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Sodium in PDB 2qzi: The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311.

Protein crystallography data

The structure of The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311., PDB code: 2qzi was solved by K.Tan, M.Zhou, L.Freeman, 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) 36.23 / 2.20
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 150.783, 150.783, 103.247, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 25.1

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311. (pdb code 2qzi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311., PDB code: 2qzi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 2qzi

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Sodium binding site 1 out of 7 in the The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311.


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 Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na101

b:57.1
occ:1.00
 O A:ALA23 2.4 74.6 1.0
O A:THR21 2.4 71.6 1.0
O A:HOH144 2.5 59.1 1.0
O A:LEU18 2.5 70.3 1.0
C A:ALA23 3.4 74.0 1.0
C A:LEU18 3.5 73.0 1.0
C A:THR21 3.5 73.5 1.0
C A:ASP22 3.7 73.3 1.0
N A:ALA23 3.8 74.2 1.0
O A:ASP22 4.0 72.9 1.0
CA A:LEU18 4.0 72.7 1.0
CA A:ASP22 4.1 74.4 1.0
O A:HOH141 4.2 48.2 1.0
CA A:ALA23 4.2 73.5 1.0
N A:ASP22 4.3 74.2 1.0
N A:PHE24 4.4 73.7 1.0
O A:GLN17 4.4 74.3 1.0
N A:THR21 4.5 73.3 1.0
CA A:THR21 4.6 74.5 1.0
CA A:PHE24 4.6 73.4 1.0
N A:ASP19 4.7 72.8 1.0
CB A:LEU18 4.8 72.5 1.0
CG2 A:THR21 4.9 71.7 1.0

Sodium binding site 2 out of 7 in 2qzi

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Sodium binding site 2 out of 7 in the The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311.


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 Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na102

b:45.6
occ:1.00
 OG1 A:THR39 2.6 77.5 1.0
O A:HOH152 2.9 41.5 1.0
O A:HIS44 2.9 71.6 1.0
O A:THR39 3.4 71.6 1.0
C A:THR39 3.5 74.1 1.0
N A:ALA41 3.5 68.3 1.0
CG A:GLU46 3.5 78.0 1.0
CB A:THR39 3.6 75.5 1.0
C A:GLN40 3.6 70.1 1.0
CB A:ALA41 3.6 67.6 1.0
N A:GLU46 3.6 73.5 1.0
N A:GLN40 3.7 72.9 1.0
CA A:GLN40 3.7 70.3 1.0
C A:TYR45 3.8 72.4 1.0
CA A:TYR45 3.8 70.7 1.0
C A:HIS44 3.8 70.7 1.0
ND1 A:HIS44 3.8 76.3 1.0
CE1 A:HIS44 3.9 74.9 1.0
CB A:GLU46 3.9 75.0 1.0
O A:HOH142 4.0 37.7 1.0
CA A:ALA41 4.2 67.8 1.0
CA A:THR39 4.2 75.4 1.0
CG A:HIS44 4.2 74.0 1.0
O A:GLN40 4.2 69.8 1.0
N A:TYR45 4.2 71.5 1.0
NE2 A:HIS44 4.3 78.4 1.0
CA A:GLU46 4.4 75.0 1.0
CD2 A:HIS44 4.5 75.5 1.0
O A:TYR45 4.5 71.5 1.0
CD A:GLU46 4.7 81.1 1.0
CG2 A:THR39 4.8 72.5 1.0
OE2 A:GLU46 4.9 80.8 1.0
CB A:HIS44 4.9 70.5 1.0
CA A:HIS44 4.9 70.6 1.0

Sodium binding site 3 out of 7 in 2qzi

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Sodium binding site 3 out of 7 in the The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311.


