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Iodine in PDB 6x2d: Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae

Enzymatic activity of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae

All present enzymatic activity of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae:
3.1.26.12;

Protein crystallography data

The structure of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae, PDB code: 6x2d was solved by G.Minasov, L.Shuvalova, O.Kiryukhina, I.Dubrovska, G.Wiersum, K.J.F.Satchell, 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) 29.41 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.614, 58.812, 47.046, 90.00, 108.16, 90.00
R / Rfree (%) 20.7 / 24.3

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae (pdb code 6x2d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae, PDB code: 6x2d:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 6x2d

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Iodine binding site 1 out of 9 in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:90.7
occ:1.00
 O A:HOH518 3.4 49.1 1.0
NH1 A:ARG336 3.6 56.4 1.0
NE A:ARG336 3.7 57.2 1.0
CD2 A:LEU338 3.9 52.5 1.0
CG2 A:ILE292 4.0 40.3 1.0
CZ A:ARG336 4.1 56.2 1.0
CD A:PRO294 4.4 46.5 1.0
CG A:PRO294 4.5 49.0 1.0
CB A:PRO294 4.7 48.1 1.0
CD A:ARG336 4.8 53.1 1.0
CD1 A:LEU338 4.8 50.9 1.0
OE1 A:GLN279 4.9 80.3 1.0
CG A:LEU338 5.0 49.8 1.0

Iodine binding site 2 out of 9 in 6x2d

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Iodine binding site 2 out of 9 in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:83.8
occ:0.70
 NE2 A:GLN332 3.7 45.6 1.0
OE1 A:GLN332 4.0 47.3 1.0
CG2 A:VAL282 4.0 46.0 1.0
CA A:GLN279 4.2 63.0 1.0
CD A:GLN332 4.2 46.6 1.0
NH2 A:ARG336 4.3 56.6 1.0
N A:GLN279 4.6 67.1 1.0
O A:GLN279 4.7 52.4 1.0
C A:GLN279 4.9 58.2 1.0
CG A:GLN279 5.0 73.7 1.0

Iodine binding site 3 out of 9 in 6x2d

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Iodine binding site 3 out of 9 in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:61.9
occ:0.70
 I A:IOD403 0.0 61.9 0.7
I A:IOD403 2.8 69.0 0.3
CB A:ARG353 4.2 49.8 1.0
NH1 A:ARG356 4.5 44.3 1.0
CD A:ARG353 4.5 61.6 1.0
NE A:ARG353 4.6 68.7 1.0
CG A:ARG353 4.8 55.0 1.0

Iodine binding site 4 out of 9 in 6x2d

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Iodine binding site 4 out of 9 in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:69.0
occ:0.30
 I A:IOD403 0.0 69.0 0.3
I A:IOD403 2.8 61.9 0.7
N A:ARG353 3.5 44.0 1.0
CB A:ARG353 3.7 49.8 1.0
N A:VAL352 3.8 44.8 1.0
CA A:ARG353 4.2 45.3 1.0
CB A:VAL352 4.3 45.1 1.0
C A:VAL352 4.4 40.7 1.0
CA A:VAL352 4.4 43.0 1.0
C A:PRO351 4.5 46.2 1.0
CA A:PRO351 4.7 50.5 1.0
CB A:PRO351 4.7 52.1 1.0
NE A:ARG353 4.9 68.7 1.0
NH1 A:ARG356 5.0 44.3 1.0

Iodine binding site 5 out of 9 in 6x2d

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Iodine binding site 5 out of 9 in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:89.8
occ:0.70
 O A:HOH525 3.1 41.4 1.0
O B:HOH528 3.4 48.1 1.0
O B:HOH512 3.4 32.5 1.0
CA B:GLY376 3.8 38.5 1.0
N B:ARG377 4.0 42.2 1.0
CE2 A:PHE381 4.1 34.9 1.0
NE A:ARG380 4.2 51.3 1.0
C B:GLY376 4.4 39.9 1.0
CD2 A:PHE381 4.4 34.9 1.0
CG A:ARG380 4.5 43.0 1.0
CB A:SER379 4.6 31.3 1.0
CD A:ARG380 4.7 48.2 1.0
O B:ARG377 4.9 36.1 1.0
NH2 B:ARG377 4.9 78.9 1.0

