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Sodium in PDB 4x9c: 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii

Protein crystallography data

The structure of 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii, PDB code: 4x9c was solved by A.D.Nikulin, S.V.Tishchenko, S.V.Nikonova, V.N.Murina, A.O.Mihailina, N.V.Lekontseva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.67 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.667, 66.857, 109.212, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 18.8

Other elements in 4x9c:

The structure of 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii (pdb code 4x9c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii, PDB code: 4x9c:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4x9c

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Sodium binding site 1 out of 5 in the 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na102

b:31.8
occ:1.00
 O B:HOH228 2.4 31.3 1.0
OH C:TYR71 2.4 21.9 1.0
O B:LEU59 3.0 12.8 1.0
O B:VAL52 3.2 14.5 1.0
CZ C:TYR71 3.3 19.3 1.0
N B:VAL52 3.5 11.0 1.0
CE1 C:TYR71 3.5 15.5 1.0
CE B:MET51 3.6 26.5 1.0
N B:LEU59 3.6 12.8 1.0
CB B:MET51 3.7 11.9 1.0
C B:LEU59 3.7 11.5 1.0
C B:VAL52 3.9 15.5 1.0
C B:MET51 3.9 11.0 1.0
CA B:MET51 4.0 10.1 1.0
CB B:ASN58 4.0 19.9 1.0
OG1 B:THR43 4.1 15.3 1.0
C B:ASN58 4.2 13.3 1.0
CA B:ASN58 4.2 15.4 1.0
CA B:VAL52 4.2 11.0 1.0
CA B:LEU59 4.3 12.4 1.0
CG B:MET51 4.6 13.2 1.0
CE2 C:TYR71 4.6 20.0 1.0
SD B:MET51 4.6 21.1 1.0
N B:LEU60 4.6 10.6 1.0
OD1 B:ASN58 4.7 29.4 1.0
CG B:ASN58 4.7 24.2 1.0
O B:HOH211 4.8 33.7 1.0
CD1 C:TYR71 4.8 15.1 1.0
O B:MET51 4.9 12.1 1.0
N B:LYS53 4.9 13.6 1.0

Sodium binding site 2 out of 5 in 4x9c

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Sodium binding site 2 out of 5 in the 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na101

b:33.6
occ:1.00
 O D:HOH228 2.7 15.4 1.0
O4 D:PEG101 2.8 42.6 1.0
C4 D:PEG101 2.8 41.8 1.0
C3 D:PEG101 2.9 35.4 1.0
ND1 C:HIS64 2.9 10.3 1.0
CG C:HIS64 3.5 9.5 1.0
CB C:HIS64 3.6 8.9 1.0
O C:HOH235 3.6 35.7 1.0
O2 D:PEG101 3.7 46.6 1.0
CE1 C:HIS64 3.8 9.7 1.0
CB D:HIS64 3.9 8.6 1.0
CA D:HIS64 4.2 7.8 1.0
O D:HOH225 4.5 15.1 1.0
CD2 C:HIS64 4.5 10.4 1.0
O B:HOH217 4.5 16.1 1.0
C2 D:PEG101 4.5 32.0 1.0
O E:HOH236 4.5 16.1 1.0
O C:HOH212 4.6 15.5 1.0
NE2 C:HIS64 4.6 9.2 1.0
O E:HOH242 4.6 26.5 1.0
O B:HOH226 4.8 23.7 1.0
N D:HIS64 5.0 7.9 1.0
O D:HOH247 5.0 38.4 1.0
O E:HOH261 5.0 41.3 1.0

Sodium binding site 3 out of 5 in 4x9c

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Sodium binding site 3 out of 5 in the 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na103

b:24.2
occ:1.00
 CL D:CL102 2.7 47.7 1.0
OD2 E:ASP67 2.8 14.8 1.0
O E:ARG33 2.9 15.5 1.0
CB D:ASN34 3.3 18.8 1.0
CA E:ARG33 3.4 9.4 1.0
CG D:ARG33 3.5 11.0 1.0
C E:ARG33 3.5 12.1 1.0
CG E:ASP67 3.6 10.9 1.0
OD1 E:ASP67 3.7 11.1 1.0
CB E:ARG33 3.7 10.3 1.0
NE D:ARG33 3.8 11.0 1.0
CD D:ARG33 3.9 12.8 1.0
N D:ASN34 3.9 16.0 1.0
CA D:ASN34 4.0 18.8 1.0
CG D:ASN34 4.1 19.2 1.0
O E:HOH254 4.2 35.6 1.0
O E:HOH218 4.4 28.1 1.0
C D:ARG33 4.4 14.7 1.0
ND2 D:ASN34 4.5 25.4 1.0
CB D:ARG33 4.6 11.4 1.0
OD1 D:ASN34 4.7 20.6 1.0
N E:ARG33 4.7 9.1 1.0
CZ D:ARG33 4.8 11.0 1.0
O D:HOH232 4.8 22.8 1.0
N E:ASN34 4.8 9.8 1.0
O D:ARG33 4.9 18.6 1.0
O E:LEU32 4.9 9.0 1.0

Sodium binding site 4 out of 5 in 4x9c

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Sodium binding site 4 out of 5 in the 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na104

b:28.5
occ:1.00
 OH F:TYR71 2.5 19.7 1.0
NZ E:LYS53 2.6 19.1 0.4
O E:LEU59 3.0 10.2 1.0
CE E:LYS53 3.1 18.3 0.4
O E:VAL52 3.3 10.8 1.0
CZ F:TYR71 3.4 16.7 1.0
CE E:MET51 3.5 20.0 1.0
N E:VAL52 3.5 8.5 1.0
CE1 F:TYR71 3.6 14.4 1.0
CB E:MET51 3.6 11.1 1.0
N E:LEU59 3.7 9.7 1.0
C E:LEU59 3.8 7.8 1.0
CA E:MET51 4.0 9.5 1.0
C E:VAL52 4.0 10.0 1.0
C E:MET51 4.0 9.3 1.0
OG1 E:THR43 4.0 16.9 1.0
CB E:ASN58 4.1 14.5 1.0
C E:ASN58 4.2 10.4 1.0
CA E:ASN58 4.3 11.2 1.0
CA E:VAL52 4.3 9.5 1.0
CA E:LEU59 4.4 8.2 1.0
O F:HOH224 4.4 35.9 1.0
SD E:MET51 4.5 15.5 1.0
CG E:MET51 4.5 12.3 1.0
O E:HOH259 4.6 38.5 1.0
CD E:LYS53 4.6 24.8 0.4
N E:LEU60 4.7 7.6 1.0
CE2 F:TYR71 4.7 16.4 1.0
OD1 E:ASN58 4.8 29.9 1.0
CG E:ASN58 4.9 21.9 1.0
CD1 F:TYR71 4.9 12.7 1.0
O E:MET51 4.9 10.8 1.0

Sodium binding site 5 out of 5 in 4x9c

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Sodium binding site 5 out of 5 in the 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na104

b:21.5
occ:1.00
 O F:HOH239 2.6 27.8 1.0
OE2 F:GLU49 2.7 12.8 1.0
NZ A:LYS63 2.8 13.0 1.0
CD F:GLU49 3.4 12.3 1.0
CE A:LYS63 3.5 10.9 1.0
CE1 F:PHE62 3.5 11.4 1.0
CB A:ALA20 3.6 13.6 1.0
CD A:LYS63 3.6 10.2 1.0
CD A:GLU18 3.8 28.2 1.0
OE1 A:GLU18 3.8 29.9 1.0
CG F:GLU49 3.8 12.2 1.0
OE2 A:GLU18 3.8 28.3 1.0
CB A:GLU18 4.0 23.7 1.0
C1 F:PEG102 4.0 37.9 1.0
CZ F:PHE62 4.2 11.1 1.0
OE1 F:GLU49 4.4 12.9 1.0
CG A:GLU18 4.4 24.5 1.0
CD1 F:PHE62 4.5 10.5 1.0
N A:ALA20 4.6 13.1 1.0
O1 F:PEG102 4.7 48.2 1.0
O A:ASN47 4.7 13.4 1.0
CA A:ALA20 4.7 12.1 1.0
O F:HOH233 4.8 18.0 1.0
CG A:LYS63 4.9 9.3 1.0
O2 F:PEG102 4.9 42.0 1.0
C2 F:PEG102 4.9 40.4 1.0

Reference:

A.D.Nikulin, S.V.Tishchenko, S.V.Nikonova, V.N.Murina, A.O.Mihailina, N.V.Lekontseva. 1.4A Crystal Structure of Hfq From Methanococcus Jannaschii To Be Published.
Page generated: Mon Oct 7 19:00:44 2024

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