Atomistry » Magnesium » PDB 3k9l-3kk1 » 3ka4
Atomistry »
  Magnesium »
    PDB 3k9l-3kk1 »
      3ka4 »

Magnesium in PDB 3ka4: Frog M-Ferritin with Cobalt

Enzymatic activity of Frog M-Ferritin with Cobalt

All present enzymatic activity of Frog M-Ferritin with Cobalt:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin with Cobalt, PDB code: 3ka4 was solved by T.Tosha, H.L.Ng, E.Theil, T.Alber, O.Bhattasali, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.40
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.765, 183.765, 183.765, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.4

Other elements in 3ka4:

The structure of Frog M-Ferritin with Cobalt also contains other interesting chemical elements:

Cobalt (Co) 8 atoms
Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Frog M-Ferritin with Cobalt (pdb code 3ka4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Frog M-Ferritin with Cobalt, PDB code: 3ka4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3ka4

Go back to Magnesium Binding Sites List in 3ka4
Magnesium binding site 1 out of 6 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg185

b:13.7
occ:0.50
O A:HOH255 2.1 16.8 1.0
O A:HOH282 2.1 12.2 0.5
O A:HOH236 4.3 15.1 1.0
O A:HOH315 4.5 25.9 1.0
CE A:LYS83 4.6 16.7 1.0
NZ A:LYS82 4.6 24.8 0.0
CD A:LYS82 4.7 15.8 1.0
O A:HOH329 4.7 28.3 1.0
CD A:LYS82 4.7 16.6 0.0
CE A:LYS82 4.9 18.9 1.0

Magnesium binding site 2 out of 6 in 3ka4

Go back to Magnesium Binding Sites List in 3ka4
Magnesium binding site 2 out of 6 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg186

b:17.1
occ:0.33
O A:HOH322 1.8 27.4 1.0
O A:HOH323 2.0 28.2 1.0
OD1 A:ASP127 3.8 17.2 1.0
OG A:SER131 4.2 20.0 1.0
OE1 A:GLU130 4.3 17.4 1.0
O A:HOH409 4.4 29.9 1.0
O A:HOH309 4.9 21.2 1.0
CG A:ASP127 4.9 13.5 1.0
CB A:GLU130 4.9 12.9 1.0

Magnesium binding site 3 out of 6 in 3ka4

Go back to Magnesium Binding Sites List in 3ka4
Magnesium binding site 3 out of 6 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg187

b:22.4
occ:1.00
O A:HOH340 2.0 24.8 1.0
O A:HOH360 2.0 27.5 1.0
O A:HOH337 2.0 20.4 1.0
OG A:SER10 2.1 18.4 1.0
O A:HOH242 2.1 17.3 1.0
O A:HOH382 2.2 27.2 1.0
CB A:SER10 3.2 13.6 1.0
CA A:SER10 3.9 12.4 1.0
O A:SER10 4.1 12.0 1.0
OE1 A:GLU13 4.2 14.2 1.0
O A:HOH264 4.2 22.3 1.0
C A:SER10 4.3 10.5 1.0
O A:HOH239 4.3 37.7 1.0
O A:HOH252 4.5 20.6 1.0
CD A:GLU13 4.7 12.5 1.0
O A:HOH207 4.9 32.0 1.0

Magnesium binding site 4 out of 6 in 3ka4

Go back to Magnesium Binding Sites List in 3ka4
Magnesium binding site 4 out of 6 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg188

b:19.8
occ:0.50
O A:HOH276 2.1 22.8 1.0
OD2 A:ASP146 4.0 15.0 1.0
O A:HOH418 4.2 30.1 1.0
O A:HOH302 4.3 20.5 1.0
O A:HOH280 4.3 27.1 1.0
O A:HOH311 4.6 23.5 1.0

Magnesium binding site 5 out of 6 in 3ka4

Go back to Magnesium Binding Sites List in 3ka4
Magnesium binding site 5 out of 6 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg196

b:31.3
occ:1.00
O A:HOH334 1.9 31.0 1.0
O A:HOH362 2.0 40.2 1.0
O A:HOH365 2.1 38.5 1.0
O A:HOH364 2.1 42.0 1.0
O A:HOH363 2.2 44.1 1.0
O A:HOH301 2.4 21.9 1.0
OD1 A:ASN21 4.2 10.5 1.0
O A:HOH310 4.4 21.3 1.0
O A:HOH295 4.4 20.4 1.0
O A:HOH314 4.4 24.8 1.0
O A:ARG18 4.4 10.8 1.0
O A:HOH343 4.5 25.0 1.0
CB A:LEU22 5.0 11.1 1.0

Magnesium binding site 6 out of 6 in 3ka4

Go back to Magnesium Binding Sites List in 3ka4
Magnesium binding site 6 out of 6 in the Frog M-Ferritin with Cobalt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Frog M-Ferritin with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg197

b:30.0
occ:1.00
O A:HOH339 2.0 19.0 1.0
O A:HOH338 2.1 19.9 1.0
O A:HOH332 2.1 22.6 1.0
O A:SER131 4.2 15.3 1.0
O A:HOH414 4.3 32.6 1.0
O A:GLU130 4.3 14.9 1.0
CA A:SER131 4.5 13.8 1.0
O A:HOH227 4.5 37.6 1.0
O A:HOH409 4.6 29.9 1.0
C A:SER131 4.7 13.6 1.0
CB A:GLU135 4.7 14.8 1.0
CG A:GLU135 4.9 15.0 1.0
CL A:CL194 5.0 20.3 1.0

Reference:

T.Tosha, H.L.Ng, O.Bhattasali, T.Alber, E.C.Theil. Moving Metal Ions Through Ferritin-Protein Nanocages From Three-Fold Pores to Catalytic Sites. J.Am.Chem.Soc. V. 132 14562 2010.
ISSN: ISSN 0002-7863
PubMed: 20866049
DOI: 10.1021/JA105583D
Page generated: Mon Dec 14 08:21:51 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy