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Sodium in PDB 3szs: Crystal Structure Analysis of Hellethionin D

Protein crystallography data

The structure of Crystal Structure Analysis of Hellethionin D, PDB code: 3szs was solved by A.Thorn, I.Uson, C.Eduardo, G.M.Sheldrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.80 / 1.95
Space group I 4 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 129.829, 129.829, 103.994, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.1

Other elements in 3szs:

The structure of Crystal Structure Analysis of Hellethionin D also contains other interesting chemical elements:

Chlorine (Cl) 33 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of Hellethionin D (pdb code 3szs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 19 binding sites of Sodium where determined in the Crystal Structure Analysis of Hellethionin D, PDB code: 3szs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 19 in 3szs

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Sodium binding site 1 out of 19 in the Crystal Structure Analysis of Hellethionin D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Hellethionin D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na52

b:24.9
occ:1.00
 O E:HOH102 2.6 12.2 1.0
O E:ASN11 2.8 20.5 1.0
OG1 A:THR25 2.9 16.6 1.0
N A:THR25 3.2 18.5 1.0
CA E:ASN11 3.5 20.8 1.0
C E:ASN11 3.5 20.5 1.0
CA A:THR25 3.5 18.3 1.0
CB E:ASN14 3.6 21.3 1.0
C A:PRO24 3.7 19.0 1.0
CB A:PRO24 3.8 19.6 1.0
CB A:THR25 3.8 18.9 1.0
N E:ALA15 3.8 20.8 1.0
CB E:ASN11 4.0 20.9 1.0
OG A:SER22 4.0 20.2 1.0
CB E:ALA15 4.2 20.6 1.0
CD1 A:ILE28 4.2 21.6 1.0
OD1 E:ASN11 4.3 21.6 1.0
O A:PRO24 4.3 19.3 1.0
CA A:PRO24 4.3 20.3 1.0
C E:ASN14 4.4 21.1 1.0
CA E:ALA15 4.5 20.8 1.0
CA E:ASN14 4.5 21.2 1.0
ND2 E:ASN14 4.5 21.9 1.0
CG E:ASN11 4.5 21.5 1.0
O E:ARG10 4.6 21.8 1.0
CG E:ASN14 4.7 21.7 1.0
N E:ASN11 4.7 21.1 1.0
CG A:PRO24 4.7 21.5 1.0
N E:ASN14 4.8 20.9 1.0
N E:CYS12 4.8 20.4 1.0
C A:THR25 5.0 19.9 1.0

Sodium binding site 2 out of 19 in 3szs

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Sodium binding site 2 out of 19 in the Crystal Structure Analysis of Hellethionin D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Hellethionin D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na53

b:34.8
occ:1.00
 O E:HOH102 2.9 12.2 1.0
O E:HOH131 2.9 24.4 1.0
O A:HOH110 3.7 21.9 1.0
CD A:PRO24 3.8 22.3 1.0
OG A:SER22 3.8 20.2 1.0
CG A:PRO24 3.8 21.5 1.0
CB A:SER22 3.9 21.8 1.0
ND2 E:ASN14 4.1 21.9 1.0
O E:HOH151 4.4 7.1 1.0
CB A:PRO24 4.7 19.6 1.0
O E:HOH103 4.7 9.5 1.0
CL A:CL51 4.8 23.6 0.5
OD1 E:ASN11 4.9 21.6 1.0

Sodium binding site 3 out of 19 in 3szs

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Sodium binding site 3 out of 19 in the Crystal Structure Analysis of Hellethionin D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of Hellethionin D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na54

b:33.9
occ:1.00
 O A:ARG17 2.6 22.5 1.0
O A:HOH106 2.7 19.8 1.0
O A:GLY21 2.9 21.7 1.0
NH1 A:ARG17 3.5 28.8 1.0
C A:GLY20 3.5 19.7 1.0
N A:GLY21 3.6 17.9 1.0
C A:ARG17 3.6 22.9 1.0
CA A:GLY20 3.7 20.9 1.0
C A:GLY21 3.8 19.5 1.0
O A:GLY20 3.8 19.2 1.0
CA A:ARG17 4.0 23.0 1.0
O A:HOH105 4.1 24.6 1.0
CZ A:ARG17 4.1 31.1 1.0
N A:GLY20 4.1 20.3 1.0
CA A:GLY21 4.3 18.1 1.0
O A:HOH104 4.3 29.2 1.0
O A:HOH113 4.4 17.3 1.0
CB A:ARG17 4.5 25.8 1.0
NE A:ARG17 4.6 30.2 1.0
CD A:ARG17 4.6 26.0 1.0
N A:SER22 4.7 19.6 1.0
NH2 A:ARG17 4.8 34.9 1.0
N A:PHE18 4.9 23.5 1.0

Sodium binding site 4 out of 19 in 3szs

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Sodium binding site 4 out of 19 in the Crystal Structure Analysis of Hellethionin D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure Analysis of Hellethionin D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na51

b:36.9
occ:1.00
 O B:HOH121 2.5 20.3 1.0
OG1 B:THR39 2.7 33.9 1.0
CB B:THR39 3.5 31.0 1.0
CG2 B:THR39 3.9 32.9 1.0
O B:HOH132 4.2 31.8 1.0
O B:HOH125 4.6 21.4 1.0
O B:CYS40 4.6 28.3 1.0
CA B:THR39 4.9 30.1 1.0

Sodium binding site 5 out of 19 in 3szs

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Sodium binding site 5 out of 19 in the Crystal Structure Analysis of Hellethionin D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure Analysis of Hellethionin D within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na52

b:33.9
occ:0.50
 O D:SER42 2.9 25.2 1.0
CA D:SER42 3.6 27.1 1.0
C D:SER42 3.6 26.3 1.0
CB D:SER42 3.7 29.1 1.0
CB D:PRO45 3.7 26.2 1.0
CG D:PRO45 3.9 26.1 1.0
O D:HOH102 4.3 16.4 1.0
O D:HOH110 4.4 35.7 1.0
CD D:PRO45 4.7 24.9 1.0
OG D:SER42 4.8 30.7 1.0
N D:SER43 4.9 26.2 1.0

Sodium binding site 6 out of 19 in 3szs

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Sodium binding site 6 out of 19 in the Crystal Structure Analysis of Hellethionin D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure Analysis of Hellethionin D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na52

b:26.0
occ:1.00
 O E:GLY21 2.8 23.5 1.0
N G:LYS1 2.9 21.5 1.0
O E:HOH111 3.0 2.0 1.0
O E:ARG17 3.2 23.2 1.0
NH1 E:ARG17 3.4 24.3 1.0
C E:GLY20 3.4 24.4 1.0
CA G:LYS1 3.4 21.9 1.0
CB G:LYS1 3.6 23.4 1.0
N E:GLY21 3.6 23.5 1.0
CA E:GLY20 3.6 24.6 1.0
C E:GLY21 3.7 23.6 1.0
O E:GLY20 3.7 25.0 1.0
CZ E:ARG17 3.8 24.2 1.0
C E:ARG17 4.1 22.6 1.0
N E:GLY20 4.2 23.9 1.0
CA E:GLY21 4.2 23.3 1.0
NE E:ARG17 4.2 23.5 1.0
CA E:ARG17 4.3 22.2 1.0
NH2 E:ARG17 4.3 24.9 1.0
CD E:ARG17 4.5 22.8 1.0
N E:SER22 4.6 23.9 1.0
CG G:LYS1 4.6 25.5 1.0
CB E:ARG17 4.7 22.3 1.0
O G:HOH109 4.7 7.9 1.0
O G:VAL35 4.8 21.0 1.0
O E:HOH127 4.8 14.9 1.0
C G:LYS1 4.9 21.0 1.0
CA E:SER22 4.9 24.2 1.0

Sodium binding site 7 out of 19 in 3szs

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Sodium binding site 7 out of 19 in the Crystal Structure Analysis of Hellethionin D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure Analysis of Hellethionin D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na54

b:37.3
occ:1.00
 O E:HOH157 2.6 13.8 1.0
OG F:SER43 2.8 25.7 1.0
O F:HOH135 2.9 17.6 1.0
ND2 E:ASN6 3.1 23.2 1.0
CB F:SER43 3.7 24.9 1.0
CG E:ARG5 3.8 25.4 1.0
CB E:ASN6 3.8 23.8 1.0
CG E:ASN6 3.9 23.1 1.0
CD1 F:ILE33 4.0 20.3 1.0
CG F:PRO41 4.2 27.1 1.0
O E:ARG5 4.3 24.5 1.0
CD E:ARG5 4.3 29.0 1.0
CL F:CL54 4.3 29.4 0.5
ND1 F:HIS44 4.3 20.2 1.0
O E:HOH150 4.4 11.6 1.0
O E:HOH136 4.4 12.6 1.0
CB F:PRO41 4.6 27.6 1.0
CE1 F:HIS44 4.7 20.4 1.0
C E:ARG5 4.7 23.7 1.0
CL E:CL65 4.7 38.0 0.5
CB E:ARG5 5.0 22.9 1.0
CA E:ASN6 5.0 23.6 1.0

Sodium binding site 8 out of 19 in 3szs

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Sodium binding site 8 out of 19 in the Crystal Structure Analysis of Hellethionin D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure Analysis of Hellethionin D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na56

b:32.5
occ:1.00
 OD1 E:ASN14 2.6 23.6 1.0
O G:HOH104 2.9 7.0 1.0
NH1 E:ARG10 3.0 22.9 1.0
CG E:ASN14 3.7 21.7 1.0
O E:HOH151 3.8 7.1 1.0
CD E:ARG10 3.9 22.3 1.0
CZ E:ARG10 4.0 23.1 1.0
ND2 E:ASN14 4.0 21.9 1.0
CD1 E:TYR13 4.1 22.5 1.0
OG1 G:THR36 4.1 25.5 1.0
OG E:SER2 4.1 23.8 1.0
CE1 E:TYR13 4.1 22.2 1.0
NE E:ARG10 4.3 22.8 1.0
CB G:THR36 4.7 22.7 1.0
O E:HOH147 4.7 21.8 1.0

Sodium binding site 9 out of 19 in 3szs

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Sodium binding site 9 out of 19 in the Crystal Structure Analysis of Hellethionin D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure Analysis of Hellethionin D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na57

b:39.2
occ:1.00
 OG1 E:THR37 2.7 30.0 1.0
CB E:THR37 3.7 31.3 1.0
O E:THR39 3.7 30.9 1.0
CG2 E:THR37 3.7 31.9 1.0
CD E:PRO41 3.9 27.2 1.0
CB E:VAL35 4.0 27.2 1.0
CG1 E:VAL35 4.0 26.8 1.0
N E:PRO41 4.1 28.2 1.0
CG2 E:VAL35 4.1 27.4 1.0
CB E:PRO41 4.1 28.2 1.0
CG E:PRO41 4.2 27.1 1.0
CL E:CL51 4.4 24.4 1.0
CA E:PRO41 4.5 28.8 1.0
C E:CYS40 4.6 28.8 1.0
C E:THR39 4.8 31.2 1.0
CA E:CYS40 4.9 28.6 1.0

Sodium binding site 10 out of 19 in 3szs

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Sodium binding site 10 out of 19 in the Crystal Structure Analysis of Hellethionin D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure Analysis of Hellethionin D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na59

b:35.5
occ:1.00
 O E:HOH123 2.7 8.2 1.0
O E:HOH158 3.6 2.9 1.0
CG2 E:THR37 4.0 31.9 1.0
O E:THR36 4.0 31.9 1.0
CA E:THR37 4.0 31.4 1.0
CB E:THR37 4.5 31.3 1.0
N E:THR37 4.6 30.7 1.0
C E:THR36 4.6 30.8 1.0
N E:THR38 5.0 33.4 1.0

Reference:

A.Thorn, I.Uson, C.Eduardo, G.M.Sheldrick. Crystal Structure Analysis of Hellethionin D To Be Published.
Page generated: Mon Oct 7 13:02:33 2024

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