Atomistry » Sodium » PDB 3fak-3fvi » 3frm
Atomistry »
  Sodium »
    PDB 3fak-3fvi »
      3frm »

Sodium in PDB 3frm: The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228.

Protein crystallography data

The structure of The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228., PDB code: 3frm was solved by K.Tan, A.Sather, S.Clancy, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.45 / 2.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.711, 126.549, 112.807, 90.00, 94.52, 90.00
R / Rfree (%) 19.7 / 26.3

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228. (pdb code 3frm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228., PDB code: 3frm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3frm

Go back to Sodium Binding Sites List in 3frm
Sodium binding site 1 out of 6 in the The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na252

b:37.4
occ:1.00
 O A:ASP159 2.1 33.7 1.0
O A:TYR156 2.5 33.1 1.0
O A:ILE161 2.8 30.6 1.0
OD1 A:ASP159 2.9 36.0 1.0
O A:ASN157 2.9 35.8 1.0
C A:ASP159 3.2 35.0 1.0
OE1 A:GLU162 3.6 40.3 1.0
C A:TYR156 3.6 31.8 1.0
C A:ASN157 3.8 34.8 1.0
C A:ILE161 4.0 30.8 1.0
CG A:ASP159 4.0 36.8 1.0
CA A:ASN157 4.1 34.5 1.0
N A:ASP160 4.1 35.4 1.0
C A:ASP160 4.1 35.1 1.0
CA A:ASP159 4.1 34.7 1.0
O A:ASP160 4.2 35.7 1.0
N A:ASP159 4.2 34.4 1.0
CA A:ASP160 4.2 36.5 1.0
N A:ASN157 4.3 33.3 1.0
NH1 A:ARG163 4.4 16.7 1.0
CD A:GLU162 4.4 38.2 1.0
N A:ILE161 4.5 33.7 1.0
CA A:TYR156 4.7 30.4 1.0
CB A:ASP159 4.7 34.8 1.0
OE2 A:GLU162 4.7 38.4 1.0
CA A:ILE161 4.8 31.5 1.0
C A:LEU158 4.8 34.3 1.0
N A:GLU162 4.9 30.2 1.0

Sodium binding site 2 out of 6 in 3frm

Go back to Sodium Binding Sites List in 3frm
Sodium binding site 2 out of 6 in the The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na252

b:28.8
occ:1.00
 OD2 B:ASP159 2.4 21.2 1.0
O B:ASP159 2.6 24.1 1.0
O B:ILE161 2.6 22.4 1.0
O B:TYR156 2.8 14.8 1.0
C B:ASP159 3.3 23.9 1.0
O B:ASN157 3.4 19.1 1.0
CG B:ASP159 3.6 24.4 1.0
C B:ASN157 3.7 18.9 1.0
C B:TYR156 3.7 15.4 1.0
C B:ILE161 3.8 22.2 1.0
OE2 B:GLU162 3.9 40.7 1.0
N B:ILE161 3.9 24.2 1.0
O B:HOH278 4.0 12.0 1.0
N B:ASP159 4.0 23.3 1.0
N B:ASP160 4.0 24.4 1.0
O B:HOH272 4.1 12.3 1.0
CA B:ASN157 4.1 17.6 1.0
CA B:ASP159 4.1 23.7 1.0
CA B:ASP160 4.1 25.5 1.0
NH1 B:ARG163 4.2 21.9 1.0
C B:ASP160 4.3 24.3 1.0
N B:ASN157 4.3 15.8 1.0
N B:LEU158 4.4 20.4 1.0
O B:SER155 4.4 16.0 1.0
CA B:ILE161 4.4 23.0 1.0
CB B:ASP159 4.5 23.3 1.0
CD B:GLU162 4.5 36.2 1.0
OD1 B:ASP159 4.5 27.6 1.0
OE1 B:GLU162 4.6 35.5 1.0
C B:LEU158 4.6 22.3 1.0
N B:GLU162 4.7 21.4 1.0
CA B:TYR156 4.8 15.1 1.0

