.2 1.0
N D:GLU36 4.4 59.3 1.0
OD1 B:ASP39 4.5 77.8 1.0
CA A:GLY38 4.5 58.1 1.0
CA D:GLU36 4.6 61.9 1.0
CA A:CYS37 4.7 61.1 1.0
CB A:GLU36 4.7 59.0 1.0
N A:ASP39 4.7 59.1 1.0
CA A:ASP39 4.8 59.7 1.0
CB D:SER35 5.0 58.0 1.0
OD1 A:ASP39 5.0 63.2 1.0

Sodium binding site 2 out of 2 in 1x0g

Go back to Sodium Binding Sites List in 1x0g
Sodium binding site 2 out of 2 in the Crystal Structure of Isca with the [2FE-2S] Cluster


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 Isca with the [2FE-2S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1001

b:55.6
occ:1.00
O D:HOH116 2.1 56.6 1.0
O B:GLU36 2.4 51.2 1.0
O C:SER35 2.5 61.2 1.0
O C:GLY38 2.7 58.4 1.0
O C:GLU36 2.8 65.5 1.0
C C:GLU36 3.3 63.3 1.0
CA C:GLU36 3.5 62.3 1.0
C B:GLU36 3.6 53.0 1.0
C C:SER35 3.6 60.8 1.0
OG B:SER35 3.6 59.3 1.0
CB B:CYS37 3.7 57.0 1.0
C C:GLY38 3.9 59.6 1.0
N C:GLU36 4.0 61.5 1.0
CA B:CYS37 4.1 56.0 1.0
OD1 D:ASP39 4.2 69.4 1.0
N C:CYS37 4.2 63.5 1.0
N B:CYS37 4.2 53.7 1.0
N C:GLY38 4.3 62.5 1.0
N B:GLU36 4.3 50.4 1.0
C C:CYS37 4.4 63.6 1.0
CB B:SER35 4.6 52.1 1.0
CA C:GLY38 4.6 60.2 1.0
CA B:GLU36 4.6 53.0 1.0
CA C:CYS37 4.6 63.5 1.0
O C:CYS37 4.8 65.8 1.0
CB C:GLU36 4.8 62.4 1.0
CA C:SER35 4.8 60.2 1.0
N C:ASP39 4.9 59.9 1.0
CA C:ASP39 4.9 61.2 1.0

Reference:

K.Morimoto, E.Yamashita, Y.Kondou, S.J.Lee, F.Arisaka, T.Tsukihara, M.Nakai. The Asymmetric Isca Homodimer with An Exposed [2FE-2S] Cluster Suggests the Structural Basis of the Fe-S Cluster Biosynthetic Scaffold. J.Mol.Biol. V. 360 117 2006.
ISSN: ISSN 0022-2836
PubMed: 16730357
DOI: 10.1016/J.JMB.2006.04.067
Page generated: Tue Dec 15 05:41:28 2020

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