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 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy