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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: Sun Aug 17 14:52:18 2025

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