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 Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:47.4
occ:1.00
 O B:HOH169 2.3 46.7 1.0
O B:THR21 2.4 66.0 1.0
O B:LEU18 2.4 71.8 1.0
O B:ALA23 2.5 70.1 1.0
C B:LEU18 3.4 71.8 1.0
C B:THR21 3.6 70.3 1.0
C B:ALA23 3.6 72.3 1.0
CA B:LEU18 3.7 71.5 1.0
N B:ALA23 3.9 71.3 1.0
C B:ASP22 3.9 71.2 1.0
O B:GLN17 4.2 76.4 1.0
CA B:ASP22 4.3 71.4 1.0
O B:ASP22 4.3 70.3 1.0
CA B:ALA23 4.3 71.1 1.0
N B:ASP22 4.4 70.8 1.0
N B:THR21 4.5 70.2 1.0
O B:HOH108 4.5 45.0 1.0
CB B:LEU18 4.5 70.9 1.0
N B:ASP19 4.6 69.7 1.0
N B:PHE24 4.6 71.1 1.0
CA B:THR21 4.7 68.7 1.0
CA B:PHE24 4.7 70.7 1.0
OG1 B:THR21 4.7 74.0 1.0
O B:HOH129 4.9 59.6 1.0
N B:LEU18 4.9 72.0 1.0
C B:ASP19 4.9 69.0 1.0
N B:ASN20 5.0 68.8 1.0
CA B:ASP19 5.0 69.5 1.0

Sodium binding site 4 out of 7 in 2qzi

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Sodium binding site 4 out of 7 in the The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311.


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 Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na102

b:43.0
occ:1.00
 O B:HOH153 2.5 47.5 1.0
OG1 B:THR39 2.9 77.0 1.0
O B:HIS44 3.0 74.1 1.0
N B:ALA41 3.4 71.3 1.0
CG B:GLU46 3.6 78.3 1.0
CB B:ALA41 3.6 70.1 1.0
ND1 B:HIS44 3.6 74.3 1.0
C B:THR39 3.6 72.8 1.0
CE1 B:HIS44 3.7 75.3 1.0
C B:GLN40 3.7 70.4 1.0
O B:THR39 3.7 72.3 1.0
CB B:THR39 3.7 74.8 1.0
N B:GLU46 3.8 75.7 1.0
CA B:GLN40 3.8 70.5 1.0
N B:GLN40 3.9 71.0 1.0
C B:HIS44 3.9 74.5 1.0
C B:TYR45 4.0 73.8 1.0
CA B:TYR45 4.0 72.3 1.0
O B:HOH107 4.1 49.7 1.0
CB B:GLU46 4.1 75.8 1.0
CA B:ALA41 4.1 71.3 1.0
NE2 B:HIS44 4.2 76.4 1.0
CG B:HIS44 4.2 72.3 1.0
CA B:THR39 4.3 74.4 1.0
O B:GLN40 4.3 71.1 1.0
N B:TYR45 4.4 73.0 1.0
CD2 B:HIS44 4.5 70.7 1.0
CA B:GLU46 4.6 76.7 1.0
O B:TYR45 4.8 73.9 1.0
CD B:GLU46 4.8 81.8 1.0
OE2 B:GLU46 4.8 82.9 1.0
CB B:ALA23 5.0 70.3 1.0
CB B:HIS44 5.0 75.0 1.0
CA B:ALA23 5.0 71.1 1.0

Sodium binding site 5 out of 7 in 2qzi

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Sodium binding site 5 out of 7 in the The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311.


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 Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na103

b:44.5
occ:1.00
 O B:HOH156 2.6 48.7 1.0
OG B:SER95 2.7 73.6 1.0
O B:GLU93 3.2 71.2 1.0
O B:ARG84 3.4 71.7 1.0
C B:GLU93 3.7 72.5 1.0
CG2 B:VAL86 3.7 66.7 1.0
N B:SER95 3.7 72.6 1.0
CB B:SER95 3.7 73.5 1.0
CB B:GLU93 3.8 71.8 1.0
C B:ARG84 4.0 74.1 1.0
C B:ILE94 4.1 73.7 1.0
CG B:ARG84 4.1 79.2 1.0
N B:ILE94 4.2 71.8 1.0
CA B:ILE94 4.2 73.3 1.0
O B:HOH159 4.2 54.0 1.0
N B:VAL86 4.2 70.8 1.0
CA B:SER95 4.3 72.9 1.0
NE B:ARG84 4.3 89.0 1.0
O B:HOH106 4.4 46.9 1.0
CA B:GLU93 4.4 72.5 1.0
CB B:VAL86 4.4 71.1 1.0
CD B:ARG84 4.4 85.2 1.0
CB B:ARG84 4.4 75.7 1.0
OE1 B:GLU46 4.5 82.3 1.0
N B:THR85 4.6 73.3 1.0
CA B:THR85 4.7 74.0 1.0
C B:THR85 4.7 72.5 1.0
O B:ILE94 4.8 72.6 1.0
CA B:ARG84 4.8 75.5 1.0
CA B:VAL86 4.9 71.2 1.0

Sodium binding site 6 out of 7 in 2qzi

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Sodium binding site 6 out of 7 in the The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311.


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 Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na101

b:49.0
occ:1.00
 O C:HOH136 2.2 50.0 1.0
O C:LEU18 2.4 68.6 1.0
O C:THR21 2.4 70.4 1.0
O C:ALA23 2.4 70.8 1.0
C C:ALA23 3.5 70.0 1.0
C C:LEU18 3.5 71.8 1.0
C C:THR21 3.6 71.3 1.0
C C:ASP22 3.8 72.0 1.0
N C:ALA23 3.9 71.2 1.0
CA C:LEU18 4.0 72.1 1.0
CA C:ASP22 4.2 72.5 1.0
O C:ASP22 4.2 72.1 1.0
CA C:ALA23 4.2 70.8 1.0
N C:ASP22 4.3 72.4 1.0
O C:GLN17 4.4 74.5 1.0
N C:THR21 4.4 68.5 1.0
O C:HOH138 4.4 48.7 1.0
N C:PHE24 4.5 68.8 1.0
CA C:THR21 4.6 70.2 1.0
O C:HOH113 4.6 53.7 1.0
N C:ASP19 4.6 71.0 1.0
CA C:PHE24 4.7 69.8 1.0
CB C:LEU18 4.9 73.5 1.0
OG1 C:THR21 4.9 69.8 1.0
C C:ASP19 4.9 70.5 1.0
CA C:ASP19 4.9 70.9 1.0

Sodium binding site 7 out of 7 in 2qzi

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Sodium binding site 7 out of 7 in the The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na102

b:50.1
occ:1.00
 O C:HOH139 2.8 40.1 1.0
O C:HIS44 2.8 70.3 1.0
OG1 C:THR39 2.9 74.7 1.0
N C:ALA41 3.2 68.4 1.0
C C:GLN40 3.5 66.9 1.0
CB C:ALA41 3.5 66.6 1.0
CA C:GLN40 3.6 66.0 1.0
ND1 C:HIS44 3.6 66.6 1.0
CG C:GLU46 3.6 73.2 1.0
O C:THR39 3.6 66.6 1.0
C C:THR39 3.7 69.6 1.0
N C:GLN40 3.7 67.7 1.0
C C:HIS44 3.7 68.9 1.0
N C:GLU46 3.8 71.1 1.0
CE1 C:HIS44 3.8 71.8 1.0
CA C:TYR45 3.9 68.7 1.0
C C:TYR45 3.9 70.0 1.0
CB C:THR39 3.9 70.3 1.0
CA C:ALA41 4.0 68.1 1.0
CG C:HIS44 4.0 70.5 1.0
O C:HOH133 4.1 42.2 1.0
CB C:GLU46 4.2 70.5 1.0
N C:TYR45 4.3 68.2 1.0
NE2 C:HIS44 4.3 71.5 1.0
O C:GLN40 4.3 63.9 1.0
CA C:THR39 4.4 69.7 1.0
CD2 C:HIS44 4.4 72.1 1.0
CA C:GLU46 4.6 71.3 1.0
O C:TYR45 4.6 69.5 1.0
CB C:HIS44 4.7 69.0 1.0
CD C:GLU46 4.7 75.4 1.0
OE2 C:GLU46 4.7 77.9 1.0
CA C:HIS44 4.7 69.4 1.0

Reference:

K.Tan, M.Zhou, L.Freeman, A.Joachimiak. The Crystal Structure of A Conserved Protein of Unknown Function From Streptococcus Thermophilus Lmg 18311. To Be Published.
Page generated: Mon Oct 7 04:06:53 2024

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