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Sodium in PDB 5ni3: Sfgfp 204-204 Mutant Dimer

Protein crystallography data

The structure of Sfgfp 204-204 Mutant Dimer, PDB code: 5ni3 was solved by H.L.Worthy, P.J.Rizkallah, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.17 / 1.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.700, 98.020, 102.640, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.1

Other elements in 5ni3:

The structure of Sfgfp 204-204 Mutant Dimer also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Sfgfp 204-204 Mutant Dimer (pdb code 5ni3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Sfgfp 204-204 Mutant Dimer, PDB code: 5ni3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 5ni3

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Sodium binding site 1 out of 10 in the Sfgfp 204-204 Mutant Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sfgfp 204-204 Mutant Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:39.5
occ:1.00
 O A:HOH589 2.7 29.0 1.0
O A:VAL68 3.2 15.7 1.0
O A:HOH523 3.3 20.2 1.0
N A:SER72 3.5 17.9 1.0
OG A:SER72 3.6 20.4 1.0
CD1 A:LEU42 3.6 24.2 1.0
CA A:GLN69 3.6 16.6 1.0
C A:PHE71 3.7 17.4 1.0
O A:HOH406 3.7 33.9 1.0
CG2 A:VAL224 3.7 19.1 1.0
CB A:VAL224 3.9 18.6 1.0
CB A:PHE71 3.9 16.7 1.0
C A:VAL68 3.9 16.1 1.0
N A:PHE71 4.0 17.1 1.0
CA A:PHE71 4.0 17.2 1.0
CA A:SER72 4.0 18.5 1.0
C A:GLN69 4.1 17.0 1.0
O A:GLN69 4.1 17.3 1.0
N A:GLN69 4.1 16.0 1.0
O A:PHE71 4.2 17.9 1.0
CG1 A:VAL224 4.3 19.9 1.0
CB A:SER72 4.4 19.3 1.0
CG A:LEU42 4.5 21.8 1.0
CB A:GLN69 4.7 17.2 1.0
OE2 A:GLU222 4.7 31.0 1.0
CG A:GLN69 4.8 17.7 1.0
N A:CYS70 4.8 17.1 1.0

Sodium binding site 2 out of 10 in 5ni3

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Sodium binding site 2 out of 10 in the Sfgfp 204-204 Mutant Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sfgfp 204-204 Mutant Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:38.8
occ:1.00
 O A:HOH641 2.6 37.8 1.0
ND2 A:ASN170 2.9 22.6 1.0
ND2 A:ASN144 3.0 21.1 1.0
O A:HOH607 3.0 40.8 1.0
CB A:ASN170 3.5 18.6 1.0
OE2 A:GLU142 3.6 33.5 1.0
CG A:ASN170 3.7 19.7 1.0
CG A:GLU142 3.7 23.3 1.0
CD A:GLU142 3.8 30.3 1.0
CG A:ASN144 3.9 18.6 1.0
CB A:GLU142 4.1 19.9 1.0
O A:HOH633 4.1 42.5 1.0
OD1 A:ASN144 4.2 19.5 1.0
O A:HOH564 4.6 27.9 1.0
O A:HOH584 4.8 35.1 1.0
OE1 A:GLU142 4.8 36.2 1.0
OD1 A:ASN170 4.9 20.8 1.0
O A:HOH544 4.9 36.6 1.0

