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Iodine in PDB 5tw9: 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.

Protein crystallography data

The structure of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis., PDB code: 5tw9 was solved by G.Minasov, L.Shuvalova, K.Flores, I.Dubrovska, S.Grimshaw, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.61 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.037, 64.001, 173.151, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.3

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Iodine atom in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. (pdb code 5tw9). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 22 binding sites of Iodine where determined in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis., PDB code: 5tw9:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 22 in 5tw9

Go back to Iodine Binding Sites List in 5tw9
Iodine binding site 1 out of 22 in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:40.2
occ:0.30
 I A:IOD401 0.0 40.2 0.3
I A:IOD401 1.5 41.9 0.4
O D:HOH547 3.2 23.9 0.7
O A:HOH527 3.8 29.1 1.0
CB A:ASP357 4.0 18.4 0.5
N A:ALA358 4.2 15.2 1.0
ND2 D:ASN332 4.2 19.4 1.0
CB A:ALA358 4.3 15.2 1.0
CB D:ALA331 4.3 17.1 1.0
CB A:ASP357 4.5 18.7 0.5
CG D:LYS328 4.6 25.7 1.0
O D:LYS328 4.6 18.1 1.0
CA D:LYS328 4.6 20.5 1.0
CB D:LYS328 4.6 22.8 1.0
CA A:ALA358 4.7 14.7 1.0
C A:ASP357 4.8 15.6 0.5
C A:ASP357 4.9 15.6 0.5
OD2 A:ASP357 4.9 22.2 0.5
CG D:ASN332 4.9 17.0 1.0
CA A:ASP357 4.9 16.8 0.5
CG A:ASP357 4.9 20.2 0.5
CD D:LYS328 5.0 29.1 1.0
OD1 D:ASN332 5.0 17.5 1.0

Iodine binding site 2 out of 22 in 5tw9

Go back to Iodine Binding Sites List in 5tw9
Iodine binding site 2 out of 22 in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:41.9
occ:0.40
 I A:IOD401 0.0 41.9 0.4
I A:IOD401 1.5 40.2 0.3
CB D:ALA331 3.6 17.1 1.0
CB A:ASP357 3.7 18.4 0.5
O A:HOH547 3.9 36.2 1.0
N A:ALA358 4.0 15.2 1.0
CB A:ASP357 4.3 18.7 0.5
N A:ASP357 4.3 16.2 0.5
N A:ASP357 4.3 16.2 0.5
CG A:ASP357 4.4 20.2 0.5
CB A:ALA358 4.5 15.2 1.0
CA A:ASP357 4.5 16.8 0.5
OD2 A:ASP357 4.5 22.2 0.5
CA A:ASP357 4.6 16.7 0.5
C A:ASP357 4.7 15.6 0.5
CB A:THR356 4.7 16.2 1.0
O D:HOH547 4.7 23.9 0.7
C A:ASP357 4.7 15.6 0.5
CA D:LYS328 4.8 20.5 1.0
CA A:ALA358 4.8 14.7 1.0
O A:HOH527 4.8 29.1 1.0
O D:LYS328 4.9 18.1 1.0
CG D:LYS328 5.0 25.7 1.0
OG1 A:THR356 5.0 15.2 1.0

Iodine binding site 3 out of 22 in 5tw9

Go back to Iodine Binding Sites List in 5tw9
Iodine binding site 3 out of 22 in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I401

b:26.8
occ:0.80
 O B:HOH520 3.5 16.4 1.0
N B:GLU350 4.1 21.6 1.0
CB A:PRO324 4.3 20.5 1.0
CD1 B:TYR349 4.3 25.3 0.5
CB B:GLU350 4.3 20.7 1.0
CE2 B:TYR352 4.4 20.1 1.0
CA A:PRO324 4.4 19.3 1.0
CG B:GLU350 4.4 20.6 1.0
CB B:TYR349 4.7 23.8 0.5
O B:GLU350 4.7 22.0 1.0
CA B:GLU350 4.7 20.9 1.0
CG A:PRO324 4.9 22.8 1.0
OH B:TYR352 4.9 19.8 1.0
CA B:TYR349 4.9 22.8 0.5
O B:HOH552 5.0 26.1 1.0
CB B:TYR349 5.0 23.6 0.5
N A:PRO324 5.0 21.1 1.0
CA B:TYR349 5.0 22.7 0.5

