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Iodine in PDB 3km3: Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution

Enzymatic activity of Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution

All present enzymatic activity of Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution:
3.5.4.13;

Protein crystallography data

The structure of Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution, PDB code: 3km3 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 84.660, 84.660, 140.740, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 22.2

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution (pdb code 3km3). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 16 binding sites of Iodine where determined in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution, PDB code: 3km3:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 16 in 3km3

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Iodine binding site 1 out of 16 in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I186

b:49.1
occ:1.00
 CA A:HIS7 3.9 14.8 1.0
CG A:ASP6 3.9 15.9 1.0
N A:HIS7 3.9 16.2 1.0
OD2 A:ASP6 4.0 16.3 1.0
CD2 A:LEU36 4.1 15.4 1.0
CB A:ASP6 4.1 16.0 1.0
CB A:HIS7 4.1 15.8 1.0
C A:ASP6 4.2 16.2 1.0
CD A:LYS10 4.2 19.3 1.0
OD1 A:ASP6 4.3 14.5 1.0
O A:ASP6 4.4 17.0 1.0
CB A:LYS10 4.7 16.0 1.0
CA A:ASP6 4.8 16.2 1.0
O A:HOH265 4.9 24.9 1.0

Iodine binding site 2 out of 16 in 3km3

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Iodine binding site 2 out of 16 in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I187

b:67.3
occ:0.81
 O A:HOH228 3.7 20.6 1.0
CA A:GLU11 3.9 15.4 1.0
CD1 A:LEU14 4.2 21.2 1.0
CB A:GLU11 4.2 15.3 1.0
N A:GLU11 4.2 15.7 1.0
C A:LYS10 4.6 15.9 1.0
CB A:LEU14 4.6 19.4 1.0
CG A:LYS10 4.7 17.1 1.0
O A:LYS10 4.7 15.4 1.0
CE A:LYS10 4.7 19.9 1.0
CD A:LYS10 4.8 19.3 1.0
CE A:LYS15 4.8 32.9 1.0
NZ A:LYS15 4.9 34.9 1.0
CG A:LEU14 4.9 20.0 1.0

Iodine binding site 3 out of 16 in 3km3

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Iodine binding site 3 out of 16 in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution


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 Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I188

b:60.6
occ:0.61
 O A:HOH238 3.4 30.6 1.0
CD2 A:PHE77 3.6 19.2 1.0
O A:HOH283 4.0 21.6 1.0
CE1 A:TYR145 4.0 10.9 1.0
CD1 A:TYR145 4.1 11.9 1.0
CB A:ASP76 4.3 13.9 1.0
O A:ASP76 4.3 11.8 1.0
NZ A:LYS143 4.4 20.0 1.0
CE2 A:PHE77 4.4 21.8 1.0
CB A:PHE77 4.5 13.2 1.0
CG A:PHE77 4.5 15.3 1.0
CE A:LYS143 4.5 19.1 1.0
C A:ASP76 4.6 12.5 1.0
O A:HOH284 4.8 29.0 1.0

Iodine binding site 4 out of 16 in 3km3

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Iodine binding site 4 out of 16 in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution


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 Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I189

b:58.0
occ:0.81
 O A:HOH270 2.5 20.7 1.0
O A:HOH251 2.8 15.6 1.0
NZ A:LYS50 3.5 21.0 1.0
CG2 A:THR131 4.1 13.9 1.0
CB A:LEU87 4.2 11.2 1.0
CE A:LYS89 4.3 30.2 1.0
CD A:LYS50 4.3 16.8 1.0
C A:LEU87 4.3 10.2 1.0
CA A:ALA88 4.3 12.4 1.0
OG1 A:THR131 4.4 14.9 1.0
CG A:LYS89 4.4 21.0 1.0
N A:ALA88 4.4 10.1 1.0
O A:LEU87 4.4 8.9 1.0
C A:ALA88 4.4 13.5 1.0
CE A:LYS50 4.5 19.8 1.0
N A:LYS89 4.6 14.0 1.0
CD A:LYS89 4.7 25.4 1.0
NZ A:LYS89 4.7 31.3 1.0
CG A:LYS50 4.8 12.2 1.0
CB A:THR131 4.9 13.9 1.0
O A:HOH285 4.9 34.4 1.0
CA A:LEU87 4.9 10.3 1.0
O A:ALA88 4.9 16.4 1.0

Iodine binding site 5 out of 16 in 3km3

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Iodine binding site 5 out of 16 in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution


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 Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I190

b:49.3
occ:0.62
 O A:HOH219 3.5 25.5 1.0
O A:HOH274 3.5 10.6 1.0
N A:GLY106 3.7 9.8 1.0
CB A:VAL105 4.0 11.7 1.0
CA A:VAL105 4.2 12.0 1.0
CG1 A:VAL105 4.3 11.0 1.0
C A:VAL105 4.4 11.3 1.0
CA A:GLY106 4.6 9.7 1.0

Iodine binding site 6 out of 16 in 3km3

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Iodine binding site 6 out of 16 in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution


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 Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I191

b:55.0
occ:0.61
 N A:TYR129 3.5 14.0 1.0
NZ A:LYS89 3.8 31.3 1.0
O A:TYR129 3.9 14.0 1.0
CA A:GLY128 3.9 15.0 1.0
CD2 A:TYR129 3.9 15.2 1.0
CB A:TYR129 4.2 14.2 1.0
C A:GLY128 4.2 14.1 1.0
CA A:TYR129 4.3 14.3 1.0
O A:HOH303 4.4 30.2 1.0
CE A:LYS89 4.5 30.2 1.0
CG A:TYR129 4.5 15.0 1.0
C A:TYR129 4.5 13.8 1.0
CE1 A:TYR93 4.9 15.1 1.0
CD A:LYS89 4.9 25.4 1.0
CE2 A:TYR129 5.0 15.0 1.0

Iodine binding site 7 out of 16 in 3km3

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Iodine binding site 7 out of 16 in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution


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 Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I192

b:59.9
occ:0.86
 N A:SER0 4.5 24.1 1.0
N A:GLY-1 4.5 32.7 1.0
CA A:GLY-1 4.8 29.9 1.0
C A:GLY-1 4.8 27.1 1.0
CB A:SER0 4.8 22.0 1.0

Iodine binding site 8 out of 16 in 3km3

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Iodine binding site 8 out of 16 in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution


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 Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I193

b:55.2
occ:0.56
 O B:HOH214 3.2 30.2 1.0
NE A:ARG73 3.2 30.6 1.0
N A:ILE79 3.4 9.4 1.0
CZ A:ARG73 3.7 36.5 1.0
NH1 A:ARG73 3.8 38.5 1.0
CD A:ARG73 3.9 28.5 1.0
CG A:ARG73 4.0 23.7 1.0
CA A:CYS78 4.0 13.1 1.0
O B:HOH205 4.1 14.3 1.0
C A:CYS78 4.1 11.3 1.0
CB A:ILE79 4.3 9.0 1.0
CA A:ILE79 4.3 9.0 1.0
O A:ILE79 4.4 7.0 1.0
SG A:CYS78 4.4 20.9 1.0
CD1 A:ILE51 4.5 19.7 1.0
CG1 A:ILE79 4.5 10.7 1.0
NH2 A:ARG73 4.6 37.7 1.0
O A:PHE77 4.7 13.0 1.0
CD1 A:ILE79 4.8 10.2 1.0
CB A:CYS78 4.8 14.2 1.0
C A:ILE79 4.9 8.2 1.0

Iodine binding site 9 out of 16 in 3km3

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Iodine binding site 9 out of 16 in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution


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 Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I186

b:79.5
occ:0.93
 CD2 B:LEU36 4.0 16.0 1.0
CG B:ASP6 4.0 14.4 1.0
N B:HIS7 4.1 15.3 1.0
CA B:HIS7 4.1 15.5 1.0
CB B:ASP6 4.1 14.7 1.0
OD1 B:ASP6 4.2 12.6 1.0
C B:ASP6 4.3 14.9 1.0
OD2 B:ASP6 4.4 12.8 1.0
CB B:HIS7 4.4 15.8 1.0
O B:ASP6 4.6 14.8 1.0
CB B:LYS10 4.6 16.4 1.0
CA B:ASP6 4.9 14.7 1.0

Iodine binding site 10 out of 16 in 3km3

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Iodine binding site 10 out of 16 in the Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Eoxycytidine Triphosphate Deaminase From Anaplasma Phagocytophilum at 2.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I187

b:84.4
occ:0.68
 CE B:MET4 3.5 12.4 1.0
NE2 B:HIS7 3.7 17.7 1.0
CD B:PRO5 4.0 14.9 1.0
CG B:PRO5 4.1 14.5 1.0
CD2 B:HIS7 4.5 16.7 1.0
CB B:TRP8 4.6 15.2 1.0
CD1 B:TRP8 4.6 14.9 1.0
CE1 B:HIS7 4.7 17.2 1.0
CG B:TRP8 4.9 16.0 1.0

Reference:

J.Abendroth, A.S.Gardberg, J.I.Robinson, J.S.Christensen, B.L.Staker, P.J.Myler, L.J.Stewart, T.E.Edwards. Sad Phasing Using Iodide Ions in A High-Throughput Structural Genomics Environment. J.Struct.Funct.Genom. V. 12 83 2011.
ISSN: ISSN 1345-711X
PubMed: 21359836
DOI: 10.1007/S10969-011-9101-7
Page generated: Sun Aug 11 15:28:39 2024

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