Sodium binding site 3 out of 10 in 5ni3

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Sodium binding site 3 out of 10 in the Sfgfp 204-204 Mutant Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sfgfp 204-204 Mutant Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:45.6
occ:1.00
 O B:HOH622 2.3 41.1 1.0
O B:LYS45 2.8 17.2 1.0
CD1 B:ILE47 3.5 22.7 0.5
C B:LYS45 3.6 17.2 1.0
CG1 B:ILE47 3.7 21.4 0.5
CG B:GLU32 3.7 24.1 1.0
O B:ARG30 3.9 18.7 1.0
OE2 B:GLU32 4.0 34.8 1.0
CG B:LYS45 4.0 20.5 1.0
CG1 B:ILE47 4.0 21.6 0.5
N B:GLU32 4.0 17.6 1.0
CB B:LYS45 4.1 19.6 1.0
CD B:GLU32 4.2 28.3 1.0
N B:PHE46 4.2 16.7 1.0
N B:ILE47 4.3 18.1 1.0
CA B:PHE46 4.3 16.7 1.0
CA B:GLY31 4.3 16.7 1.0
C B:PHE46 4.4 17.5 1.0
CA B:LYS45 4.4 18.1 1.0
CD B:LYS45 4.4 22.6 1.0
C B:GLY31 4.5 17.0 1.0
CB B:ILE47 4.6 20.7 0.5
CB B:ILE47 4.6 20.8 0.5
CB B:GLU32 4.6 21.8 1.0
O B:HOH427 4.7 34.7 1.0
C B:ARG30 4.7 17.8 1.0
CD1 B:ILE47 4.7 22.3 0.5
CE B:LYS45 4.8 23.9 1.0
CA B:GLU32 4.9 18.8 1.0
N B:GLY31 4.9 16.8 1.0
O B:GLU32 4.9 18.0 1.0

Sodium binding site 4 out of 10 in 5ni3

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Sodium binding site 4 out of 10 in the Sfgfp 204-204 Mutant Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Sfgfp 204-204 Mutant Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:39.6
occ:1.00
 O C:HOH567 2.9 43.6 1.0
O C:HOH440 3.1 36.8 1.0
CD1 C:ILE128 3.7 28.8 1.0
CG2 C:THR105 3.9 19.4 1.0
CB C:THR105 4.1 19.4 1.0
OG1 C:THR105 4.2 21.1 1.0
CG1 C:ILE128 4.3 26.2 1.0
O C:HOH439 4.4 26.2 1.0
CD C:LYS107 4.7 21.2 1.0
OD2 C:ASP129 5.0 28.5 1.0

Sodium binding site 5 out of 10 in 5ni3

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Sodium binding site 5 out of 10 in the Sfgfp 204-204 Mutant Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Sfgfp 204-204 Mutant Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:37.3
occ:1.00
 O C:HOH412 4.1 40.8 1.0

Sodium binding site 6 out of 10 in 5ni3

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Sodium binding site 6 out of 10 in the Sfgfp 204-204 Mutant Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Sfgfp 204-204 Mutant Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:40.9
occ:1.00
 O C:HOH498 2.4 28.2 1.0
O C:PHE145 2.8 22.4 1.0
O C:SER205 3.0 34.3 1.0
N C:PHE145 3.2 19.6 1.0
O B:HOH562 3.4 36.1 1.0
C C:PHE145 3.6 19.3 1.0
CA C:PHE145 3.8 19.6 1.0
O B:HOH602 4.0 39.2 1.0
C C:ASN144 4.1 19.0 1.0
CB C:ASN144 4.1 20.4 1.0
CB C:PHE145 4.1 20.3 1.0
C C:SER205 4.1 28.8 1.0
CA C:ASN144 4.2 19.6 1.0
CA C:VAL206 4.3 23.2 1.0
O C:HOH547 4.3 22.4 1.0
O B:HOH641 4.4 42.5 1.0
N C:LEU207 4.6 20.4 1.0
N C:VAL206 4.7 23.7 1.0
O C:HOH639 4.8 41.3 1.0
N C:ASN146 4.8 18.6 1.0
O C:HOH450 4.8 28.4 1.0
O C:HOH585 4.8 37.9 1.0

Sodium binding site 7 out of 10 in 5ni3

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Sodium binding site 7 out of 10 in the Sfgfp 204-204 Mutant Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Sfgfp 204-204 Mutant Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:32.7
occ:1.00
 OG D:SER175 2.9 23.3 1.0
ND2 D:ASN135 3.0 21.4 1.0
CB D:SER175 3.8 24.0 1.0
CG D:ASN135 4.0 21.3 1.0
OD1 D:ASN135 4.1 22.1 1.0
CG2 D:VAL171 4.1 19.9 1.0
CG1 D:VAL171 4.5 20.6 1.0
OD2 D:ASP173 4.6 28.8 1.0
CB D:VAL171 4.6 20.2 1.0
OD1 D:ASP173 4.7 24.5 1.0
O D:VAL176 4.8 22.6 1.0
NE2 D:GLN177 4.9 19.8 1.0

Sodium binding site 8 out of 10 in 5ni3

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Sodium binding site 8 out of 10 in the Sfgfp 204-204 Mutant Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Sfgfp 204-204 Mutant Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:32.7
occ:1.00
 OD2 D:ASP103 2.7 24.8 1.0
N D:ASN135 2.9 22.1 1.0
NE2 D:GLN177 3.0 19.8 1.0
CG D:ASP103 3.5 24.0 1.0
CB D:ASN135 3.5 20.5 1.0
ND2 D:ASN135 3.5 21.4 1.0
CG D:ASN135 3.6 21.3 1.0
CB D:ASP103 3.6 23.6 1.0
CA D:ASN135 3.8 20.9 1.0
CA D:GLY134 3.9 25.7 1.0
C D:GLY134 3.9 23.6 1.0
CD1 D:ILE136 4.1 22.5 1.0
CD D:GLN177 4.2 19.6 1.0
OD1 D:ASN135 4.4 22.1 1.0
O D:ASP102 4.5 27.6 1.0
N D:ILE136 4.6 19.9 1.0
O D:HOH453 4.7 21.2 1.0
OD1 D:ASP103 4.7 25.1 1.0
O D:LYS101 4.7 24.2 1.0
C D:ASN135 4.7 19.9 1.0
OE1 D:GLN177 4.7 20.5 1.0
CA D:ASP103 4.9 24.6 1.0
C D:ASP102 5.0 26.9 1.0

Sodium binding site 9 out of 10 in 5ni3

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Sodium binding site 9 out of 10 in the Sfgfp 204-204 Mutant Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Sfgfp 204-204 Mutant Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:38.4
occ:1.00
 O D:HOH439 2.5 28.7 1.0
O A:HOH640 2.7 34.0 1.0
O D:HOH603 2.8 27.4 1.0
CG1 D:VAL219 3.8 17.0 1.0
O D:HOH618 3.9 39.6 1.0
OG D:SER208 4.3 18.6 1.0
O D:HOH532 4.4 27.7 1.0
O D:HOH598 4.4 39.1 1.0
O A:HOH638 4.5 40.3 1.0
O D:HOH503 4.6 19.8 1.0
O D:HOH616 4.9 38.1 1.0
O A:HOH655 5.0 39.7 1.0

Sodium binding site 10 out of 10 in 5ni3

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Sodium binding site 10 out of 10 in the Sfgfp 204-204 Mutant Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Sfgfp 204-204 Mutant Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na305

b:46.0
occ:1.00
 OE1 D:GLU132 2.4 55.0 1.0
NE2 D:HIS25 2.8 35.3 1.0
OE2 D:GLU132 2.8 54.2 1.0
O D:HOH401 3.0 37.2 1.0
CD D:GLU132 3.0 48.5 1.0
CE1 D:HIS25 3.6 36.1 1.0
CD2 D:HIS25 3.8 32.4 1.0
CD1 D:LEU137 4.1 24.1 1.0
CG D:GLU132 4.5 46.0 1.0
ND1 D:HIS25 4.8 35.5 1.0
CG D:HIS25 4.9 30.9 1.0

Reference:

H.L.Worthy, P.J.Rizkallah, J.Pope, D.D.Jones, D.Watkins. Sfgfp 204-204 Mutant Dimer To Be Published.
Page generated: Tue Dec 15 11:20:58 2020

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