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Sodium in PDB 3gsd: 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis

Protein crystallography data

The structure of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis, PDB code: 3gsd was solved by G.Minasov, Z.Wawrzak, T.Skarina, O.Onopriyenko, S.N.Peterson, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.59 / 2.05
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 140.782, 157.914, 157.132, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 20

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Sodium atom in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis (pdb code 3gsd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 22 binding sites of Sodium where determined in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis, PDB code: 3gsd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 22 in 3gsd

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Sodium binding site 1 out of 22 in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na120

b:21.5
occ:1.00
 OE1 A:GLN32 2.3 18.0 1.0
O I:HOH139 2.5 16.7 1.0
NA A:NA122 3.2 41.4 1.0
CB A:GLN32 3.3 17.7 1.0
CD A:GLN32 3.3 23.6 1.0
O A:HOH521 3.6 29.9 1.0
O A:HOH401 3.7 31.5 1.0
CG A:GLN32 3.9 16.1 1.0
OD1 A:ASN33 4.1 19.8 1.0
NE2 A:GLN32 4.4 20.2 1.0
O A:ALA29 4.6 19.0 1.0
CA A:GLN32 4.6 16.4 1.0
OE1 B:GLN65 4.7 24.4 1.0
C A:GLN32 4.8 17.8 1.0
N A:ASN33 4.8 16.6 1.0
CA A:ALA29 5.0 19.8 1.0

Sodium binding site 2 out of 22 in 3gsd

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Sodium binding site 2 out of 22 in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na121

b:38.0
occ:1.00
 O A:HOH373 2.3 26.0 1.0
O C:HOH206 2.4 26.1 1.0
O B:HOH481 2.4 25.4 1.0
O B:HOH417 2.5 28.5 1.0
O A:HOH564 2.6 32.9 1.0
O C:HOH325 2.6 24.9 1.0
O C:HOH984 3.4 33.8 0.5
O A:HOH565 3.9 28.6 1.0
O F:HOH157 3.9 30.6 1.0
O C:HOH265 3.9 26.9 1.0
O A:PRO51 4.1 21.8 1.0
O B:PRO51 4.2 20.3 1.0
O C:PRO51 4.2 17.2 1.0
O F:HOH162 4.4 20.0 1.0
O I:HOH147 4.5 17.2 1.0
O A:HOH563 4.5 33.6 1.0
O F:HOH135 4.6 18.1 1.0
O B:HOH615 4.6 35.7 1.0
O C:HOH652 4.7 29.8 1.0
O F:HOH149 4.9 19.9 1.0

Sodium binding site 3 out of 22 in 3gsd

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Sodium binding site 3 out of 22 in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na122

b:41.4
occ:1.00
 O A:HOH521 2.3 29.9 1.0
O A:HOH401 2.3 31.5 1.0
O A:HOH1114 2.5 44.6 1.0
OE1 A:GLN32 2.6 18.0 1.0
NA A:NA120 3.2 21.5 1.0
CD A:GLN32 3.5 23.6 1.0
NE2 A:GLN32 3.6 20.2 1.0
O I:HOH139 4.2 16.7 1.0
O A:HOH954 4.2 41.0 1.0
O A:HOH1157 4.5 48.3 1.0
CG A:GLN32 4.9 16.1 1.0

Sodium binding site 4 out of 22 in 3gsd

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Sodium binding site 4 out of 22 in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na120

