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Sodium in PDB 5xm5: Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli

Protein crystallography data

The structure of Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli, PDB code: 5xm5 was solved by J.Chen, L.Wang, J.Guo, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.23 / 1.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.021, 65.724, 73.532, 90.00, 91.24, 90.00
R / Rfree (%) 17.9 / 23.4

Other elements in 5xm5:

The structure of Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli (pdb code 5xm5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli, PDB code: 5xm5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5xm5

Go back to Sodium Binding Sites List in 5xm5
Sodium binding site 1 out of 5 in the Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli


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 Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:26.8
occ:1.00
H A:LYS134 2.4 32.6 1.0
H A:SER102 2.5 25.7 1.0
HA A:THR101 3.0 23.8 1.0
HA A:SER133 3.1 35.4 1.0
HB A:THR101 3.2 24.5 1.0
HG A:SER133 3.2 34.3 1.0
N A:LYS134 3.2 27.2 1.0
N A:SER102 3.3 21.4 1.0
HB2 A:LYS134 3.4 35.2 1.0
O A:SER102 3.5 21.4 1.0
HG22 A:THR101 3.7 29.6 1.0
CA A:THR101 3.7 19.8 1.0
CB A:THR101 3.8 20.4 1.0
H A:ALA135 3.8 30.3 1.0
CA A:SER133 3.9 29.5 1.0
OG A:SER133 3.9 28.6 1.0
C A:THR101 4.0 22.4 1.0
C A:SER133 4.1 30.4 1.0
HD2 A:LYS134 4.1 52.5 1.0
CA A:LYS134 4.1 27.7 1.0
CB A:LYS134 4.2 29.3 1.0
CG2 A:THR101 4.2 24.7 1.0
N A:ALA135 4.2 25.2 1.0
C A:SER102 4.3 22.6 1.0
CA A:SER102 4.4 22.3 1.0
CB A:SER133 4.4 28.6 1.0
HB2 A:ALA135 4.5 28.1 1.0
C A:LYS134 4.5 25.6 1.0
O A:HOH414 4.6 49.3 1.0
HB2 A:SER133 4.6 34.3 1.0
OG A:SER102 4.6 26.8 1.0
HG21 A:THR101 4.7 29.6 1.0
CD A:LYS134 4.8 43.7 1.0
HD3 A:LYS134 4.8 52.5 1.0
O A:GLU132 4.8 35.3 1.0
O A:THR100 4.9 27.0 1.0
HB3 A:LYS134 4.9 35.2 1.0
CG A:LYS134 4.9 32.9 1.0
HG3 A:LYS134 5.0 39.5 1.0
N A:THR101 5.0 23.1 1.0

Sodium binding site 2 out of 5 in 5xm5

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Sodium binding site 2 out of 5 in the Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli


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 Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:48.3
occ:1.00
HD11 A:ILE82 2.2 36.4 1.0
HG3 A:PRO136 2.7 32.9 1.0
O A:HOH508 2.9 39.8 1.0
CD1 A:ILE82 3.0 30.4 1.0
HD12 A:ILE82 3.0 36.4 1.0
HH21 A:ARG96 3.2 64.2 1.0
HG2 A:PRO136 3.3 32.9 1.0
HD13 A:ILE82 3.4 36.4 1.0
CG A:PRO136 3.4 27.4 1.0
HH22 A:ARG96 3.5 64.2 1.0
HB3 A:MET158 3.6 22.0 1.0
NH2 A:ARG96 3.6 53.5 1.0
SD A:MET158 3.6 14.8 1.0
O A:HOH536 3.6 52.8 1.0
HB2 A:MET158 3.9 22.0 1.0
HD3 A:PRO136 3.9 30.2 1.0
HE3 A:MET158 4.1 29.5 1.0
CB A:MET158 4.1 18.3 1.0
CG1 A:ILE82 4.2 22.9 1.0
HG13 A:ILE82 4.2 27.5 1.0
CD A:PRO136 4.2 25.1 1.0
CE A:MET158 4.3 24.6 1.0
HE1 A:MET158 4.4 29.5 1.0
O A:HOH424 4.4 47.4 1.0
HG12 A:ILE82 4.4 27.5 1.0
CG A:MET158 4.5 17.3 1.0
HB3 A:PRO136 4.5 28.8 1.0
CB A:PRO136 4.6 24.0 1.0
HD2 A:PRO136 4.7 30.2 1.0
CZ A:ARG96 4.8 52.7 1.0
HG2 A:MET158 4.8 20.8 1.0
HB3 A:PHE94 4.8 21.4 1.0
HD2 A:PHE94 4.9 19.1 1.0
CD2 A:PHE94 5.0 15.9 1.0

Sodium binding site 3 out of 5 in 5xm5

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Sodium binding site 3 out of 5 in the Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:23.1
occ:1.00
O A:HOH564 1.9 22.8 1.0
ZN A:ZN203 2.2 15.4 1.0
O A:HOH556 2.3 27.3 1.0
HE1 A:HIS144 2.6 18.3 1.0
O A:HOH460 2.8 16.2 1.0
O A:HOH480 2.9 16.3 1.0
NE2 A:HIS155 2.9 12.6 1.0
NE2 A:HIS144 3.0 14.5 1.0
CE1 A:HIS144 3.1 15.3 1.0
HE1 A:HIS155 3.2 15.4 1.0
CE1 A:HIS155 3.3 12.8 1.0
O A:HOH552 3.7 22.4 1.0
CD2 A:HIS155 3.9 13.0 1.0
O A:HOH544 3.9 43.5 1.0
HD2 A:HIS155 4.2 15.6 1.0
O A:HOH501 4.2 28.7 1.0
CD2 A:HIS144 4.3 13.7 1.0
ND1 A:HIS155 4.3 12.7 1.0
ND1 A:HIS144 4.4 16.2 1.0
NE2 A:HIS153 4.4 15.7 1.0
CG A:HIS155 4.7 13.6 1.0
O A:HOH439 4.7 26.5 1.0
O A:HOH543 4.7 41.5 1.0
HD2 A:HIS144 4.9 16.4 1.0

Sodium binding site 4 out of 5 in 5xm5

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Sodium binding site 4 out of 5 in the Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:31.6
occ:1.00
O B:HOH385 1.9 18.6 1.0
O B:HOH504 2.3 28.2 1.0
O B:HOH403 2.8 26.9 1.0
O B:HOH516 2.9 40.0 1.0
O B:HOH483 3.4 31.2 1.0
HE1 B:HIS144 3.7 19.0 1.0
O B:HOH491 3.9 47.3 1.0
O B:HOH457 3.9 18.3 1.0
HE1 B:TYR74 4.1 20.9 1.0
O B:HOH503 4.1 36.2 1.0
ZN B:ZN201 4.1 16.6 0.9
O B:HOH417 4.3 19.9 1.0
O B:HOH511 4.3 22.4 1.0
HH B:TYR73 4.3 33.1 1.0
HE1 B:HIS155 4.3 17.2 1.0
CE1 B:HIS144 4.5 15.8 1.0
NE2 B:HIS155 4.5 14.9 1.0
CE1 B:HIS155 4.6 14.4 1.0
O B:HOH466 4.7 31.9 1.0
CZ3 B:TRP173 4.7 16.8 1.0
HZ3 B:TRP173 4.7 20.2 1.0
HE2 B:TYR73 4.8 26.8 1.0
NE2 B:HIS144 4.8 16.2 1.0
CH2 B:TRP173 4.9 14.7 1.0
CE1 B:TYR74 5.0 17.4 1.0

Sodium binding site 5 out of 5 in 5xm5

Go back to Sodium Binding Sites List in 5xm5
Sodium binding site 5 out of 5 in the Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:44.9
occ:1.00
HA B:ASP81 3.0 28.5 1.0
HE2 B:TYR43 3.2 22.1 1.0
O B:THR80 3.3 17.2 1.0
HD2 B:TYR43 3.4 24.0 1.0
HB3 B:ASP81 3.6 33.1 1.0
HE22 B:GLN47 3.9 36.5 1.0
CA B:ASP81 3.9 23.8 1.0
CE2 B:TYR43 3.9 18.4 1.0
CD2 B:TYR43 4.0 20.0 1.0
C B:THR80 4.0 18.3 1.0
CB B:ASP81 4.2 27.6 1.0
O B:HOH518 4.2 52.4 1.0
N B:ASP81 4.3 23.5 1.0
HB2 B:ASP81 4.4 33.1 1.0
O B:HOH434 4.4 48.9 1.0
NE2 B:GLN47 4.5 30.5 1.0
O B:HOH363 4.5 44.4 1.0
H B:THR80 4.5 20.8 1.0
OE1 B:GLN47 4.6 30.9 1.0
O B:HOH382 4.8 21.6 1.0
CD B:GLN47 4.9 30.5 1.0
H B:ASP81 5.0 28.2 1.0

Reference:

J.Chen, L.Wang, J.Guo, Y.Xu. Crystal Structure of Zinc Binding Protein Zint at 1.49 Angstrom From E. Coli To Be Published.
Page generated: Tue Dec 15 11:50:08 2020

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