Atomistry » Iodine » PDB 3g2t-3kxf » 3km3
Atomistry »
  Iodine »
    PDB 3g2t-3kxf »
      3km3 »

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

Go back to Iodine Binding Sites List in 3km3
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

Go back to Iodine Binding Sites List in 3km3
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

Go back to Iodine Binding Sites List in 3km3
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

Go back to Iodine Binding Sites List in 3km3
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

Go back to Iodine Binding Sites List in 3km3
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

Go back to Iodine Binding Sites List in 3km3
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

Go back to Iodine Binding Sites List in 3km3
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

Go back to Iodine Binding Sites List in 3km3
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

Go back to Iodine Binding Sites List in 3km3
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

Go back to Iodine Binding Sites List in 3km3
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy