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Chlorine in PDB 5xhm: Crystal Structure of Frog M-Ferritin D40A Mutant

Enzymatic activity of Crystal Structure of Frog M-Ferritin D40A Mutant

All present enzymatic activity of Crystal Structure of Frog M-Ferritin D40A Mutant:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Frog M-Ferritin D40A Mutant, PDB code: 5xhm was solved by M.K.Jagdev, D.Vasudevan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.98 / 1.70
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.170, 184.170, 184.170, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18.7

Other elements in 5xhm:

The structure of Crystal Structure of Frog M-Ferritin D40A Mutant also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Frog M-Ferritin D40A Mutant (pdb code 5xhm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Frog M-Ferritin D40A Mutant, PDB code: 5xhm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5xhm

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Chlorine binding site 1 out of 8 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:32.2
occ:1.00
 O A:HOH525 2.9 33.0 1.0
N A:SER10 3.0 12.3 1.0
CB A:SER10 3.6 14.0 1.0
CD2 A:HIS9 3.7 17.9 1.0
CG A:HIS9 3.7 14.9 1.0
CA A:HIS9 3.8 12.7 1.0
O A:HOH486 3.8 33.5 1.0
ND1 A:HIS9 3.8 14.8 1.0
CE1 A:HIS9 3.9 18.6 1.0
NE2 A:HIS9 3.9 17.8 1.0
C A:HIS9 3.9 13.3 1.0
CA A:SER10 3.9 12.5 1.0
CB A:HIS9 4.3 13.8 1.0
O A:TYR8 4.4 12.9 1.0
O A:HOH504 4.9 30.6 1.0
N A:HIS9 4.9 12.3 1.0
O A:HOH494 5.0 41.0 1.0

Chlorine binding site 2 out of 8 in 5xhm

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Chlorine binding site 2 out of 8 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:21.5
occ:1.00
 O A:HOH486 3.3 33.5 1.0
N A:TYR8 3.3 11.8 1.0
N A:ASN7 3.4 12.5 1.0
O A:TYR8 3.6 12.9 1.0
CD A:ARG5 3.6 15.0 1.0
CG A:ARG5 3.6 15.1 1.0
NE A:ARG5 3.6 14.6 1.0
O A:HOH458 3.9 20.1 1.0
C A:GLN6 3.9 10.9 1.0
CA A:GLN6 4.0 12.1 1.0
C A:TYR8 4.1 11.8 1.0
CA A:TYR8 4.1 12.0 1.0
CA A:ASN7 4.1 10.9 1.0
N A:GLN6 4.1 12.4 1.0
C A:ASN7 4.2 11.0 1.0
C A:ARG5 4.3 13.5 1.0
CB A:TYR8 4.4 11.3 1.0
O A:ARG5 4.5 14.5 1.0
O A:HOH547 4.5 43.5 1.0
CB A:ARG5 4.5 14.2 1.0
O A:GLN6 4.8 10.9 1.0
CZ A:ARG5 4.9 14.1 1.0

Chlorine binding site 3 out of 8 in 5xhm

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Chlorine binding site 3 out of 8 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:27.7
occ:0.95
 O A:HOH320 2.7 34.9 1.0
O A:HOH546 3.0 34.1 1.0
N A:ASP87 3.1 15.2 1.0
N A:GLU88 3.7 13.0 1.0
CA A:ARG86 3.7 15.1 1.0
CB A:ARG86 3.8 16.3 1.0
C A:ARG86 3.9 15.2 1.0
CA A:ASP87 4.0 16.1 1.0
CB A:ASP87 4.0 17.6 1.0
CG A:GLU88 4.2 18.6 1.0
O A:GLU88 4.2 16.1 1.0
CG A:ARG86 4.2 16.3 1.0
C A:ASP87 4.3 17.9 1.0
O A:HOH460 4.5 36.2 1.0
OD2 A:ASP87 4.5 21.7 1.0
CG A:ASP87 4.6 21.6 1.0
OE2 A:GLU88 4.6 28.3 1.0
NE A:ARG86 4.7 18.1 1.0
CA A:GLU88 4.7 13.8 1.0
CB A:GLU88 4.9 16.4 1.0
C A:GLU88 4.9 15.1 1.0
CD A:GLU88 4.9 23.0 1.0

Chlorine binding site 4 out of 8 in 5xhm

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Chlorine binding site 4 out of 8 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl214

b:27.4
occ:1.00
 O A:HOH341 2.8 19.1 1.0
O A:HOH390 3.2 27.4 1.0
O A:HOH487 3.3 45.3 1.0
ND2 A:ASN150 3.6 11.7 1.0
CB A:ASP146 3.8 11.6 1.0
CD1 A:PHE147 4.2 15.4 1.0
CE1 A:PHE147 4.2 18.0 1.0
O A:ASP146 4.4 11.8 1.0
C A:ASP146 4.5 12.3 1.0
OD2 A:ASP146 4.5 14.4 1.0
CG A:ASN150 4.5 12.1 1.0
CG A:ASP146 4.6 13.0 1.0
CA A:ASP146 4.7 11.5 1.0
N A:PHE147 4.7 12.2 1.0

Chlorine binding site 5 out of 8 in 5xhm

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Chlorine binding site 5 out of 8 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl215

b:43.2
occ:1.00
 O A:HOH344 3.0 28.0 1.0
ND2 A:ASN159 3.2 23.3 1.0
O A:HOH472 3.6 35.6 1.0
CA A:GLY155 3.8 13.5 1.0
O A:HOH502 3.8 24.8 1.0
CB A:ASN159 4.0 14.1 1.0
CG A:ASN159 4.1 18.4 1.0
O A:GLY155 4.4 13.5 1.0
O A:HOH526 4.6 43.4 1.0
C A:GLY155 4.6 12.4 1.0
N A:GLY155 4.7 12.6 1.0
O A:LEU154 4.8 14.8 1.0
O A:HOH459 4.8 28.4 1.0

Chlorine binding site 6 out of 8 in 5xhm

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Chlorine binding site 6 out of 8 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl216

b:22.8
occ:0.95
 O A:HOH516 2.9 29.8 1.0
O A:HOH359 3.1 21.8 1.0
N A:GLU136 3.2 15.9 1.0
N A:TYR133 3.3 14.0 1.0
C A:GLU132 3.3 15.6 1.0
N A:GLU135 3.4 13.9 1.0
O A:SER131 3.5 18.0 1.0
C A:TYR133 3.6 15.3 1.0
O A:GLU132 3.6 15.8 1.0
CB A:GLU135 3.8 18.3 1.0
C A:SER131 3.8 16.1 1.0
CA A:TYR133 3.9 14.3 1.0
N A:LEU134 3.9 14.9 1.0
CA A:GLU135 3.9 16.0 1.0
CA A:GLU132 3.9 14.6 1.0
O A:HOH395 3.9 30.9 1.0
CB A:GLU136 3.9 22.5 1.0
N A:GLU132 3.9 14.6 1.0
CG A:GLU136 4.0 24.1 1.0
O A:TYR133 4.0 13.3 1.0
C A:GLU135 4.0 15.7 1.0
O A:GLU130 4.0 18.0 1.0
CA A:GLU136 4.1 17.0 1.0
C A:LEU134 4.4 13.5 1.0
CG A:GLU135 4.5 17.5 1.0
O A:HOH560 4.6 23.9 1.0
CA A:SER131 4.7 14.4 1.0
CA A:LEU134 4.7 14.4 1.0
C A:GLU130 4.8 17.0 1.0
O A:HOH453 4.9 21.7 1.0

Chlorine binding site 7 out of 8 in 5xhm

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Chlorine binding site 7 out of 8 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:47.4
occ:0.95
 NH2 A:ARG5 3.0 15.0 1.0
N A:SER2 3.0 24.2 1.0
O A:HOH482 3.2 35.7 1.0
CB A:VAL1 3.4 49.1 1.0
CA A:VAL1 3.4 41.6 1.0
O A:GLY73 3.6 13.8 1.0
CG1 A:VAL1 3.6 51.2 1.0
CD A:ARG5 3.6 15.0 1.0
C A:VAL1 3.7 35.0 1.0
O A:HOH416 3.8 20.1 1.0
O A:HOH382 3.8 25.9 1.0
CB A:SER2 3.9 22.1 1.0
CZ A:ARG5 4.0 14.1 1.0
CA A:SER2 4.1 22.3 1.0
NE A:ARG5 4.2 14.6 1.0
CG A:ARG5 4.6 15.1 1.0
CB A:ARG5 4.6 14.2 1.0
O A:HOH504 4.6 30.6 1.0
C A:GLY73 4.7 14.3 1.0
N A:VAL1 4.8 44.4 1.0
CG2 A:VAL1 4.8 50.9 1.0
O A:VAL1 4.9 34.9 1.0

Chlorine binding site 8 out of 8 in 5xhm

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Chlorine binding site 8 out of 8 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:49.9
occ:0.50
 O A:HOH379 2.4 26.9 1.0
O A:HOH307 3.3 21.8 1.0
NE A:ARG59 3.7 29.4 1.0
NH2 A:ARG59 4.2 34.8 1.0
CG A:ARG59 4.3 32.5 1.0
CZ A:ARG59 4.4 35.3 1.0
CD1 A:ILE81 4.5 11.9 1.0
CD2 A:LEU24 4.5 14.9 1.0
CD A:ARG59 4.6 33.0 1.0
OG A:SER27 4.6 7.0 0.3

Reference:

B.Subhadarshanee, A.Mohanty, M.K.Jagdev, D.Vasudevan, R.K.Behera. Surface Charge Dependent Separation of Modified and Hybrid Ferritin in Native Page: Impact of Lysine 104 Biochim. Biophys. Acta V.1865 1267 2017.
ISSN: ISSN 0006-3002
PubMed: 28739445
DOI: 10.1016/J.BBAPAP.2017.07.012
Page generated: Fri Jul 26 20:56:15 2024

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