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Sodium in PDB 6zhv: Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic

Protein crystallography data

The structure of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic, PDB code: 6zhv was solved by C.F.Sousa, J.Morais-Cabral, P.Gameiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.30 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.029, 112.005, 131.568, 90, 90, 90
R / Rfree (%) 19.8 / 23.3

Other elements in 6zhv:

The structure of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic (pdb code 6zhv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic, PDB code: 6zhv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 6zhv

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Sodium binding site 1 out of 12 in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:35.9
occ:1.00
 O A:HOH539 2.3 27.1 1.0
O B:ALA97 2.5 24.8 1.0
N A:THR103 2.8 18.4 1.0
O B:HOH532 2.8 20.8 1.0
C B:ALA97 3.4 22.9 1.0
O B:HOH533 3.4 21.7 1.0
CB B:ALA97 3.4 21.9 1.0
CA A:LYS102 3.6 21.3 1.0
CA B:ALA97 3.6 23.9 1.0
CB A:THR103 3.7 20.6 1.0
C A:LYS102 3.7 21.0 1.0
CA A:THR103 3.7 21.9 1.0
CB A:LYS102 3.8 18.6 1.0
OG1 A:THR103 4.0 21.3 1.0
O A:THR103 4.0 19.2 1.0
O B:SER92 4.0 21.6 1.0
O B:GLN88 4.3 18.5 1.0
C A:THR103 4.3 20.0 1.0
CB B:ASN91 4.4 18.8 1.0
N B:GLN98 4.6 22.1 1.0
ND2 B:ASN91 4.6 17.3 1.0
CE1 A:TYR85 4.9 20.6 1.0
N A:LYS102 4.9 16.9 1.0
O A:LYS102 4.9 18.4 1.0
NE2 B:GLN98 5.0 38.5 1.0

Sodium binding site 2 out of 12 in 6zhv

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Sodium binding site 2 out of 12 in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:45.0
occ:1.00
 O B:HOH544 2.2 27.2 1.0
O A:HOH541 2.2 30.3 1.0
O C:HOH536 2.3 30.9 1.0
OH B:TYR85 3.5 30.3 1.0
OH A:TYR85 3.6 28.6 1.0
CE1 B:PHE87 3.7 19.9 1.0
CE2 B:TYR85 3.8 23.8 1.0
CZ B:TYR85 3.8 21.8 1.0
CZ A:TYR85 4.0 22.8 1.0
CE1 C:PHE87 4.0 21.0 1.0
CE2 A:TYR85 4.1 20.7 1.0
OH C:TYR85 4.2 28.7 1.0
CE1 A:PHE87 4.2 18.9 1.0
OE1 C:GLN98 4.3 40.5 1.0
CD1 B:PHE87 4.5 17.0 1.0
CE2 C:TYR85 4.5 21.1 1.0
CZ C:TYR85 4.5 21.2 1.0
CZ B:PHE87 4.6 16.4 1.0
ND2 B:ASN101 4.7 20.8 1.0
CD2 B:TYR85 4.7 17.8 1.0
OE1 A:GLN98 4.8 41.0 1.0
CE1 B:TYR85 4.8 20.2 1.0
CZ C:PHE87 4.8 20.5 1.0
CE1 A:TYR85 4.8 20.6 1.0
CD1 C:PHE87 4.8 17.5 1.0
OE1 B:GLN98 4.9 43.3 1.0
CZ A:PHE87 5.0 20.8 1.0
CD1 A:PHE87 5.0 14.8 1.0

Sodium binding site 3 out of 12 in 6zhv

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Sodium binding site 3 out of 12 in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:39.4
occ:1.00
 O B:SER350 2.3 26.6 1.0
O B:ASN338 2.4 28.2 1.0
O B:HOH550 2.4 44.0 1.0
O B:ILE340 2.6 31.7 1.0
C B:SER350 3.4 28.7 1.0
C B:ASN338 3.4 27.1 1.0
C B:ILE340 3.8 29.4 1.0
CB B:SER350 3.9 33.5 1.0
CA B:SER350 3.9 28.8 1.0
C B:GLN339 4.1 32.8 1.0
N B:ILE340 4.1 30.0 1.0
CB B:ASN338 4.1 27.2 1.0
N B:GLN339 4.2 25.2 1.0
CA B:GLN339 4.2 27.2 1.0
CA B:ASN338 4.4 26.5 1.0
CG B:ASN338 4.4 24.7 1.0
CA B:ILE340 4.5 27.1 1.0
O B:GLN339 4.5 27.8 1.0
N B:ASP351 4.5 27.8 1.0
OG B:SER350 4.6 34.2 1.0
OD1 B:ASN338 4.7 22.2 1.0
N B:ASP341 4.8 35.3 1.0
OD1 B:ASP352 4.8 27.8 1.0
CA B:ASP341 4.8 39.1 1.0
CA B:ASP351 4.9 29.4 1.0
ND2 B:ASN338 5.0 23.2 1.0
N B:ASN338 5.0 25.8 1.0

Sodium binding site 4 out of 12 in 6zhv

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Sodium binding site 4 out of 12 in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:45.7
occ:1.00
 O B:GLN225 2.2 27.9 1.0
O B:HOH553 2.4 42.5 1.0
O B:GLY228 2.5 36.0 1.0
O B:GLU223 2.9 40.2 1.0
C B:GLN225 3.4 26.4 1.0
C B:GLY228 3.7 33.8 1.0
C B:GLU223 3.9 34.8 1.0
N B:GLN225 4.1 28.8 1.0
NA B:NA406 4.2 44.9 1.0
OE2 B:GLU223 4.3 44.9 1.0
C B:PRO226 4.3 32.2 1.0
N B:PRO226 4.3 25.2 1.0
CA B:GLN225 4.4 29.4 1.0
CA B:ASN229 4.4 36.5 1.0
O B:PRO226 4.4 31.1 1.0
C B:ALA224 4.4 36.8 1.0
CA B:PRO226 4.4 32.1 1.0
N B:ASN229 4.5 34.2 1.0
C B:LEU227 4.5 29.3 1.0
CB B:ASN229 4.5 37.8 1.0
O B:LEU227 4.5 27.2 1.0
N B:GLY228 4.6 27.2 1.0
N B:LEU227 4.6 27.1 1.0
CA B:GLY228 4.7 29.4 1.0
CA B:GLU223 4.7 31.1 1.0
O B:GLN222 4.7 27.8 1.0
N B:ALA224 4.8 32.4 1.0
O B:ALA224 4.9 31.3 1.0
CA B:ALA224 4.9 34.8 1.0

Sodium binding site 5 out of 12 in 6zhv

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Sodium binding site 5 out of 12 in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:44.9
occ:1.00
 NH2 B:ARG218 2.7 26.5 1.0
O B:LEU227 2.8 27.2 1.0
O B:GLN222 2.9 27.8 1.0
O B:GLY228 3.2 36.0 1.0
NH1 B:ARG218 3.4 34.4 1.0
CZ B:ARG218 3.5 31.1 1.0
C B:GLY228 3.5 33.8 1.0
CA B:GLY228 3.6 29.4 1.0
C B:LEU227 3.7 29.3 1.0
CD2 B:PHE272 3.8 28.1 1.0
C B:GLN222 3.8 28.8 1.0
CB B:GLN225 4.0 27.3 1.0
N B:PHE272 4.1 27.0 1.0
N B:GLY228 4.1 27.2 1.0
O B:GLN225 4.2 27.9 1.0
CB B:PHE272 4.2 23.4 1.0
NA B:NA405 4.2 45.7 1.0
CG B:PHE272 4.4 26.5 1.0
N B:ASN229 4.5 34.2 1.0
N B:GLU223 4.6 28.6 1.0
CA B:GLU223 4.6 31.1 1.0
CA B:GLY271 4.7 26.0 1.0
N B:GLN225 4.7 28.8 1.0
CA B:PHE272 4.7 27.1 1.0
C B:GLN225 4.7 26.4 1.0
CA B:GLN225 4.7 29.4 1.0
CG B:GLN225 4.7 28.9 1.0
CA B:GLN222 4.7 29.0 1.0
C B:GLY271 4.7 28.2 1.0
CE2 B:PHE272 4.8 25.5 1.0
NE B:ARG218 4.8 39.2 1.0
O B:PHE272 4.8 26.5 1.0
C B:GLU223 4.9 34.8 1.0
O B:GLU223 4.9 40.2 1.0
CB B:GLN222 4.9 24.6 1.0

Sodium binding site 6 out of 12 in 6zhv

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Sodium binding site 6 out of 12 in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:46.4
occ:1.00
 O A:GLN225 2.3 32.2 1.0
O A:GLY228 2.3 38.4 1.0
O A:GLU223 2.8 48.5 1.0
C A:GLN225 3.5 32.7 1.0
C A:GLY228 3.5 38.5 1.0
C A:GLU223 3.9 41.7 1.0
C A:PRO226 4.2 40.8 1.0
O A:PRO226 4.2 37.8 1.0
OE2 A:GLU223 4.2 49.5 1.0
N A:GLN225 4.3 36.4 1.0
CA A:PRO226 4.3 35.9 1.0
NA A:NA405 4.3 43.5 1.0
N A:PRO226 4.3 32.3 1.0
CA A:ASN229 4.3 42.6 1.0
N A:ASN229 4.4 42.9 1.0
N A:GLY228 4.5 37.5 1.0
CA A:GLN225 4.5 37.2 1.0
CA A:GLY228 4.5 36.9 1.0
C A:ALA224 4.5 44.2 1.0
C A:LEU227 4.5 36.5 1.0
O A:LEU227 4.5 35.6 1.0
CA A:GLU223 4.6 42.3 1.0
O A:GLN222 4.6 36.2 1.0
CB A:ASN229 4.7 48.1 1.0
N A:LEU227 4.7 34.0 1.0
N A:ALA224 4.8 40.5 1.0
O A:ALA224 4.9 41.4 1.0
OD1 A:ASN229 4.9 58.6 1.0
CA A:ALA224 4.9 38.5 1.0

Sodium binding site 7 out of 12 in 6zhv

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Sodium binding site 7 out of 12 in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:44.8
occ:1.00
 OD2 A:ASP312 2.4 36.4 1.0
O A:HOH550 2.7 32.0 1.0
OD1 A:ASP341 3.1 64.4 1.0
CG A:ASP312 3.2 34.1 1.0
CB A:ASP312 3.4 30.1 1.0
ND2 A:ASN315 3.7 33.9 1.0
CA A:ILE340 3.9 25.7 1.0
CD1 A:ILE340 4.0 28.6 1.0
O A:GLN339 4.0 29.4 1.0
N A:ASP341 4.1 32.9 1.0
CB A:ASN315 4.2 25.9 1.0
O A:HOH549 4.2 38.0 1.0
CG A:ASP341 4.3 53.9 1.0
CG A:ASN315 4.4 30.7 1.0
OD1 A:ASP312 4.4 34.4 1.0
N A:ILE340 4.5 29.7 1.0
C A:ILE340 4.6 31.8 1.0
C A:GLN339 4.6 30.4 1.0
CB A:ILE340 4.8 28.3 1.0
CG1 A:ILE340 4.9 28.3 1.0
CA A:ASP312 4.9 30.0 1.0

Sodium binding site 8 out of 12 in 6zhv

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Sodium binding site 8 out of 12 in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:37.7
occ:1.00
 O A:HOH538 2.4 28.0 1.0
OE1 A:GLN361 2.6 47.3 1.0
OG A:SER330 2.9 24.3 1.0
CD A:GLN361 3.4 43.3 1.0
N A:SER330 3.5 19.2 1.0
CB A:SER330 3.5 22.9 1.0
C A:MET329 3.6 25.0 1.0
CG A:GLN361 3.7 34.1 1.0
CG1 A:VAL359 3.7 24.1 1.0
O A:VAL359 3.8 20.9 1.0
N A:MET329 3.8 21.1 1.0
CA A:MET329 3.8 20.7 1.0
C A:ASN328 3.9 25.4 1.0
O A:ASN328 3.9 25.6 1.0
CB A:VAL359 4.0 22.4 1.0
CA A:SER330 4.1 19.8 1.0
O A:MET329 4.3 23.3 1.0
C A:VAL359 4.4 22.4 1.0
O A:LYS327 4.6 26.5 1.0
NE2 A:GLN361 4.6 48.0 1.0
CB A:GLN361 4.7 24.3 1.0
CA A:ASN328 4.7 23.9 1.0
N A:GLN361 4.8 22.4 1.0
CD1 A:TYR324 4.9 27.7 1.0
CE1 A:TYR324 4.9 28.6 1.0
CA A:VAL359 4.9 20.0 1.0
O A:ASN326 5.0 27.1 1.0

Sodium binding site 9 out of 12 in 6zhv

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Sodium binding site 9 out of 12 in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:43.5
occ:1.00
 NH2 A:ARG218 2.4 40.0 1.0
O A:LEU227 2.6 35.6 1.0
O A:GLN222 2.9 36.2 1.0
CZ A:ARG218 3.4 40.3 1.0
O A:GLY228 3.5 38.4 1.0
CD1 A:PHE272 3.5 29.8 1.0
NH1 A:ARG218 3.6 38.4 1.0
CA A:GLY228 3.6 36.9 1.0
C A:LEU227 3.7 36.5 1.0
N A:PHE272 3.7 29.0 1.0
CB A:GLN225 3.8 36.2 1.0
C A:GLY228 3.8 38.5 1.0
C A:GLN222 3.9 39.9 1.0
CB A:PHE272 4.1 29.1 1.0
N A:GLY228 4.1 37.5 1.0
CA A:GLY271 4.2 29.6 1.0
O A:GLN225 4.2 32.2 1.0
CG A:PHE272 4.3 28.6 1.0
NA A:NA402 4.3 46.4 1.0
CG A:GLN225 4.4 34.6 1.0
C A:GLY271 4.4 31.0 1.0
CA A:PHE272 4.5 32.6 1.0
CE1 A:PHE272 4.5 28.5 1.0
CA A:GLN225 4.6 37.2 1.0
C A:GLN225 4.6 32.7 1.0
NE A:ARG218 4.6 37.3 1.0
CA A:GLN222 4.7 34.9 1.0
N A:GLN225 4.7 36.4 1.0
N A:GLU223 4.7 37.3 1.0
O A:PHE272 4.8 32.1 1.0
CA A:GLU223 4.8 42.3 1.0
N A:ASN229 4.8 42.9 1.0
CB A:GLN222 4.9 32.2 1.0
CA A:LEU227 4.9 33.0 1.0
C A:GLU223 5.0 41.7 1.0

Sodium binding site 10 out of 12 in 6zhv

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Sodium binding site 10 out of 12 in the Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:34.6
occ:1.00
 O C:GLN225 2.3 28.1 1.0
O C:GLY228 2.3 28.8 1.0
O C:GLU223 2.6 31.9 1.0
C C:GLN225 3.5 26.1 1.0
C C:GLY228 3.5 29.2 1.0
C C:GLU223 3.7 28.7 1.0
N C:GLN225 4.1 26.6 1.0
CA C:ASN229 4.2 30.5 1.0
OE2 C:GLU223 4.3 37.0 1.0
N C:ASN229 4.4 24.3 1.0
C C:PRO226 4.4 30.8 1.0
CA C:GLU223 4.4 27.5 1.0
C C:ALA224 4.4 32.0 1.0
CA C:GLN225 4.4 30.3 1.0
NA C:NA404 4.4 36.2 1.0
CA C:PRO226 4.4 25.9 1.0
N C:PRO226 4.4 28.7 1.0
O C:GLN222 4.5 23.0 1.0
O C:PRO226 4.5 26.1 1.0
N C:GLY228 4.5 24.2 1.0
CB C:ASN229 4.5 32.0 1.0
CA C:GLY228 4.5 24.2 1.0
C C:LEU227 4.6 28.5 1.0
O C:LEU227 4.6 27.1 1.0
OD1 C:ASN229 4.6 48.2 1.0
N C:ALA224 4.6 25.6 1.0
N C:LEU227 4.7 24.7 1.0
O C:ALA224 4.8 28.7 1.0
CA C:ALA224 4.8 30.1 1.0

Reference:

C.F.Sousa, J.Morais-Cabral, P.Gameiro. Crystal Structure of Ompf Porin Soaked in Ciprofloxacin Metaloantibiotic To Be Published.
Page generated: Tue Oct 8 15:28:37 2024

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