Atomistry » Iron » PDB 4m71-4n0k » 4mdz
Atomistry »
  Iron »
    PDB 4m71-4n0k »
      4mdz »

Iron in PDB 4mdz: Metallo-Enzyme From P. Marina

Protein crystallography data

The structure of Metallo-Enzyme From P. Marina, PDB code: 4mdz was solved by D.Bellini, M.A.Walsh, Oxford Protein Production Facility (Oppf), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.54 / 2.68
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.190, 183.010, 233.460, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.8

Iron Binding Sites:

The binding sites of Iron atom in the Metallo-Enzyme From P. Marina (pdb code 4mdz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Metallo-Enzyme From P. Marina, PDB code: 4mdz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4mdz

Go back to Iron Binding Sites List in 4mdz
Iron binding site 1 out of 4 in the Metallo-Enzyme From P. Marina


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Metallo-Enzyme From P. Marina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:21.1
occ:0.50
O4 A:SIN404 1.9 57.4 0.8
O A:HOH501 2.0 40.9 1.0
NE2 A:HIS277 2.1 44.9 1.0
OD1 A:ASP222 2.2 46.3 1.0
NE2 A:HIS276 2.2 53.2 1.0
NE2 A:HIS250 2.3 43.8 1.0
CD2 A:HIS277 3.1 43.8 1.0
C4 A:SIN404 3.1 70.4 0.8
CE1 A:HIS276 3.1 54.5 1.0
CE1 A:HIS277 3.1 42.4 1.0
CG A:ASP222 3.1 47.2 1.0
CE1 A:HIS250 3.2 46.6 1.0
CD2 A:HIS250 3.2 46.2 1.0
CD2 A:HIS276 3.3 52.6 1.0
OD2 A:ASP222 3.4 52.4 1.0
FE A:FE402 3.5 50.8 0.5
O3 A:SIN404 3.7 76.9 0.8
ND1 A:HIS277 4.2 42.8 1.0
CG A:HIS277 4.3 43.8 1.0
C3 A:SIN404 4.3 72.1 0.8
CD2 A:HIS221 4.3 40.9 1.0
ND1 A:HIS276 4.3 54.5 1.0
ND1 A:HIS250 4.4 45.9 1.0
CG A:HIS250 4.4 45.9 1.0
CG A:HIS276 4.4 49.6 1.0
CB A:ASP222 4.5 40.6 1.0
O1 A:SIN405 4.6 64.8 0.5
CE A:LYS225 4.8 52.6 1.0
NE2 A:HIS221 4.9 45.7 1.0
CA A:ASP222 4.9 40.3 1.0

Iron binding site 2 out of 4 in 4mdz

Go back to Iron Binding Sites List in 4mdz
Iron binding site 2 out of 4 in the Metallo-Enzyme From P. Marina


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Metallo-Enzyme From P. Marina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:50.8
occ:0.50
OD2 A:ASP222 2.1 52.4 1.0
O3 A:SIN404 2.1 76.9 0.8
O A:HOH501 2.2 40.9 1.0
FE A:FE403 2.8 51.1 0.5
C4 A:SIN404 2.9 70.4 0.8
O1 A:SIN405 2.9 64.8 0.5
O4 A:SIN404 3.0 57.4 0.8
O2 A:SIN405 3.1 54.7 0.5
CG A:ASP222 3.1 47.2 1.0
OE1 A:GLU185 3.2 87.5 1.0
C1 A:SIN405 3.4 60.4 0.5
OE2 A:GLU185 3.4 93.9 1.0
FE A:FE401 3.5 21.1 0.5
NZ A:LYS225 3.5 53.5 1.0
OD1 A:ASP222 3.6 46.3 1.0
CD A:GLU185 3.7 90.0 1.0
O A:HOH508 4.0 60.4 1.0
NE2 A:HIS221 4.1 45.7 1.0
CE A:LYS225 4.3 52.6 1.0
O A:HOH509 4.3 97.2 1.0
C3 A:SIN404 4.4 72.1 0.8
CB A:ASP222 4.4 40.6 1.0
OD2 A:ASP305 4.4 54.0 1.0
CD2 A:HIS221 4.5 40.9 1.0
O A:HOH503 4.6 73.8 1.0
NE2 A:HIS277 4.8 44.9 1.0
CE1 A:HIS277 4.9 42.4 1.0
OD1 A:ASP305 4.9 60.2 1.0
C2 A:SIN405 4.9 58.8 0.5
NE2 A:HIS276 4.9 53.2 1.0

Iron binding site 3 out of 4 in 4mdz

Go back to Iron Binding Sites List in 4mdz
Iron binding site 3 out of 4 in the Metallo-Enzyme From P. Marina


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Metallo-Enzyme From P. Marina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:51.1
occ:0.50
OD1 A:ASP305 2.6 60.2 1.0
O A:HOH508 2.7 60.4 1.0
NE2 A:HIS189 2.7 44.5 1.0
OE1 A:GLU185 2.7 87.5 1.0
FE A:FE402 2.8 50.8 0.5
NE2 A:HIS221 3.0 45.7 1.0
O2 A:SIN405 3.0 54.7 0.5
OE2 A:GLU185 3.3 93.9 1.0
O A:HOH510 3.3 71.9 1.0
C1 A:SIN405 3.3 60.4 0.5
CD A:GLU185 3.4 90.0 1.0
CE1 A:HIS189 3.4 44.6 1.0
CG A:ASP305 3.4 53.5 1.0
O1 A:SIN405 3.5 64.8 0.5
OD2 A:ASP305 3.5 54.0 1.0
OD2 A:ASP222 3.7 52.4 1.0
CE1 A:HIS221 3.7 41.6 1.0
O A:HOH501 3.7 40.9 1.0
CD2 A:HIS189 3.7 44.2 1.0
CD2 A:HIS221 4.2 40.9 1.0
C2 A:SIN405 4.3 58.8 0.5
ND1 A:HIS189 4.6 44.3 1.0
CG A:ASP222 4.6 47.2 1.0
CG A:HIS189 4.8 42.3 1.0
CG A:GLU185 4.8 81.7 1.0
O3 A:SIN404 4.8 76.9 0.8
CB A:ASP305 4.8 45.3 1.0
ND1 A:HIS221 5.0 42.1 1.0

Iron binding site 4 out of 4 in 4mdz

Go back to Iron Binding Sites List in 4mdz
Iron binding site 4 out of 4 in the Metallo-Enzyme From P. Marina


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Metallo-Enzyme From P. Marina within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:55.4
occ:1.00
NE2 B:HIS277 2.1 53.4 1.0
OD2 B:ASP222 2.1 50.0 1.0
O B:HOH546 2.3 43.7 1.0
NE2 B:HIS250 2.4 61.9 1.0
NE2 B:HIS276 2.4 53.1 1.0
CD2 B:HIS277 3.1 51.4 1.0
CE1 B:HIS277 3.1 48.2 1.0
CG B:ASP222 3.2 48.6 1.0
CD2 B:HIS276 3.3 54.6 1.0
CE1 B:HIS250 3.3 60.8 1.0
CD2 B:HIS250 3.4 57.8 1.0
CE1 B:HIS276 3.4 51.0 1.0
O B:HOH545 3.5 42.8 1.0
OD1 B:ASP222 3.6 49.7 1.0
CD2 B:HIS221 4.1 49.6 1.0
ND1 B:HIS277 4.2 45.7 1.0
O B:HOH511 4.2 99.0 1.0
CG B:HIS277 4.2 47.9 1.0
OD2 B:ASP305 4.4 57.0 1.0
CG B:HIS276 4.5 51.1 1.0
ND1 B:HIS250 4.5 59.3 1.0
ND1 B:HIS276 4.5 49.6 1.0
CG B:HIS250 4.5 58.8 1.0
CB B:ASP222 4.6 46.4 1.0
NE2 B:HIS221 4.6 54.6 1.0
C5A B:C2E402 4.8 85.5 1.0
CA B:ASP222 4.8 43.9 1.0
CE B:LYS225 5.0 60.0 1.0

Reference:

D.Bellini, D.L.Caly, Y.Mccarthy, M.Bumann, S.Q.An, J.M.Dow, R.P.Ryan, M.A.Walsh. Crystal Structure of An Hd-Gyp Domain Cyclic-Di-Gmp Phosphodiesterase Reveals An Enzyme with A Novel Trinuclear Catalytic Iron Centre. Mol.Microbiol. V. 91 26 2014.
ISSN: ISSN 0950-382X
PubMed: 24176013
DOI: 10.1111/MMI.12447
Page generated: Mon Aug 5 06:52:59 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy