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Magnesium in PDB 6a4u: The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin

Enzymatic activity of The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin

All present enzymatic activity of The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin:
1.16.3.1;

Protein crystallography data

The structure of The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin, PDB code: 6a4u was solved by T.Masuda, B.Mikami, J.Zang, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.59 / 1.16
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 124.872, 124.872, 175.683, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 15.7

Other elements in 6a4u:

The structure of The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin (pdb code 6a4u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin, PDB code: 6a4u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6a4u

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Magnesium binding site 1 out of 5 in the The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg212

b:44.4
occ:1.00
 OG1 C:THR160 2.9 18.9 1.0
N C:THR160 3.1 13.4 1.0
C C:GLY158 3.2 11.1 0.7
N C:PRO159 3.2 11.2 0.7
O C:GLY158 3.3 12.8 0.7
CD C:PRO159 3.4 12.4 0.7
O C:THR160 3.5 16.0 1.0
CD C:PRO159 3.5 15.4 0.3
N C:PRO159 3.6 14.7 0.3
C C:GLY158 3.7 13.4 0.3
CA C:THR160 3.7 14.8 1.0
CG C:PRO159 3.8 15.9 0.3
CB C:THR160 3.8 17.6 1.0
CA C:GLY158 3.9 12.5 0.3
C C:THR160 3.9 14.0 1.0
CA C:GLY158 3.9 10.4 0.7
C C:PRO159 4.0 11.8 0.7
C C:PRO159 4.1 14.7 0.3
CA C:PRO159 4.1 11.2 0.7
O C:GLY158 4.3 13.7 0.3
CA C:PRO159 4.3 15.1 0.3
O2 C:EDO204 4.4 23.8 1.0
CG C:PRO159 4.4 12.4 0.7
O C:HOH394 4.4 45.1 1.0
CG2 C:THR160 4.5 19.3 1.0
CB C:PRO159 4.7 15.7 0.3
C2 C:EDO204 4.7 26.2 1.0
O1 C:EDO204 4.7 25.7 1.0

Magnesium binding site 2 out of 5 in 6a4u

Go back to Magnesium Binding Sites List in 6a4u
Magnesium binding site 2 out of 5 in the The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg213

b:36.3
occ:1.00
 N C:ASN8 3.2 8.9 1.0
O C:HOH421 3.9 14.9 1.0
CA C:GLN7 4.0 9.4 1.0
O C:HOH438 4.1 27.9 1.0
CA C:ASN8 4.1 9.3 1.0
C C:GLN7 4.1 8.8 1.0
O C:HOH426 4.1 25.6 1.0
CG C:GLN7 4.3 9.7 1.0
O1 C:EDO209 4.6 50.3 1.0
CB C:GLN7 4.8 9.6 1.0
CB C:ASN8 5.0 9.9 1.0

Magnesium binding site 3 out of 5 in 6a4u

Go back to Magnesium Binding Sites List in 6a4u
Magnesium binding site 3 out of 5 in the The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg208

b:28.1
occ:1.00
 O D:HOH440 2.2 44.4 1.0
O D:GLY75 2.8 10.1 1.0
NH2 D:ARG6 3.0 12.3 1.0
N D:SER3 3.0 14.1 1.0
OG D:SER3 3.3 13.5 0.1
CD D:ARG6 3.5 11.6 1.0
CB D:SER3 3.5 12.3 0.9
CB D:SER3 3.6 13.3 0.1
CA D:ALA2 3.8 20.7 1.0
CB D:ALA2 3.8 21.5 1.0
C D:ALA2 3.9 17.1 1.0
CA D:SER3 3.9 12.2 0.9
CA D:SER3 3.9 12.8 0.1
C D:GLY75 3.9 8.3 1.0
CZ D:ARG6 4.0 10.8 1.0
CB D:ARG6 4.1 9.6 1.0
CG D:ARG6 4.1 9.8 1.0
O D:HOH339 4.2 20.9 1.0
NE D:ARG6 4.2 11.9 1.0
CA D:GLY75 4.7 8.3 1.0
O D:HOH400 4.8 38.3 1.0
N D:GLY76 4.8 8.5 1.0
OG D:SER3 4.8 11.9 0.9
CA D:GLY76 4.9 9.1 1.0
O D:SER3 4.9 11.6 1.0
C D:SER3 5.0 11.1 1.0

Magnesium binding site 4 out of 5 in 6a4u

Go back to Magnesium Binding Sites List in 6a4u
Magnesium binding site 4 out of 5 in the The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg209

b:36.5
occ:1.00
 N D:ASN8 3.2 8.3 1.0
O D:HOH425 3.8 13.8 1.0
O D:HOH428 3.8 30.0 1.0
CA D:GLN7 3.9 8.2 1.0
C D:GLN7 4.1 7.8 1.0
CA D:ASN8 4.1 8.4 1.0
O D:HOH419 4.2 24.6 1.0
CG D:GLN7 4.3 9.4 1.0
CB D:GLN7 4.7 8.7 1.0
O D:ARG6 4.9 9.7 1.0
N D:GLN7 4.9 8.4 1.0
CB D:ASN8 5.0 9.1 1.0

Magnesium binding site 5 out of 5 in 6a4u

Go back to Magnesium Binding Sites List in 6a4u
Magnesium binding site 5 out of 5 in the The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg210

b:35.5
occ:1.00
 O F:HOH460 2.2 40.7 1.0
N F:ASN8 3.1 8.5 1.0
O F:HOH421 3.7 13.4 1.0
CA F:GLN7 3.9 8.4 1.0
CA F:ASN8 4.0 8.7 1.0
C F:GLN7 4.0 7.9 1.0
O F:HOH433 4.1 25.6 1.0
O B:HOH306 4.3 29.2 1.0
O B:HOH315 4.3 41.1 1.0
CG F:GLN7 4.4 9.3 1.0
CB F:GLN7 4.7 8.9 1.0
CB F:ASN8 4.9 9.2 1.0
O F:ARG6 4.9 9.9 1.0
N F:GLN7 4.9 8.2 1.0

Reference:

T.Masuda, J.Zang, G.Zhao, B.Mikami. The First Crystal Structure of Crustacean Ferritin That Is A Hybrid Type of H and L Ferritin Protein Sci. V. 27 1955 2018.
ISSN: ESSN 1469-896X
PubMed: 30099791
DOI: 10.1002/PRO.3495
Page generated: Mon Sep 30 18:58:01 2024

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