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Iron in PDB 3qga: 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae

Enzymatic activity of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae

All present enzymatic activity of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae:
3.5.1.5;

Protein crystallography data

The structure of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae, PDB code: 3qga was solved by D.E.Tronrud, A.Robbins, P.A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.29 / 3.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 166.980, 223.940, 395.870, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 18.9

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (pdb code 3qga). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae, PDB code: 3qga:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 3qga

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Iron binding site 1 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe774

b:23.4
occ:1.00
 O C:HOH780 2.1 73.7 1.0
OQ1 C:KCX218 2.2 23.5 1.0
NE2 C:HIS273 2.2 27.1 1.0
ND1 C:HIS247 2.3 20.4 1.0
CX C:KCX218 3.2 23.1 1.0
CE1 C:HIS273 3.2 27.2 1.0
CD2 C:HIS273 3.2 27.2 1.0
CG C:HIS247 3.3 19.7 1.0
CE1 C:HIS247 3.3 19.6 1.0
FE C:FE775 3.4 34.1 1.0
OQ2 C:KCX218 3.5 24.5 1.0
CB C:HIS247 3.5 17.0 1.0
O C:GLY278 3.6 35.4 1.0
NE2 C:HIS220 3.6 20.6 1.0
CD2 C:HIS220 3.9 20.6 1.0
ND1 C:HIS273 4.3 28.0 1.0
CG C:HIS273 4.4 25.7 1.0
NZ C:KCX218 4.4 20.7 1.0
NE2 C:HIS247 4.4 20.1 1.0
CD2 C:HIS247 4.4 20.4 1.0
NE2 C:HIS135 4.5 28.3 1.0
CE1 C:HIS135 4.6 28.4 1.0
C C:GLY278 4.6 34.8 1.0
OD1 C:ASP361 4.7 38.5 1.0
CE1 C:HIS220 4.7 20.6 1.0
O C:ALA168 4.7 26.6 1.0
OD2 C:ASP361 4.7 44.3 1.0
CA C:HIS247 4.8 16.5 1.0
CE C:KCX218 4.9 20.2 1.0

Iron binding site 2 out of 12 in 3qga

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Iron binding site 2 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe775

b:34.1
occ:1.00
 OD1 C:ASP361 1.9 38.5 1.0
NE2 C:HIS137 2.1 28.7 1.0
O C:HOH780 2.1 73.7 1.0
OQ2 C:KCX218 2.3 24.5 1.0
NE2 C:HIS135 2.4 28.3 1.0
CE1 C:HIS137 2.8 28.4 1.0
CG C:ASP361 3.1 38.9 1.0
CD2 C:HIS137 3.3 28.7 1.0
CX C:KCX218 3.3 23.1 1.0
CE1 C:HIS135 3.4 28.4 1.0
CD2 C:HIS135 3.4 28.1 1.0
FE C:FE774 3.4 23.4 1.0
OD2 C:ASP361 3.6 44.3 1.0
OQ1 C:KCX218 3.6 23.5 1.0
O C:ALA364 4.0 64.1 1.0
O C:ALA168 4.0 26.6 1.0
ND1 C:HIS137 4.0 28.9 1.0
CG C:HIS137 4.3 27.1 1.0
CB C:ASP361 4.3 33.3 1.0
CG2 C:THR170 4.3 16.6 1.0
NZ C:KCX218 4.5 20.7 1.0
CG C:HIS135 4.5 26.2 1.0
ND1 C:HIS135 4.5 28.7 1.0
CB C:ALA364 4.5 52.8 1.0
CA C:ASP361 4.5 31.8 1.0
NE2 C:HIS273 4.7 27.1 1.0
CD2 C:HIS273 4.8 27.2 1.0
O C:ASP361 4.9 35.0 1.0

Iron binding site 3 out of 12 in 3qga

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Iron binding site 3 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe774

b:26.7
occ:1.00
 O F:HOH780 2.1 73.2 1.0
NE2 F:HIS273 2.2 24.4 1.0
OQ1 F:KCX218 2.2 26.4 1.0
ND1 F:HIS247 2.3 26.2 1.0
CX F:KCX218 3.1 24.9 1.0
CD2 F:HIS273 3.1 24.6 1.0
CE1 F:HIS247 3.1 26.2 1.0
CE1 F:HIS273 3.2 24.7 1.0
OQ2 F:KCX218 3.2 24.9 1.0
CG F:HIS247 3.4 24.8 1.0
FE F:FE775 3.4 25.1 1.0
NE2 F:HIS220 3.6 22.4 1.0
O F:GLY278 3.7 44.3 1.0
CB F:HIS247 3.8 21.1 1.0
CD2 F:HIS220 3.9 22.5 1.0
CG F:HIS273 4.3 23.4 1.0
NZ F:KCX218 4.3 23.1 1.0
NE2 F:HIS247 4.3 26.6 1.0
ND1 F:HIS273 4.3 25.7 1.0
CD2 F:HIS247 4.5 26.8 1.0
NE2 F:HIS135 4.5 31.7 1.0
OD1 F:ASP361 4.5 41.6 1.0
OD2 F:ASP361 4.5 43.0 1.0
C F:GLY278 4.5 43.2 1.0
CE1 F:HIS135 4.5 31.6 1.0
O F:ALA168 4.6 20.9 1.0
CE1 F:HIS220 4.6 22.3 1.0
CG F:ASP361 4.9 41.0 1.0
CE F:KCX218 4.9 22.1 1.0

Iron binding site 4 out of 12 in 3qga

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Iron binding site 4 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe775

b:25.1
occ:1.00
 OD1 F:ASP361 1.9 41.6 1.0
OQ2 F:KCX218 2.0 24.9 1.0
O F:HOH780 2.1 73.2 1.0
NE2 F:HIS137 2.2 28.1 1.0
NE2 F:HIS135 2.4 31.7 1.0
CE1 F:HIS137 3.0 27.7 1.0
CG F:ASP361 3.1 41.0 1.0
CX F:KCX218 3.1 24.9 1.0
CD2 F:HIS137 3.3 28.1 1.0
CD2 F:HIS135 3.3 31.7 1.0
CE1 F:HIS135 3.4 31.6 1.0
FE F:FE774 3.4 26.7 1.0
OQ1 F:KCX218 3.5 26.4 1.0
OD2 F:ASP361 3.7 43.0 1.0
CG2 F:THR170 4.1 20.9 1.0
O F:ALA168 4.1 20.9 1.0
CB F:ASP361 4.2 34.6 1.0
NZ F:KCX218 4.2 23.1 1.0
O F:ALA364 4.2 61.3 1.0
ND1 F:HIS137 4.2 27.8 1.0
CG F:HIS137 4.3 25.9 1.0
CA F:ASP361 4.4 32.9 1.0
CG F:HIS135 4.5 29.7 1.0
CB F:ALA364 4.5 50.2 1.0
ND1 F:HIS135 4.5 32.0 1.0
NE2 F:HIS273 4.7 24.4 1.0
CD2 F:HIS273 4.7 24.6 1.0

Iron binding site 5 out of 12 in 3qga

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Iron binding site 5 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe774

b:25.6
occ:1.00
 O I:HOH780 2.1 73.3 1.0
ND1 I:HIS247 2.1 27.2 1.0
NE2 I:HIS273 2.3 31.3 1.0
OQ1 I:KCX218 2.3 25.9 1.0
CE1 I:HIS247 2.9 26.6 1.0
CX I:KCX218 3.2 25.3 1.0
CD2 I:HIS273 3.2 31.7 1.0
CE1 I:HIS273 3.3 31.4 1.0
CG I:HIS247 3.3 25.7 1.0
OQ2 I:KCX218 3.3 27.6 1.0
FE I:FE775 3.4 29.3 1.0
NE2 I:HIS220 3.5 26.4 1.0
O I:GLY278 3.6 45.9 1.0
CD2 I:HIS220 3.7 26.4 1.0
CB I:HIS247 3.8 21.9 1.0
NE2 I:HIS247 4.2 27.1 1.0
CD2 I:HIS247 4.4 27.2 1.0
CG I:HIS273 4.4 30.4 1.0
NZ I:KCX218 4.4 21.4 1.0
ND1 I:HIS273 4.4 32.1 1.0
CE1 I:HIS135 4.4 29.8 1.0
O I:ALA168 4.5 28.4 1.0
C I:GLY278 4.5 44.7 1.0
OD2 I:ASP361 4.6 44.6 1.0
NE2 I:HIS135 4.6 29.7 1.0
OD1 I:ASP361 4.6 36.2 1.0
CE1 I:HIS220 4.7 26.1 1.0
CG I:HIS220 5.0 24.0 1.0
CA I:HIS247 5.0 20.8 1.0

Iron binding site 6 out of 12 in 3qga

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Iron binding site 6 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe775

b:29.3
occ:1.00
 O I:HOH780 2.1 73.3 1.0
NE2 I:HIS137 2.1 31.7 1.0
OQ2 I:KCX218 2.1 27.6 1.0
NE2 I:HIS135 2.2 29.7 1.0
OD1 I:ASP361 2.2 36.2 1.0
CE1 I:HIS137 2.9 31.2 1.0
CE1 I:HIS135 3.0 29.8 1.0
CX I:KCX218 3.1 25.3 1.0
CG I:ASP361 3.3 37.8 1.0
CD2 I:HIS137 3.3 31.6 1.0
CD2 I:HIS135 3.3 29.7 1.0
FE I:FE774 3.4 25.6 1.0
OQ1 I:KCX218 3.5 25.9 1.0
OD2 I:ASP361 3.7 44.6 1.0
ND1 I:HIS137 4.1 31.3 1.0
ND1 I:HIS135 4.2 30.4 1.0
O I:ALA168 4.2 28.4 1.0
O I:ALA364 4.2 60.7 1.0
NZ I:KCX218 4.3 21.4 1.0
CG2 I:THR170 4.3 15.0 1.0
CG I:HIS137 4.3 29.1 1.0
CG I:HIS135 4.4 28.4 1.0
CB I:ASP361 4.5 32.5 1.0
CA I:ASP361 4.6 31.0 1.0
NE2 I:HIS273 4.7 31.3 1.0
CB I:ALA364 4.7 51.0 1.0
CD2 I:HIS273 4.7 31.7 1.0

Iron binding site 7 out of 12 in 3qga

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Iron binding site 7 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe774

b:24.1
occ:1.00
 O L:HOH780 2.1 73.8 1.0
OQ1 L:KCX218 2.1 21.5 1.0
ND1 L:HIS247 2.2 27.3 1.0
NE2 L:HIS273 2.3 30.1 1.0
CE1 L:HIS247 3.1 26.7 1.0
CX L:KCX218 3.1 20.8 1.0
CD2 L:HIS273 3.2 30.4 1.0
CG L:HIS247 3.3 25.6 1.0
CE1 L:HIS273 3.3 30.4 1.0
OQ2 L:KCX218 3.4 21.3 1.0
FE L:FE775 3.4 31.9 1.0
NE2 L:HIS220 3.6 28.2 1.0
CB L:HIS247 3.6 22.0 1.0
O L:GLY278 3.7 42.4 1.0
CD2 L:HIS220 3.8 28.1 1.0
NE2 L:HIS247 4.3 27.1 1.0
NZ L:KCX218 4.3 19.1 1.0
CD2 L:HIS247 4.4 26.9 1.0
CE1 L:HIS135 4.4 31.5 1.0
CG L:HIS273 4.4 29.5 1.0
ND1 L:HIS273 4.4 31.2 1.0
OD1 L:ASP361 4.5 41.7 1.0
NE2 L:HIS135 4.5 31.6 1.0
OD2 L:ASP361 4.5 48.8 1.0
C L:GLY278 4.6 40.4 1.0
O L:ALA168 4.7 23.2 1.0
CE1 L:HIS220 4.8 28.0 1.0
CE L:KCX218 4.9 19.1 1.0
CG L:ASP361 4.9 42.9 1.0
CA L:HIS247 4.9 21.1 1.0

Iron binding site 8 out of 12 in 3qga

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Iron binding site 8 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe775

b:31.9
occ:1.00
 OD1 L:ASP361 1.9 41.7 1.0
NE2 L:HIS137 2.0 31.5 1.0
O L:HOH780 2.1 73.8 1.0
OQ2 L:KCX218 2.2 21.3 1.0
NE2 L:HIS135 2.2 31.6 1.0
CE1 L:HIS137 2.9 31.3 1.0
CG L:ASP361 3.0 42.9 1.0
CE1 L:HIS135 3.1 31.5 1.0
CD2 L:HIS137 3.1 31.8 1.0
CX L:KCX218 3.2 20.8 1.0
CD2 L:HIS135 3.3 31.8 1.0
FE L:FE774 3.4 24.1 1.0
OQ1 L:KCX218 3.5 21.5 1.0
OD2 L:ASP361 3.6 48.8 1.0
O L:ALA364 4.0 64.5 1.0
ND1 L:HIS137 4.1 32.2 1.0
CG L:HIS137 4.2 30.1 1.0
O L:ALA168 4.2 23.2 1.0
CB L:ASP361 4.2 34.0 1.0
ND1 L:HIS135 4.3 31.8 1.0
NZ L:KCX218 4.4 19.1 1.0
CG L:HIS135 4.4 29.7 1.0
CA L:ASP361 4.4 31.9 1.0
CG2 L:THR170 4.5 25.1 1.0
CB L:ALA364 4.5 53.3 1.0
NE2 L:HIS273 4.8 30.1 1.0
CD2 L:HIS273 4.8 30.4 1.0

Iron binding site 9 out of 12 in 3qga

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Iron binding site 9 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe774

b:31.5
occ:1.00
 O O:HOH780 2.1 73.1 1.0
ND1 O:HIS247 2.2 33.3 1.0
OQ1 O:KCX218 2.2 30.7 1.0
NE2 O:HIS273 2.3 30.1 1.0
CE1 O:HIS247 3.0 33.2 1.0
CE1 O:HIS273 3.2 30.5 1.0
CX O:KCX218 3.2 29.9 1.0
CD2 O:HIS273 3.2 30.1 1.0
CG O:HIS247 3.3 31.7 1.0
FE O:FE775 3.4 28.5 1.0
OQ2 O:KCX218 3.6 28.9 1.0
O O:GLY278 3.6 41.1 1.0
CB O:HIS247 3.7 28.0 1.0
NE2 O:HIS220 3.7 26.3 1.0
CD2 O:HIS220 4.0 26.5 1.0
NE2 O:HIS247 4.3 33.8 1.0
CG O:HIS273 4.4 28.7 1.0
CD2 O:HIS247 4.4 33.6 1.0
ND1 O:HIS273 4.4 31.4 1.0
NE2 O:HIS135 4.4 28.4 1.0
NZ O:KCX218 4.4 29.4 1.0
CE1 O:HIS135 4.4 28.1 1.0
OD1 O:ASP361 4.6 45.3 1.0
O O:ALA168 4.6 29.3 1.0
C O:GLY278 4.6 40.8 1.0
OD2 O:ASP361 4.7 51.5 1.0
CE1 O:HIS220 4.8 26.3 1.0
CE O:KCX218 4.9 28.8 1.0
CA O:HIS247 4.9 27.2 1.0

Iron binding site 10 out of 12 in 3qga

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Iron binding site 10 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe775

b:28.5
occ:1.00
 OD1 O:ASP361 2.0 45.3 1.0
O O:HOH780 2.1 73.1 1.0
NE2 O:HIS137 2.2 33.3 1.0
NE2 O:HIS135 2.2 28.4 1.0
OQ2 O:KCX218 2.3 28.9 1.0
CE1 O:HIS137 3.1 33.1 1.0
CG O:ASP361 3.1 45.5 1.0
CX O:KCX218 3.2 29.9 1.0
CD2 O:HIS135 3.2 28.4 1.0
CE1 O:HIS135 3.2 28.1 1.0
CD2 O:HIS137 3.3 33.5 1.0
OQ1 O:KCX218 3.4 30.7 1.0
FE O:FE774 3.4 31.5 1.0
OD2 O:ASP361 3.7 51.5 1.0
O O:ALA364 4.1 62.9 1.0
O O:ALA168 4.2 29.3 1.0
ND1 O:HIS137 4.3 33.6 1.0
CB O:ASP361 4.3 37.7 1.0
CG O:HIS135 4.3 26.4 1.0
NZ O:KCX218 4.3 29.4 1.0
ND1 O:HIS135 4.3 28.5 1.0
CG2 O:THR170 4.4 16.2 1.0
CG O:HIS137 4.4 31.8 1.0
CA O:ASP361 4.5 36.1 1.0
CB O:ALA364 4.5 54.1 1.0
NE2 O:HIS273 4.6 30.1 1.0
CD2 O:HIS273 4.7 30.1 1.0
CD2 O:TYR272 4.9 24.6 1.0
O O:ASP361 5.0 41.7 1.0

Reference:

E.L.Carter, D.E.Tronrud, S.R.Taber, P.A.Karplus, R.P.Hausinger. Iron-Containing Urease in A Pathogenic Bacterium. Proc.Natl.Acad.Sci.Usa V. 108 13095 2011.
ISSN: ISSN 0027-8424
PubMed: 21788478
DOI: 10.1073/PNAS.1106915108
Page generated: Sun Aug 4 18:39:05 2024

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