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Chlorine in PDB 5u1a: Ferritin with Gc Mtre Loop 1 Inserted at HIS34

Enzymatic activity of Ferritin with Gc Mtre Loop 1 Inserted at HIS34

All present enzymatic activity of Ferritin with Gc Mtre Loop 1 Inserted at HIS34:
1.16.3.2;

Protein crystallography data

The structure of Ferritin with Gc Mtre Loop 1 Inserted at HIS34, PDB code: 5u1a was solved by S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 128.412, 128.412, 165.041, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.6

Other elements in 5u1a:

The structure of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 also contains other interesting chemical elements:

Iron (Fe) 6 atoms
Sodium (Na) 30 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34 (pdb code 5u1a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34, PDB code: 5u1a:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5u1a

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Chlorine binding site 1 out of 8 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl204

b:24.5
occ:0.50
 O D:HOH385 2.9 42.4 1.0
OG C:SER87 3.3 40.0 1.0
N C:SER87 3.3 23.4 1.0
CB C:SER87 3.7 28.8 1.0
CB C:THR86 4.0 25.0 1.0
CA C:THR86 4.1 23.5 1.0
CA C:SER87 4.2 26.9 1.0
C C:THR86 4.2 26.3 1.0
CB D:ALA90 4.3 23.3 1.0
CG2 C:THR86 4.5 24.3 1.0
O C:SER87 5.0 24.4 1.0

Chlorine binding site 2 out of 8 in 5u1a

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Chlorine binding site 2 out of 8 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl204

b:34.0
occ:0.50
 OG C:SER87 2.6 40.0 1.0
O D:HOH311 2.8 36.0 1.0
N D:ALA90 3.1 21.5 1.0
CA D:SER89 3.4 33.7 1.0
CB D:SER89 3.4 37.6 1.0
C D:SER89 3.7 27.3 1.0
CB C:SER87 3.9 28.8 1.0
CB D:ALA90 4.1 23.3 1.0
CA D:ALA90 4.1 21.2 1.0
O D:ALA90 4.4 22.4 1.0
CA C:SER87 4.7 26.9 1.0
OG D:SER89 4.7 40.6 1.0
O D:ILE88 4.8 38.0 1.0
N D:SER89 4.8 31.7 1.0
C D:ALA90 4.8 22.0 1.0
O D:SER89 4.9 29.5 1.0

Chlorine binding site 3 out of 8 in 5u1a

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Chlorine binding site 3 out of 8 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl209

b:22.5
occ:1.00
 O F:HOH387 3.0 23.0 1.0
O1 F:GOL207 3.1 34.1 1.0
O F:HOH366 3.3 34.1 1.0
OG1 F:THR86 3.4 15.9 1.0
CB F:ASN15 3.7 14.2 1.0
C1 F:GOL207 3.8 41.2 1.0
CG2 F:THR86 3.9 15.7 1.0
ND2 F:ASN15 4.1 17.6 1.0
CB F:THR86 4.1 15.3 1.0
CG F:ASN15 4.2 16.2 1.0
NA F:NA204 4.3 23.1 1.0
CG F:GLU12 4.5 18.6 1.0
CA F:GLU12 4.6 15.7 1.0
O F:GLU12 4.8 13.6 1.0
CB F:GLU12 4.9 17.4 1.0
C2 F:GOL207 5.0 44.4 1.0
C3 F:GOL207 5.0 50.4 1.0

Chlorine binding site 4 out of 8 in 5u1a

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Chlorine binding site 4 out of 8 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl204

b:34.8
occ:1.00
 O G:HOH368 3.1 46.2 1.0
NE1 G:TRP30 3.2 22.4 1.0
N G:PHE95 3.3 26.7 1.0
O G:PHE95 3.3 22.4 1.0
CD1 G:TRP30 3.6 20.7 1.0
O G:GLY34 3.7 44.9 1.0
CA G:LYS94 3.7 34.9 1.0
C G:LYS94 3.9 31.4 1.0
CB G:LYS94 4.0 40.9 1.0
C G:PHE95 4.2 24.4 1.0
C G:GLY34 4.2 39.8 1.0
O G:HIS93 4.3 33.8 1.0
CA G:PHE95 4.4 25.0 1.0
CE2 G:TRP30 4.5 21.2 1.0
CB G:SER47 4.7 47.7 1.0
CG G:LYS94 4.7 48.3 1.0
N G:LYS94 4.8 31.6 1.0
CG G:TRP30 5.0 17.8 1.0

Chlorine binding site 5 out of 8 in 5u1a

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Chlorine binding site 5 out of 8 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl204

b:32.4
occ:1.00
 O K:HOH367 2.9 19.2 1.0
O K:HOH317 3.3 34.6 1.0
OG1 K:THR86 3.3 21.1 1.0
CG K:GLU12 4.0 22.6 1.0
CG2 K:THR86 4.0 21.7 1.0
CA K:GLU12 4.1 16.6 1.0
CB K:ASN15 4.1 16.0 1.0
ND2 K:ASN15 4.1 19.5 1.0
CB K:THR86 4.2 20.3 1.0
O K:ASN11 4.3 14.1 1.0
CG K:ASN15 4.3 17.3 1.0
N K:GLU12 4.4 16.2 1.0
O K:HOH341 4.5 25.3 1.0
C K:ASN11 4.5 16.2 1.0
CB K:GLU12 4.6 19.8 1.0
O K:GLN84 4.7 21.1 1.0
N K:THR86 4.8 18.4 1.0

Chlorine binding site 6 out of 8 in 5u1a

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Chlorine binding site 6 out of 8 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl208

b:21.1
occ:1.00
 O L:HOH410 3.0 19.1 1.0
OG1 L:THR86 3.3 15.1 1.0
O L:HOH379 3.3 29.9 1.0
CB L:ASN15 3.5 12.8 1.0
CG2 L:THR86 3.8 15.7 1.0
ND2 L:ASN15 4.1 14.8 1.0
CG L:ASN15 4.1 14.3 1.0
CB L:THR86 4.1 15.0 1.0
NA L:NA201 4.3 19.5 1.0
CG L:GLU12 4.7 20.6 1.0
O L:HOH401 4.7 30.0 1.0
CA L:GLU12 4.7 15.5 1.0
O L:GLU12 4.8 13.8 1.0
CA L:ASN15 4.9 12.9 1.0
CB L:GLU12 5.0 17.8 1.0
O L:HOH428 5.0 29.8 1.0

Chlorine binding site 7 out of 8 in 5u1a

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Chlorine binding site 7 out of 8 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl209

b:35.3
occ:1.00
 N L:GLU96 3.2 22.1 1.0
O L:HOH418 3.2 47.5 1.0
CE L:LYS104 3.4 37.6 1.0
CB L:GLN100 3.6 29.3 1.0
NZ L:LYS104 3.6 42.2 1.0
CA L:PHE95 3.7 21.9 1.0
CB L:GLU96 3.8 30.2 1.0
CG L:GLU96 3.9 39.4 1.0
C L:PHE95 3.9 22.7 1.0
CB L:PHE95 4.0 21.8 1.0
CA L:GLU96 4.1 24.8 1.0
CD1 L:PHE95 4.1 22.5 1.0
CD L:LYS104 4.2 28.6 1.0
CG L:GLN100 4.4 34.9 1.0
C L:GLN100 4.5 22.8 1.0
CG L:PHE95 4.6 20.9 1.0
CA L:GLN100 4.6 25.8 1.0
O L:GLN100 4.7 22.9 1.0
OE1 L:GLU92 4.8 45.7 1.0
O L:LYS94 4.8 23.9 1.0
N L:GLY97 4.9 21.4 1.0
N L:ILE101 4.9 21.1 1.0
N L:PHE95 5.0 21.8 1.0
C L:GLU96 5.0 24.5 1.0

Chlorine binding site 8 out of 8 in 5u1a

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Chlorine binding site 8 out of 8 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl210

b:35.7
occ:1.00
 OG1 L:THR131 2.9 17.5 1.0
N L:THR131 3.1 15.8 1.0
NA L:NA205 3.2 43.0 1.0
CB L:ASP128 3.3 29.9 1.0
CA L:ASP128 3.4 28.5 1.0
CB L:THR131 3.4 18.1 1.0
C L:ASP128 3.5 23.5 1.0
O L:ASP128 3.6 20.0 1.0
CD2 L:LEU2 3.6 39.6 1.0
N L:ALA130 3.8 19.3 1.0
CB L:ALA130 3.8 20.6 1.0
CA L:THR131 3.9 16.6 1.0
C L:ALA130 4.0 17.8 1.0
N L:HIS129 4.0 22.4 1.0
CA L:ALA130 4.1 19.6 1.0
CG L:ASP128 4.3 39.7 1.0
OD1 L:ASP128 4.3 39.6 1.0
O L:HOH431 4.5 43.5 1.0
C L:HIS129 4.6 21.4 1.0
N L:ASP128 4.8 28.2 1.0
CG2 L:THR131 4.8 18.3 1.0
CA L:HIS129 4.9 23.6 1.0

Reference:

L.Wang, D.Xing, A.Le Van, A.E.Jerse, S.Wang. Structure-Based Design of Ferritin Nanoparticle Immunogens Displaying Antigenic Loops of Neisseria Gonorrhoeae. Febs Open Bio V. 7 1196 2017.
ISSN: ESSN 2211-5463
PubMed: 28781959
DOI: 10.1002/2211-5463.12267
Page generated: Fri Jul 26 17:52:08 2024

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