Iodine binding site 4 out of 22 in 5tw9

Go back to Iodine Binding Sites List in 5tw9
Iodine binding site 4 out of 22 in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I402

b:19.4
occ:0.90
 O B:HOH540 3.5 33.3 1.0
O B:HOH508 3.6 21.1 1.0
N B:ALA358 3.7 14.9 1.0
CB B:ALA358 4.0 14.4 1.0
CB B:ASP357 4.1 18.1 0.3
CB B:ASP357 4.2 19.0 0.7
N B:ASP357 4.2 16.6 0.3
N B:ASP357 4.2 16.9 0.7
CB B:THR356 4.3 16.1 1.0
O B:HOH561 4.3 26.4 1.0
OG1 B:THR356 4.4 16.1 1.0
CA B:ALA358 4.4 14.5 1.0
CA B:ASP357 4.5 16.8 0.3
C B:ASP357 4.5 15.7 0.3
CA B:ASP357 4.6 17.2 0.7
C B:ASP357 4.6 15.8 0.7
O B:HOH526 4.9 27.8 1.0
CG B:ASP357 4.9 19.9 0.3
OD2 B:ASP357 5.0 21.2 0.3

Iodine binding site 5 out of 22 in 5tw9

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Iodine binding site 5 out of 22 in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I403

b:25.9
occ:0.30
 CZ B:ARG378 2.1 26.4 0.5
NH1 B:ARG378 2.2 27.5 0.5
NH2 B:ARG378 2.3 27.5 0.5
NE B:ARG378 3.0 24.4 0.5
NE B:ARG378 3.1 25.1 0.5
O A:HOH522 3.3 35.1 1.0
NH2 B:ARG378 3.6 28.6 0.5
CZ B:ARG378 3.8 27.5 0.5
CD B:ARG378 3.8 23.1 0.5
CA B:ALA375 4.0 16.0 1.0
CB A:ALA371 4.1 19.1 1.0
CD B:ARG378 4.1 24.4 0.5
CG B:LEU374 4.1 16.1 1.0
CD2 B:LEU374 4.2 17.7 1.0
CB B:ALA375 4.3 17.1 1.0
N B:ALA375 4.3 14.9 1.0
C B:LEU374 4.6 14.2 1.0
O B:LEU374 4.6 13.9 1.0
CB B:ARG378 4.7 19.6 0.5
CB B:ARG378 4.7 20.0 0.5
O B:HOH518 4.8 36.7 1.0
CG B:ARG378 4.9 21.4 0.5
CB B:LEU374 5.0 14.8 1.0

Iodine binding site 6 out of 22 in 5tw9

Go back to Iodine Binding Sites List in 5tw9
Iodine binding site 6 out of 22 in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I401

b:24.9
occ:0.50
 I D:IOD401 2.6 25.8 0.6
OH D:TYR352 3.2 27.3 1.0
N C:LEU325 3.5 22.3 1.0
CA C:PRO324 3.5 26.2 1.0
O D:HOH512 3.6 19.2 0.4
CG D:GLU350 3.7 25.5 1.0
CB C:PRO324 3.7 26.6 1.0
CE2 D:TYR352 3.9 27.9 1.0
O D:HOH512 3.9 17.2 0.6
CZ D:TYR352 4.0 26.9 1.0
C C:PRO324 4.0 23.0 1.0
N D:GLU350 4.2 27.6 1.0
CB D:GLU350 4.2 26.1 1.0
CB C:LEU325 4.6 23.1 1.0
CA C:LEU325 4.6 21.4 1.0
CG C:LEU325 4.7 24.8 1.0
CG C:PRO324 4.7 28.3 1.0
N C:PRO324 4.7 27.6 1.0
O C:HOH507 4.7 35.9 1.0
CA D:GLU350 4.8 26.2 1.0
CD D:GLU350 4.9 24.6 1.0

Iodine binding site 7 out of 22 in 5tw9

Go back to Iodine Binding Sites List in 5tw9
Iodine binding site 7 out of 22 in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I402

b:39.7
occ:0.40
 O C:HOH537 2.4 25.9 0.6
I C:IOD403 2.6 34.2 0.4
CG C:LYS328 3.9 23.4 1.0
CB C:LYS328 4.0 20.5 1.0
ND2 C:ASN332 4.1 20.4 1.0
CD C:LYS328 4.1 26.3 1.0
CA C:LYS328 4.2 18.5 1.0
O C:HOH504 4.4 36.7 1.0
O C:HOH513 4.5 27.7 1.0
O C:LYS328 4.5 17.3 1.0
C C:LYS328 4.9 17.4 1.0
CB C:ALA331 4.9 16.6 1.0
CG C:ASN332 4.9 17.4 1.0

Iodine binding site 8 out of 22 in 5tw9

Go back to Iodine Binding Sites List in 5tw9
Iodine binding site 8 out of 22 in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I403

b:34.2
occ:0.40
 I C:IOD402 2.6 39.7 0.4
O C:HOH538 2.9 32.1 0.6
CB C:ALA331 3.6 16.6 1.0
O C:HOH502 3.7 33.1 1.0
CD C:LYS323 4.1 41.3 1.0
NZ C:LYS323 4.4 45.2 1.0
CA C:LYS328 4.4 18.5 1.0
O C:GLN327 4.7 17.9 1.0
CG C:LYS328 4.7 23.4 1.0
CE C:LYS323 4.8 44.3 1.0
CB C:LYS328 5.0 20.5 1.0

Iodine binding site 9 out of 22 in 5tw9

Go back to Iodine Binding Sites List in 5tw9
Iodine binding site 9 out of 22 in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I404

b:26.4
occ:0.30
 OE1 C:GLU353 1.8 33.5 0.5
CD C:GLU353 2.3 31.9 0.5
OE2 C:GLU353 2.5 33.7 0.5
CG C:GLU353 3.6 28.9 0.5
CD C:GLU353 4.0 27.5 0.5
CG C:GLU353 4.1 28.2 0.5
OE2 C:GLU353 4.2 28.1 0.5
OE1 C:GLU353 4.4 27.1 0.5
O C:HOH543 4.4 32.5 0.5
CB C:GLU353 4.5 28.1 0.5
CB C:GLU353 4.7 27.4 0.5

Iodine binding site 10 out of 22 in 5tw9

Go back to Iodine Binding Sites List in 5tw9
Iodine binding site 10 out of 22 in the 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322- 384) of Iron Uptake System Component Efeo From Yersinia Pestis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I405

b:42.9
occ:0.30
 O C:HOH555 2.4 27.7 0.6
OG1 C:THR368 3.3 25.2 1.0
CE C:LYS364 3.8 37.7 1.0
CB C:THR368 3.8 24.2 1.0
CG C:LYS364 3.9 29.6 1.0
O C:LYS364 3.9 20.3 1.0
CG2 C:THR368 4.2 26.8 1.0
CA C:GLY365 4.2 20.7 1.0
C C:LYS364 4.2 21.4 1.0
CD C:LYS364 4.2 34.4 1.0
N C:GLY365 4.3 20.8 1.0
NZ C:LYS364 4.5 38.9 1.0
CB C:LYS364 4.7 25.4 1.0
O C:HOH524 4.7 33.7 1.0
O D:HOH505 4.9 38.8 1.0

Reference:

G.Minasov, L.Shuvalova, K.Flores, I.Dubrovska, S.Grimshaw, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.50 Angstrom Crystal Structure of C-Terminal Fragment (Residues 322-384) of Iron Uptake System Component Efeo From Yersinia Pestis. To Be Published.
Page generated: Sun Aug 11 21:53:20 2024

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