Sodium binding site 3 out of 6 in 3frm

Go back to Sodium Binding Sites List in 3frm
Sodium binding site 3 out of 6 in the The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na252

b:24.3
occ:1.00
 O C:ASP159 2.4 21.7 1.0
O C:ILE161 2.5 24.2 1.0
O C:HOH296 2.6 21.6 1.0
OD2 C:ASP159 2.7 25.3 1.0
O C:TYR156 2.7 12.9 1.0
O C:ASN157 3.3 18.1 1.0
C C:ASP159 3.5 22.3 1.0
O C:HOH266 3.6 20.7 1.0
C C:ASN157 3.7 17.8 1.0
C C:TYR156 3.7 13.5 1.0
C C:ILE161 3.7 21.8 1.0
CG C:ASP159 4.0 22.6 1.0
CA C:ASN157 4.0 16.6 1.0
N C:ILE161 4.1 22.7 1.0
OE2 C:GLU162 4.2 27.2 1.0
N C:ASP159 4.2 21.0 1.0
N C:ASN157 4.3 14.7 1.0
CA C:ASP159 4.3 21.2 1.0
NH1 C:ARG163 4.3 24.2 1.0
C C:ASP160 4.4 23.1 1.0
N C:LEU158 4.4 18.5 1.0
N C:ASP160 4.4 23.4 1.0
O C:HOH256 4.5 18.4 1.0
O C:SER155 4.5 14.0 1.0
CA C:ILE161 4.5 21.5 1.0
CD C:GLU162 4.5 27.2 1.0
CA C:ASP160 4.5 24.1 1.0
C C:LEU158 4.6 20.8 1.0
OE1 C:GLU162 4.7 25.5 1.0
CA C:TYR156 4.7 13.3 1.0
N C:GLU162 4.7 20.2 1.0
CB C:ASP159 4.8 21.2 1.0
OD1 C:ASP159 4.8 24.2 1.0
CA C:GLU162 4.9 19.7 1.0
O C:HOH276 5.0 26.9 1.0

Sodium binding site 4 out of 6 in 3frm

Go back to Sodium Binding Sites List in 3frm
Sodium binding site 4 out of 6 in the The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na252

b:37.9
occ:1.00
 OD1 D:ASP159 2.4 30.7 1.0
O D:ILE161 2.6 24.6 1.0
O D:ASP159 2.6 28.1 1.0
O D:TYR156 2.7 27.7 1.0
O D:HOH299 3.4 31.9 1.0
C D:ASP159 3.5 28.4 1.0
CG D:ASP159 3.6 29.1 1.0
C D:TYR156 3.7 26.7 1.0
C D:ILE161 3.8 24.1 1.0
OE2 D:GLU162 3.9 39.0 1.0
O D:ASN157 4.0 28.1 1.0
N D:ILE161 4.0 26.9 1.0
N D:ASP159 4.1 27.4 1.0
C D:ASN157 4.2 27.5 1.0
CA D:ASP159 4.2 28.0 1.0
N D:ASP160 4.3 28.5 1.0
NH1 D:ARG163 4.4 15.1 1.0
CD D:GLU162 4.4 35.1 1.0
N D:ASN157 4.5 27.0 1.0
OD2 D:ASP159 4.5 28.1 1.0
C D:ASP160 4.5 28.4 1.0
CA D:ASN157 4.5 27.3 0.5
CA D:ASP160 4.5 29.5 1.0
CA D:ILE161 4.5 25.6 1.0
CB D:ASP159 4.6 28.1 1.0
CA D:ASN157 4.6 27.2 0.5
OE1 D:GLU162 4.6 36.3 1.0
O D:SER155 4.6 24.0 1.0
C D:LEU158 4.6 27.6 1.0
CA D:TYR156 4.7 25.7 1.0
N D:GLU162 4.7 21.9 1.0
N D:LEU158 4.7 27.9 1.0
CA D:GLU162 4.8 20.5 1.0
CG1 D:ILE161 5.0 26.8 1.0

Sodium binding site 5 out of 6 in 3frm

Go back to Sodium Binding Sites List in 3frm
Sodium binding site 5 out of 6 in the The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na252

b:41.7
occ:1.00
 OD1 E:ASP159 2.5 29.8 1.0
O E:TYR156 2.5 31.0 1.0
O E:ASP159 2.7 33.5 1.0
O E:ILE161 2.8 28.0 1.0
C E:ASP159 3.4 33.5 1.0
C E:TYR156 3.7 30.6 1.0
CG E:ASP159 3.8 33.3 1.0
C E:ILE161 3.9 28.4 1.0
N E:ASP160 4.0 33.7 1.0
NH1 E:ARG163 4.0 20.8 1.0
N E:ASP159 4.2 33.9 1.0
N E:ILE161 4.2 31.1 1.0
CA E:ASP159 4.2 33.7 1.0
CA E:ASP160 4.3 34.7 1.0
C E:ASP160 4.4 33.1 1.0
CA E:TYR156 4.5 30.1 1.0
CB E:ASP159 4.6 33.1 1.0
N E:LEU158 4.7 34.4 1.0
CA E:ILE161 4.7 29.9 1.0
C E:LEU158 4.7 34.3 1.0
OD2 E:ASP159 4.7 33.2 1.0
N E:ASN157 4.7 31.9 1.0
O E:SER155 4.7 29.6 1.0
C E:ASN157 4.7 33.6 1.0
N E:GLU162 4.8 26.3 1.0
CA E:ASN157 4.9 33.3 1.0
CA E:GLU162 4.9 24.6 1.0
O E:LEU158 5.0 33.9 1.0

Sodium binding site 6 out of 6 in 3frm

Go back to Sodium Binding Sites List in 3frm
Sodium binding site 6 out of 6 in the The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na252

b:30.7
occ:1.00
 OD1 F:ASP159 2.5 23.5 1.0
O F:TYR156 2.6 20.7 1.0
O F:ILE161 2.8 21.9 1.0
O F:ASP159 2.9 22.5 1.0
O F:HOH315 3.3 15.8 1.0
OE1 F:GLU162 3.5 34.6 1.0
C F:ASP159 3.6 22.8 1.0
C F:TYR156 3.7 20.1 1.0
CG F:ASP159 3.8 24.2 1.0
C F:ILE161 3.8 22.3 1.0
NH1 F:ARG163 3.9 21.8 1.0
N F:ILE161 4.0 23.5 1.0
N F:ASP159 4.1 22.1 1.0
N F:ASP160 4.3 23.6 1.0
CA F:ASP159 4.3 22.2 1.0
O F:ASN157 4.4 22.4 1.0
CD F:GLU162 4.4 33.7 1.0
C F:ASP160 4.5 24.6 1.0
CA F:ILE161 4.5 23.3 1.0
C F:ASN157 4.5 22.1 1.0
CA F:TYR156 4.5 19.1 1.0
OD2 F:ASP159 4.6 24.9 1.0
CA F:ASP160 4.6 25.3 1.0
CB F:ASP159 4.6 22.9 1.0
O F:HOH303 4.7 8.1 1.0
N F:ASN157 4.7 20.8 1.0
N F:GLU162 4.7 20.7 1.0
OE2 F:GLU162 4.7 38.6 1.0
C F:LEU158 4.7 22.2 1.0
CA F:ASN157 4.8 21.3 1.0
N F:LEU158 5.0 22.8 1.0
CA F:GLU162 5.0 19.8 1.0

Reference:

K.Tan, A.Sather, S.Clancy, A.Joachimiak. The Crystal Structure of A Functionally Unknown Conserved Protein From Staphylococcus Epidermidis Atcc 12228. To Be Published.
Page generated: Mon Oct 7 09:49:16 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy