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Iron in PDB 3bv6: Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold

Protein crystallography data

The structure of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold, PDB code: 3bv6 was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, X.Yang, F.R.Collart, A.Joachimiak, W.F.Anderson, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 83.433, 94.839, 94.591, 99.69, 97.90, 116.13
R / Rfree (%) 16.7 / 20.8

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold (pdb code 3bv6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold, PDB code: 3bv6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 3bv6

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Iron binding site 1 out of 12 in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:34.1
occ:0.80
 O A:HOH452 1.9 14.7 0.8
O A:HOH533 2.0 28.7 1.0
NE2 A:HIS117 2.1 32.2 1.0
ND1 A:HIS119 2.2 38.0 1.0
OD1 A:ASP227 2.2 31.1 1.0
OD2 A:ASP184 2.4 23.1 1.0
CD2 A:HIS117 2.8 29.0 1.0
CG A:ASP227 3.0 27.8 1.0
CE1 A:HIS119 3.1 36.6 1.0
CE1 A:HIS117 3.1 31.0 1.0
OD2 A:ASP227 3.2 28.9 1.0
O A:HOH452 3.3 2.4 0.2
CG A:HIS119 3.3 37.2 1.0
CG A:ASP184 3.4 21.7 1.0
O A:HOH570 3.6 29.6 1.0
CB A:HIS119 3.7 36.4 1.0
OD1 A:ASP184 3.8 23.7 1.0
O A:HOH459 3.8 24.9 1.0
CG A:HIS117 3.9 32.3 1.0
ND1 A:HIS117 4.0 33.5 1.0
FE A:FE402 4.2 30.6 1.0
NE2 A:HIS119 4.2 30.8 1.0
O A:HOH477 4.3 25.7 1.0
NE2 A:HIS122 4.3 25.8 1.0
CB A:ASP227 4.4 24.2 1.0
CD2 A:HIS119 4.4 32.3 1.0
CD2 A:HIS122 4.5 28.1 1.0
N A:ASP227 4.7 20.7 1.0
CB A:ASP184 4.7 20.9 1.0
O A:ASP227 4.8 18.6 1.0
CA A:ASP227 4.8 22.0 1.0
O A:HOH697 4.9 44.4 1.0
O A:HOH572 4.9 25.5 0.7
CE1 A:HIS122 4.9 29.5 1.0

Iron binding site 2 out of 12 in 3bv6

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Iron binding site 2 out of 12 in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:30.6
occ:1.00
 OD2 A:ASP227 2.1 28.9 1.0
O A:HOH452 2.1 2.4 0.2
NE2 A:HIS122 2.2 25.8 1.0
NE2 A:HIS282 2.2 24.7 1.0
O A:HOH572 2.3 25.5 0.7
OD2 A:ASP121 2.5 37.0 1.0
O A:HOH452 2.8 14.7 0.8
CD2 A:HIS122 3.0 28.1 1.0
CE1 A:HIS282 3.1 20.7 1.0
CG A:ASP121 3.2 34.5 1.0
OD1 A:ASP121 3.2 31.7 1.0
CG A:ASP227 3.2 27.8 1.0
CD2 A:HIS282 3.2 20.6 1.0
CE1 A:HIS122 3.3 29.5 1.0
O A:HOH572 3.9 14.7 0.3
NZ A:LYS260 4.0 26.3 1.0
OD1 A:ASP227 4.0 31.1 1.0
O A:HOH570 4.1 29.6 1.0
FE A:FE401 4.2 34.1 0.8
CB A:ASP227 4.2 24.2 1.0
CG A:HIS122 4.2 27.1 1.0
ND1 A:HIS282 4.2 20.4 1.0
ND1 A:HIS122 4.3 27.4 1.0
CG A:HIS282 4.3 16.2 1.0
NE2 A:HIS117 4.6 32.2 1.0
CB A:ASP121 4.6 29.5 1.0
SG A:CYS45 4.6 21.5 1.0
CE A:LYS260 4.7 33.4 1.0
CE1 A:HIS117 4.8 31.0 1.0
O A:HOH533 4.9 28.7 1.0

Iron binding site 3 out of 12 in 3bv6

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Iron binding site 3 out of 12 in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:32.3
occ:1.00
 O B:HOH643 2.0 4.0 0.2
NE2 B:HIS122 2.1 28.6 1.0
NE2 B:HIS282 2.2 25.2 1.0
O B:HOH773 2.2 27.8 0.7
OD2 B:ASP227 2.2 32.1 1.0
OD2 B:ASP121 2.3 35.0 1.0
O B:HOH643 2.8 16.5 0.8
CD2 B:HIS122 3.0 29.8 1.0
CE1 B:HIS282 3.0 22.3 1.0
CG B:ASP121 3.1 34.8 1.0
CE1 B:HIS122 3.2 27.2 1.0
OD1 B:ASP121 3.2 34.4 1.0
CG B:ASP227 3.3 27.7 1.0
CD2 B:HIS282 3.3 21.5 1.0
O B:HOH773 3.6 15.1 0.3
OD1 B:ASP227 4.0 36.9 1.0
NZ B:LYS260 4.0 32.3 1.0
O B:HOH514 4.1 29.1 1.0
FE B:FE402 4.2 32.7 0.8
CB B:ASP227 4.2 25.7 1.0
CG B:HIS122 4.2 27.6 1.0
ND1 B:HIS282 4.2 23.1 1.0
ND1 B:HIS122 4.3 27.8 1.0
CG B:HIS282 4.4 18.2 1.0
CB B:ASP121 4.5 29.0 1.0
NE2 B:HIS117 4.5 32.9 1.0
CE B:LYS260 4.6 31.3 1.0
SG B:CYS45 4.6 22.9 1.0
CE1 B:HIS117 4.8 33.9 1.0
O B:HOH644 4.9 29.5 1.0

Iron binding site 4 out of 12 in 3bv6

Go back to Iron Binding Sites List in 3bv6
Iron binding site 4 out of 12 in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:32.7
occ:0.80
 O B:HOH643 1.8 16.5 0.8
O B:HOH644 1.9 29.5 1.0
NE2 B:HIS117 2.1 32.9 1.0
OD1 B:ASP227 2.2 36.9 1.0
ND1 B:HIS119 2.4 38.2 1.0
OD2 B:ASP184 2.4 21.9 1.0
CD2 B:HIS117 2.7 31.1 1.0
O B:HOH643 2.8 4.0 0.2
CG B:ASP227 3.0 27.7 1.0
OD2 B:ASP227 3.1 32.1 1.0
CE1 B:HIS117 3.1 33.9 1.0
CE1 B:HIS119 3.2 38.3 1.0
CG B:HIS119 3.4 36.9 1.0
CG B:ASP184 3.4 21.8 1.0
O B:HOH514 3.7 29.1 1.0
CB B:HIS119 3.7 35.6 1.0
OD1 B:ASP184 3.8 21.4 1.0
CG B:HIS117 3.9 32.6 1.0
O B:HOH455 3.9 23.6 1.0
ND1 B:HIS117 4.0 35.1 1.0
FE B:FE401 4.2 32.3 1.0
O B:HOH470 4.2 27.2 1.0
NE2 B:HIS122 4.3 28.6 1.0
CB B:ASP227 4.3 25.7 1.0
NE2 B:HIS119 4.4 33.8 1.0
CD2 B:HIS122 4.4 29.8 1.0
CD2 B:HIS119 4.5 34.6 1.0
N B:ASP227 4.7 21.5 1.0
CB B:ASP184 4.7 20.9 1.0
O B:ASP227 4.8 21.8 1.0
CA B:ASP227 4.8 23.1 1.0
O B:HOH773 4.8 27.8 0.7
CE1 B:HIS122 4.9 27.2 1.0

Iron binding site 5 out of 12 in 3bv6

Go back to Iron Binding Sites List in 3bv6
Iron binding site 5 out of 12 in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:34.2
occ:0.80
 O C:HOH784 2.0 31.1 1.0
O C:HOH417 2.0 23.8 1.0
NE2 C:HIS117 2.2 32.5 1.0
OD1 C:ASP227 2.3 26.8 1.0
ND1 C:HIS119 2.3 38.6 1.0
OD2 C:ASP184 2.3 22.6 1.0
CD2 C:HIS117 2.9 30.6 1.0
CG C:ASP227 3.0 29.1 1.0
CE1 C:HIS119 3.1 37.9 1.0
OD2 C:ASP227 3.2 30.9 1.0
CE1 C:HIS117 3.2 33.5 1.0
CG C:HIS119 3.4 38.5 1.0
CG C:ASP184 3.4 22.2 1.0
O C:HOH546 3.7 32.0 1.0
OD1 C:ASP184 3.7 20.5 1.0
CB C:HIS119 3.8 36.5 1.0
O C:HOH540 3.8 25.5 1.0
CG C:HIS117 4.0 33.2 1.0
FE C:FE402 4.1 33.1 1.0
ND1 C:HIS117 4.1 33.4 1.0
NE2 C:HIS122 4.3 29.6 1.0
O C:HOH510 4.3 32.3 1.0
NE2 C:HIS119 4.3 33.2 1.0
CB C:ASP227 4.4 24.5 1.0
CD2 C:HIS122 4.4 28.7 1.0
CD2 C:HIS119 4.4 36.2 1.0
CB C:ASP184 4.7 21.4 1.0
O C:ASP227 4.7 22.4 1.0
N C:ASP227 4.7 22.3 1.0
CA C:ASP227 4.8 23.4 1.0
O C:HOH785 4.9 26.2 0.7
CE1 C:HIS122 5.0 31.1 1.0

Iron binding site 6 out of 12 in 3bv6

Go back to Iron Binding Sites List in 3bv6
Iron binding site 6 out of 12 in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:33.1
occ:1.00
 NE2 C:HIS282 2.2 25.5 1.0
OD2 C:ASP227 2.2 30.9 1.0
NE2 C:HIS122 2.2 29.6 1.0
OD2 C:ASP121 2.2 34.7 1.0
O C:HOH785 2.3 26.2 0.7
O C:HOH417 2.7 23.8 1.0
CE1 C:HIS282 3.0 23.2 1.0
CD2 C:HIS122 3.1 28.7 1.0
CG C:ASP121 3.1 34.0 1.0
CG C:ASP227 3.2 29.1 1.0
OD1 C:ASP121 3.3 35.9 1.0
CE1 C:HIS122 3.3 31.1 1.0
CD2 C:HIS282 3.3 23.4 1.0
O C:HOH785 3.6 14.6 0.3
OD1 C:ASP227 3.9 26.8 1.0
NZ C:LYS260 4.0 29.3 1.0
FE C:FE401 4.1 34.2 0.8
CB C:ASP227 4.1 24.5 1.0
O C:HOH546 4.2 32.0 1.0
ND1 C:HIS282 4.2 24.3 1.0
CG C:HIS122 4.3 27.2 1.0
ND1 C:HIS122 4.4 31.2 1.0
CG C:HIS282 4.4 21.9 1.0
CB C:ASP121 4.5 28.4 1.0
CE C:LYS260 4.6 32.4 1.0
SG C:CYS45 4.6 23.9 1.0
NE2 C:HIS117 4.6 32.5 1.0
CE1 C:HIS117 4.9 33.5 1.0
O C:HOH784 4.9 31.1 1.0

Iron binding site 7 out of 12 in 3bv6

Go back to Iron Binding Sites List in 3bv6
Iron binding site 7 out of 12 in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:30.6
occ:0.80
 O D:HOH731 2.1 27.0 1.0
NE2 D:HIS117 2.1 32.2 1.0
O D:HOH739 2.1 29.1 1.0
ND1 D:HIS119 2.2 36.1 1.0
OD1 D:ASP227 2.2 29.1 1.0
OD2 D:ASP184 2.3 20.5 1.0
CD2 D:HIS117 2.8 29.9 1.0
CG D:ASP227 3.0 30.6 1.0
CE1 D:HIS119 3.0 36.4 1.0
CE1 D:HIS117 3.2 32.0 1.0
OD2 D:ASP227 3.2 30.8 1.0
CG D:HIS119 3.3 34.8 1.0
CG D:ASP184 3.3 22.9 1.0
O D:HOH990 3.6 36.2 1.0
OD1 D:ASP184 3.7 24.1 1.0
CB D:HIS119 3.7 33.7 1.0
O D:HOH714 3.8 29.1 1.0
CG D:HIS117 4.0 30.8 1.0
FE D:FE402 4.1 30.1 1.0
ND1 D:HIS117 4.1 32.2 1.0
NE2 D:HIS119 4.2 29.8 1.0
O D:HOH751 4.2 28.6 1.0
NE2 D:HIS122 4.3 27.9 1.0
CD2 D:HIS119 4.4 33.1 1.0
CB D:ASP227 4.4 25.4 1.0
CD2 D:HIS122 4.5 30.1 1.0
CB D:ASP184 4.6 20.8 1.0
N D:ASP227 4.7 22.6 1.0
O D:ASP227 4.7 23.0 1.0
O D:HOH875 4.8 26.8 0.8
CA D:ASP227 4.8 24.4 1.0

Iron binding site 8 out of 12 in 3bv6

Go back to Iron Binding Sites List in 3bv6
Iron binding site 8 out of 12 in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:30.1
occ:1.00
 OD2 D:ASP121 2.1 32.9 1.0
OD2 D:ASP227 2.1 30.8 1.0
NE2 D:HIS282 2.2 22.8 1.0
NE2 D:HIS122 2.3 27.9 1.0
O D:HOH875 2.3 26.8 0.8
O D:HOH731 2.5 27.0 1.0
CG D:ASP121 3.0 32.6 1.0
CE1 D:HIS282 3.1 20.6 1.0
CD2 D:HIS122 3.1 30.1 1.0
CG D:ASP227 3.1 30.6 1.0
OD1 D:ASP121 3.2 32.7 1.0
CD2 D:HIS282 3.3 22.6 1.0
CE1 D:HIS122 3.4 31.9 1.0
O D:HOH875 3.8 9.9 0.2
OD1 D:ASP227 3.8 29.1 1.0
NZ D:LYS260 4.0 24.0 1.0
FE D:FE401 4.1 30.6 0.8
CB D:ASP227 4.1 25.4 1.0
O D:HOH990 4.2 36.2 1.0
ND1 D:HIS282 4.2 21.9 1.0
CG D:HIS122 4.3 27.0 1.0
CB D:ASP121 4.4 28.4 1.0
CG D:HIS282 4.4 17.8 1.0
ND1 D:HIS122 4.4 27.6 1.0
CE D:LYS260 4.5 33.4 1.0
NE2 D:HIS117 4.6 32.2 1.0
SG D:CYS45 4.7 24.2 1.0
CE1 D:HIS117 4.7 32.0 1.0
O D:HOH739 4.9 29.1 1.0

Iron binding site 9 out of 12 in 3bv6

Go back to Iron Binding Sites List in 3bv6
Iron binding site 9 out of 12 in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:37.3
occ:0.80
 O E:HOH877 2.2 38.7 1.0
NE2 E:HIS117 2.2 33.2 1.0
OD1 E:ASP227 2.2 33.7 1.0
O E:HOH1067 2.2 34.5 1.0
ND1 E:HIS119 2.3 43.7 1.0
OD2 E:ASP184 2.4 29.4 1.0
CD2 E:HIS117 2.8 35.3 1.0
CG E:ASP227 3.0 36.9 1.0
CE1 E:HIS119 3.1 42.4 1.0
OD2 E:ASP227 3.1 37.2 1.0
CE1 E:HIS117 3.3 37.3 1.0
CG E:HIS119 3.4 41.2 1.0
CG E:ASP184 3.4 31.5 1.0
O E:HOH1089 3.5 43.0 1.0
OD1 E:ASP184 3.8 27.1 1.0
CB E:HIS119 3.8 37.8 1.0
O E:HOH803 3.8 32.1 1.0
CG E:HIS117 4.0 34.9 1.0
FE E:FE402 4.1 33.9 1.0
ND1 E:HIS117 4.2 35.6 1.0
NE2 E:HIS122 4.2 27.3 1.0
O E:HOH808 4.3 31.7 1.0
NE2 E:HIS119 4.3 39.8 1.0
CD2 E:HIS122 4.4 28.0 1.0
CB E:ASP227 4.4 31.9 1.0
CD2 E:HIS119 4.5 42.1 1.0
CB E:ASP184 4.7 27.1 1.0
O E:ASP227 4.8 31.2 1.0
N E:ASP227 4.8 28.1 1.0
CA E:ASP227 4.9 31.1 1.0
O E:HOH1068 4.9 31.9 1.0
CE1 E:HIS122 4.9 31.4 1.0

Iron binding site 10 out of 12 in 3bv6

Go back to Iron Binding Sites List in 3bv6
Iron binding site 10 out of 12 in the Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe402

b:33.9
occ:1.00
 NE2 E:HIS282 2.2 28.3 1.0
OD2 E:ASP227 2.2 37.2 1.0
OD2 E:ASP121 2.2 38.0 1.0
NE2 E:HIS122 2.2 27.3 1.0
O E:HOH1068 2.3 31.9 1.0
O E:HOH1067 2.4 34.5 1.0
CE1 E:HIS282 2.9 23.4 1.0
CG E:ASP121 3.1 35.9 1.0
CD2 E:HIS122 3.2 28.0 1.0
CG E:ASP227 3.2 36.9 1.0
OD1 E:ASP121 3.2 35.6 1.0
CE1 E:HIS122 3.3 31.4 1.0
CD2 E:HIS282 3.4 23.4 1.0
OD1 E:ASP227 3.9 33.7 1.0
O E:HOH1089 4.0 43.0 1.0
NZ E:LYS260 4.0 32.6 1.0
FE E:FE401 4.1 37.3 0.8
ND1 E:HIS282 4.2 24.5 1.0
CB E:ASP227 4.2 31.9 1.0
CG E:HIS122 4.3 26.5 1.0
ND1 E:HIS122 4.4 27.9 1.0
CG E:HIS282 4.4 24.7 1.0
CB E:ASP121 4.5 31.1 1.0
CE E:LYS260 4.5 34.4 1.0
NE2 E:HIS117 4.5 33.2 1.0
SG E:CYS45 4.6 26.1 1.0
O E:HOH877 4.9 38.7 1.0
CE1 E:HIS117 4.9 37.3 1.0

Reference:

G.Minasov, L.Shuvalova, J.S.Brunzelle, X.Yang, F.R.Collart, W.F.Anderson. Crystal Structure of Uncharacterized Metallo Protein From Vibrio Cholerae with Beta-Lactamase Like Fold. To Be Published.
Page generated: Sun Aug 4 08:03:29 2024

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