b:35.1
occ:1.00
 O B:HOH974 2.3 37.8 1.0
O F:HOH175 2.3 24.9 1.0
O J:HOH357 2.4 27.9 1.0
O J:HOH435 2.5 25.0 1.0
O B:HOH975 2.5 34.7 1.0
O I:HOH542 2.6 25.9 1.0
NA I:NA121 3.7 23.1 1.0
OE1 J:GLU41 3.9 23.7 1.0
O B:HOH254 4.1 26.9 1.0
O B:HOH1083 4.2 41.1 1.0
O B:LEU119 4.2 33.5 1.0
O J:HOH302 4.2 25.6 1.0
OXT B:LEU119 4.3 32.2 1.0
OE2 I:GLU41 4.3 26.2 1.0
O E:HOH161 4.4 30.7 1.0
O J:HOH1082 4.5 47.9 1.0
O J:HOH980 4.6 32.7 1.0
OE1 I:GLU41 4.7 24.3 1.0
C B:LEU119 4.7 32.5 1.0
NZ B:LYS42 4.8 51.5 1.0
CD J:GLU41 4.9 26.1 1.0
O J:HOH1197 5.0 43.3 1.0
CD I:GLU41 5.0 25.0 1.0

Sodium binding site 5 out of 22 in 3gsd

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Sodium binding site 5 out of 22 in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na121

b:22.2
occ:1.00
 O I:HOH129 2.3 18.2 1.0
O E:HOH159 2.3 21.3 1.0
OE1 E:GLN32 2.4 18.9 1.0
O I:HOH130 2.4 19.7 1.0
OE1 B:GLN32 2.4 24.7 1.0
CB E:GLN32 3.3 18.5 1.0
NA E:NA120 3.3 37.1 1.0
CB B:GLN32 3.3 18.7 1.0
CD E:GLN32 3.4 21.4 1.0
CD B:GLN32 3.5 24.5 1.0
O E:HOH609 3.7 30.7 1.0
O B:HOH473 3.7 27.2 1.0
CG E:GLN32 3.9 18.7 1.0
CG B:GLN32 4.0 18.6 1.0
OD1 B:ASN33 4.0 19.8 1.0
OD1 E:ASN33 4.1 16.7 1.0
O E:ALA29 4.5 19.2 1.0
NE2 E:GLN32 4.5 18.6 1.0
O B:ALA29 4.6 21.8 1.0
NE2 B:GLN32 4.6 23.1 1.0
CA E:GLN32 4.6 18.1 1.0
CA B:GLN32 4.6 18.9 1.0
N E:ASN33 4.7 18.1 1.0
C E:GLN32 4.7 18.0 1.0
OE1 F:GLN65 4.7 26.6 1.0
C B:GLN32 4.8 18.3 1.0
OE1 C:GLN65 4.8 30.1 1.0
N B:ASN33 4.8 16.8 1.0
CG B:ASN33 5.0 17.6 1.0
CG E:ASN33 5.0 16.9 1.0

Sodium binding site 6 out of 22 in 3gsd

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Sodium binding site 6 out of 22 in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na120

b:20.7
occ:1.00
 O E:HOH125 2.3 20.1 1.0
O F:HOH203 2.3 18.4 1.0
OE1 C:GLN32 2.4 23.4 1.0
CB C:GLN32 3.3 19.3 1.0
CD C:GLN32 3.4 22.1 1.0
O F:HOH131 3.6 27.2 1.0
O C:HOH653 3.9 29.6 1.0
CG C:GLN32 4.0 20.8 1.0
OD1 C:ASN33 4.1 21.1 1.0
NE2 C:GLN32 4.5 21.0 1.0
O C:ALA29 4.6 20.0 1.0
CA C:GLN32 4.6 19.9 1.0
OE1 A:GLN65 4.7 28.2 1.0
C C:GLN32 4.8 19.7 1.0
N C:ASN33 4.8 18.4 1.0
CG C:ASN33 5.0 19.9 1.0

Sodium binding site 7 out of 22 in 3gsd

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Sodium binding site 7 out of 22 in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na120

b:19.9
occ:1.00
 OE1 D:GLN32 2.3 21.1 1.0
O I:HOH133 2.4 20.4 1.0
CD D:GLN32 3.3 24.9 1.0
CB D:GLN32 3.4 21.2 1.0
O D:HOH530 3.7 26.7 1.0
CG D:GLN32 3.9 18.7 1.0
OD1 D:ASN33 4.2 18.7 1.0
NE2 D:GLN32 4.5 21.3 1.0
O D:ALA29 4.6 18.5 1.0
CA D:GLN32 4.7 21.0 1.0
OE1 E:GLN65 4.7 24.6 1.0
C D:GLN32 4.8 21.9 1.0
N D:ASN33 4.9 20.4 1.0

Sodium binding site 8 out of 22 in 3gsd

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Sodium binding site 8 out of 22 in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na121

b:33.9
occ:1.00
 O E:HOH146 2.3 25.0 1.0
O F:HOH136 2.3 21.2 1.0
O E:HOH123 2.4 24.6 1.0
O D:HOH227 2.4 29.6 1.0
O F:HOH229 2.4 30.4 1.0
O E:HOH224 2.5 27.4 1.0
O F:HOH190 3.6 29.8 1.0
O D:HOH969 3.7 31.4 0.5
O E:HOH205 3.8 27.3 1.0
O F:HOH168 3.9 28.3 1.0
O D:PRO51 4.1 19.6 1.0
O F:PRO51 4.1 18.3 1.0
O E:PRO51 4.2 18.7 1.0
O D:HOH275 4.3 20.4 1.0
O I:HOH146 4.4 17.1 1.0
O E:HOH208 4.4 19.4 1.0
O F:HOH504 4.6 29.9 1.0
O D:HOH259 4.6 29.2 1.0
O E:HOH248 4.8 33.9 1.0
O F:HOH152 5.0 20.9 1.0

Sodium binding site 9 out of 22 in 3gsd

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Sodium binding site 9 out of 22 in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na120

b:37.1
occ:1.00
 O B:HOH473 2.2 27.2 1.0
O E:HOH609 2.3 30.7 1.0
OE1 E:GLN32 2.4 18.9 1.0
O B:HOH610 2.6 48.4 1.0
O E:HOH1105 2.6 45.4 1.0
OE1 B:GLN32 2.6 24.7 1.0
CD E:GLN32 3.3 21.4 1.0
NA B:NA121 3.3 22.2 1.0
NE2 E:GLN32 3.5 18.6 1.0
CD B:GLN32 3.6 24.5 1.0
NE2 B:GLN32 3.8 23.1 1.0
O I:HOH129 4.1 18.2 1.0
O B:HOH606 4.2 41.2 1.0
O E:HOH1107 4.2 32.8 0.5
O I:HOH130 4.2 19.7 1.0
O E:HOH1106 4.5 47.6 1.0
CG E:GLN32 4.7 18.7 1.0

Sodium binding site 10 out of 22 in 3gsd

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Sodium binding site 10 out of 22 in the 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na120

b:19.8
occ:1.00
 OE1 F:GLN32 2.3 20.1 1.0
O F:HOH184 2.4 18.6 1.0
O I:HOH128 2.4 18.8 1.0
NA F:NA122 3.1 38.3 1.0
CB F:GLN32 3.3 17.6 1.0
CD F:GLN32 3.4 23.7 1.0
O F:HOH756 3.6 30.6 1.0
O F:HOH318 3.8 28.6 1.0
CG F:GLN32 3.9 17.1 1.0
OD1 F:ASN33 4.0 21.1 1.0
NE2 F:GLN32 4.5 22.9 1.0
CA F:GLN32 4.6 18.4 1.0
O F:ALA29 4.6 21.8 1.0
C F:GLN32 4.8 17.4 1.0
N F:ASN33 4.8 16.8 1.0
OE1 D:GLN65 4.8 29.0 1.0
CG F:ASN33 5.0 20.9 1.0

Reference:

G.Minasov, Z.Wawrzak, T.Skarina, O.Onopriyenko, S.N.Peterson, A.Savchenko, W.F.Anderson. 2.05 Angstrom Structure of A Divalent-Cation Tolerance Protein (Cuta) From Yersinia Pestis To Be Published.
Page generated: Mon Oct 7 10:17:05 2024

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