Iodine binding site 6 out of 9 in 6x2d

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Iodine binding site 6 out of 9 in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I401

b:62.7
occ:0.70
 CZ B:ARG356 3.5 52.0 1.0
NE B:ARG356 3.6 47.9 1.0
NH2 B:ARG356 3.7 52.1 1.0
CD B:ARG356 3.8 46.6 1.0
NH1 B:ARG356 4.1 55.8 1.0

Iodine binding site 7 out of 9 in 6x2d

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Iodine binding site 7 out of 9 in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I402

b:72.5
occ:0.70
 I B:IOD402 0.0 72.5 0.7
I B:IOD402 3.3 78.7 0.3
NH1 B:ARG336 3.7 53.6 1.0
CD2 B:LEU338 3.7 53.5 1.0
CG2 B:ILE292 4.1 40.6 1.0
CD B:ARG336 4.2 48.4 1.0
CG B:PRO294 4.3 49.0 1.0
CD B:PRO294 4.3 46.1 1.0
O B:HOH533 4.4 56.5 1.0
CB B:PRO294 4.6 48.1 1.0
CZ B:ARG336 4.7 50.8 1.0
CG B:LEU338 4.9 53.4 1.0
NE B:ARG336 4.9 50.1 1.0
CG B:ARG336 4.9 50.4 1.0
CB B:ARG336 5.0 49.5 1.0

Iodine binding site 8 out of 9 in 6x2d

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Iodine binding site 8 out of 9 in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I402

b:78.7
occ:0.30
 I B:IOD402 0.0 78.7 0.3
O B:ILE292 3.0 38.6 1.0
I B:IOD402 3.3 72.5 0.7
NH1 B:ARG336 3.4 53.6 1.0
CD B:PRO294 3.8 46.1 1.0
C B:ILE292 3.9 39.5 1.0
CB B:ILE292 4.0 39.7 1.0
CG2 B:ILE292 4.0 40.6 1.0
CA B:ARG280 4.0 57.6 1.0
O B:GLN279 4.4 57.1 1.0
CB B:ARG280 4.4 59.3 1.0
CG B:PRO294 4.5 49.0 1.0
CA B:ILE292 4.5 38.5 1.0
CZ B:ARG336 4.6 50.8 1.0
CG B:ARG280 4.6 58.0 1.0
N B:ARG280 4.7 62.1 1.0
N B:ASP293 4.8 40.5 1.0
C B:GLN279 4.9 65.1 1.0
O B:ARG280 5.0 48.0 1.0
N B:PRO294 5.0 44.6 1.0

Iodine binding site 9 out of 9 in 6x2d

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Iodine binding site 9 out of 9 in the Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I403

b:0.9
occ:0.70
 N B:ARG390 3.3 62.9 1.0
CB B:ARG390 3.7 69.0 1.0
CA B:ARG390 4.0 65.5 1.0
N B:GLY340 4.0 43.1 1.0
CA B:GLY339 4.1 45.9 1.0
C B:GLN389 4.1 60.2 1.0
O B:ARG388 4.2 42.2 1.0
CA B:GLN389 4.2 58.0 1.0
C B:ARG390 4.3 64.0 1.0
C B:GLY339 4.4 45.3 1.0
NE B:ARG390 4.6 84.4 1.0
CG B:ARG390 4.8 75.3 1.0
CG B:GLN389 4.9 71.7 1.0
CA B:GLY340 4.9 41.2 1.0

Reference:

G.Minasov, L.Shuvalova, O.Kiryukhina, I.Dubrovska, G.Wiersum, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Dnase I Domain of Ribonuclease E From Vibrio Cholerae. To Be Published.
Page generated: Fri Aug 8 22:28:10 2025

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