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Magnesium in PDB 3ajp: Crystal Structure of Human H Ferritin E140A Mutant

Enzymatic activity of Crystal Structure of Human H Ferritin E140A Mutant

All present enzymatic activity of Crystal Structure of Human H Ferritin E140A Mutant:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Human H Ferritin E140A Mutant, PDB code: 3ajp was solved by T.Masuda, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.50 / 1.90
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.974, 182.974, 182.974, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human H Ferritin E140A Mutant (pdb code 3ajp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Human H Ferritin E140A Mutant, PDB code: 3ajp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3ajp

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Magnesium binding site 1 out of 10 in the Crystal Structure of Human H Ferritin E140A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human H Ferritin E140A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg183

b:20.6
occ:1.00
 OE2 A:GLU27 2.1 18.1 1.0
O A:HOH226 2.2 16.3 1.0
O A:HOH272 2.2 24.5 1.0
OE2 A:GLU62 2.2 22.7 1.0
ND1 A:HIS65 2.3 27.2 1.0
CD A:GLU27 3.1 13.7 1.0
CD A:GLU62 3.2 23.5 1.0
CE1 A:HIS65 3.2 32.7 1.0
CG A:HIS65 3.4 26.8 1.0
OE1 A:GLU27 3.4 17.3 1.0
OE1 A:GLU62 3.4 29.8 1.0
CB A:HIS65 3.7 11.9 1.0
O A:HOH341 3.9 28.0 1.0
OE1 A:GLN141 4.0 25.2 1.0
CG1 A:VAL110 4.3 14.6 1.0
NE2 A:HIS65 4.4 32.6 1.0
CG A:GLU27 4.4 12.9 1.0
CD2 A:HIS65 4.5 23.8 1.0
CG A:GLU62 4.5 14.7 1.0
CA A:GLU62 4.6 13.6 1.0
CB A:GLU27 4.7 13.1 1.0
CB A:GLU62 4.8 13.3 1.0
CD A:GLN141 4.9 16.4 1.0
CA A:GLU27 5.0 12.7 1.0

Magnesium binding site 2 out of 10 in 3ajp

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Magnesium binding site 2 out of 10 in the Crystal Structure of Human H Ferritin E140A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human H Ferritin E140A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg184

b:40.8
occ:1.00
 O A:HOH275 2.3 36.6 1.0
O A:HOH274 2.4 27.3 1.0
OE1 A:GLN58 2.5 34.4 1.0
OE1 A:GLU61 2.5 43.5 1.0
O A:HOH273 2.6 30.2 1.0
O A:HOH372 2.7 48.6 1.0
O A:HOH367 3.2 38.8 1.0
CD A:GLN58 3.5 31.9 1.0
CD A:GLU61 3.7 44.3 1.0
NE2 A:GLN58 4.0 33.5 1.0
O A:HOH225 4.2 37.9 1.0
O A:HOH205 4.2 26.9 1.0
CB A:GLU61 4.3 17.4 1.0
CB A:ALA144 4.5 19.0 1.0
OE2 A:GLU61 4.5 51.8 1.0
O A:HOH347 4.6 29.4 1.0
O A:HOH349 4.6 33.4 1.0
CG A:GLU61 4.6 26.5 1.0
OE1 A:GLU62 4.7 29.8 1.0
OE2 A:GLU107 4.7 40.6 1.0
CG A:GLN58 4.8 21.4 1.0
CE1 A:HIS65 4.8 32.7 1.0
CA A:GLN58 4.8 16.4 1.0
CB A:GLN58 4.9 16.0 1.0

Magnesium binding site 3 out of 10 in 3ajp

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Magnesium binding site 3 out of 10 in the Crystal Structure of Human H Ferritin E140A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human H Ferritin E140A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg185

b:34.8
occ:0.71
 O A:HOH295 2.2 19.6 1.0
O A:HOH296 2.4 21.2 1.0
O A:HOH298 2.5 21.4 0.2
O A:HOH299 2.6 17.2 0.5
O A:HOH297 4.0 18.3 1.0
O A:HOH375 4.5 28.4 1.0
CE A:LYS87 4.5 25.1 0.6
O A:HOH376 4.5 32.9 1.0
NZ A:LYS86 4.9 32.7 1.0
CD A:LYS86 4.9 20.5 1.0
CG A:LYS87 5.0 17.0 0.6

Magnesium binding site 4 out of 10 in 3ajp

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Magnesium binding site 4 out of 10 in the Crystal Structure of Human H Ferritin E140A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human H Ferritin E140A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg186

b:27.1
occ:0.47
 O A:HOH256 2.3 15.8 1.0
O A:HOH249 2.4 15.3 1.0
OE2 A:GLU134 3.8 15.1 1.0
O A:HOH310 4.2 17.1 1.0
O A:HOH312 4.3 22.3 1.0
OE1 A:GLU134 4.3 23.6 1.0
CD A:GLU134 4.5 16.5 1.0

Magnesium binding site 5 out of 10 in 3ajp

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Magnesium binding site 5 out of 10 in the Crystal Structure of Human H Ferritin E140A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human H Ferritin E140A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg187

b:29.9
occ:1.00
 O A:HOH319 2.3 28.6 1.0
O A:HOH316 2.3 29.8 1.0
O A:HOH315 2.3 27.5 1.0
O A:HOH317 2.3 29.6 1.0
O A:HOH314 2.3 26.2 1.0
O A:HOH318 2.5 25.3 1.0
OD2 A:ASP131 3.8 26.1 1.0
O A:HOH196 4.3 38.3 1.0
OG1 A:THR135 4.3 21.0 1.0
CG2 A:THR135 4.4 17.8 1.0
OD1 A:ASP131 4.5 20.7 1.0
O A:HOH212 4.6 29.4 1.0
CG A:ASP131 4.6 19.9 1.0
O A:HOH292 4.7 22.6 1.0
CB A:THR135 4.9 17.6 1.0

Magnesium binding site 6 out of 10 in 3ajp

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Magnesium binding site 6 out of 10 in the Crystal Structure of Human H Ferritin E140A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human H Ferritin E140A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg188

b:49.7
occ:0.50
 OD1 A:ASP131 3.3 20.7 1.0
O A:HOH224 3.8 50.4 0.5
OE1 A:GLU134 3.9 23.6 1.0
O A:HOH318 4.4 25.3 1.0
CG A:ASP131 4.5 19.9 1.0
OG1 A:THR135 4.7 21.0 1.0
CD A:GLU134 4.8 16.5 1.0
CB A:ASP131 5.0 18.1 1.0
CB A:GLU134 5.0 18.9 1.0

Magnesium binding site 7 out of 10 in 3ajp

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Magnesium binding site 7 out of 10 in the Crystal Structure of Human H Ferritin E140A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human H Ferritin E140A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg189

b:12.4
occ:0.31
 NE2 A:HIS173 3.1 24.4 1.0
CE1 A:HIS173 3.8 26.0 1.0
CD2 A:LEU169 4.1 15.9 1.0
CD2 A:HIS173 4.3 21.6 1.0

Magnesium binding site 8 out of 10 in 3ajp

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Magnesium binding site 8 out of 10 in the Crystal Structure of Human H Ferritin E140A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Human H Ferritin E140A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg190

b:21.4
occ:0.28
 CE1 A:HIS173 3.8 26.0 1.0
ND1 A:HIS173 4.4 26.5 1.0
NE2 A:HIS173 4.7 24.4 1.0

Magnesium binding site 9 out of 10 in 3ajp

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Magnesium binding site 9 out of 10 in the Crystal Structure of Human H Ferritin E140A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Human H Ferritin E140A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg191

b:28.9
occ:1.00
 O A:HOH201 3.6 20.5 0.6
CB A:ASN25 3.6 12.3 1.0
CG A:GLN83 3.8 22.2 1.0
CG A:ASN25 3.8 14.3 1.0
CB A:GLN83 4.1 18.9 1.0
CA A:ARG22 4.1 15.2 0.7
CA A:ARG22 4.1 15.3 0.3
OD1 A:ASN25 4.2 14.2 1.0
CG A:ARG22 4.2 19.8 0.3
CG A:ARG22 4.3 19.8 0.7
ND2 A:ASN25 4.4 10.2 1.0
CB A:ARG22 4.5 18.6 0.7
CB A:ARG22 4.5 18.6 0.3
O A:ASN21 4.6 13.8 1.0
O A:ARG22 4.6 12.6 1.0
N A:ARG22 4.8 14.6 1.0
C A:ARG22 4.9 17.9 1.0

Magnesium binding site 10 out of 10 in 3ajp

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Magnesium binding site 10 out of 10 in the Crystal Structure of Human H Ferritin E140A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Human H Ferritin E140A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg192

b:40.4
occ:1.00
 OD1 A:ASP89 2.5 41.6 0.5
OD2 A:ASP89 2.5 44.0 0.5
SG A:CYS102 2.7 20.3 0.3
CG A:ASP89 2.8 35.6 0.5
O A:HOH378 3.0 30.3 1.0
CZ3 A:TRP93 3.5 33.3 1.0
O A:HOH342 3.7 30.4 1.0
CB A:CYS102 3.8 16.6 0.7
CB A:CYS102 3.9 16.6 0.3
SG A:CYS102 3.9 22.8 0.7
CH2 A:TRP93 3.9 36.1 1.0
CB A:ASP89 4.2 34.4 0.5
CB A:ASP89 4.3 34.5 0.5
SG A:CYS90 4.7 48.8 0.7
CA A:CYS102 4.7 17.3 0.3
CA A:CYS102 4.7 17.3 0.7
OD1 A:ASP89 4.7 41.7 0.5
CE3 A:TRP93 4.7 29.7 1.0
O A:CYS102 4.9 16.1 1.0
CG A:ASP89 4.9 42.4 0.5

Reference:

T.Masuda, F.Goto, T.Yoshihara, B.Mikami. The Universal Mechanism For Iron Translocation to the Ferroxidase Site in Ferritin, Which Is Mediated By the Well Conserved Transit Site Biochem.Biophys.Res.Commun. V. 400 94 2010.
ISSN: ISSN 0006-291X
PubMed: 20705053
DOI: 10.1016/J.BBRC.2010.08.017
Page generated: Wed Aug 14 08:36:56 2024

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