Iodine in PDB 6ptr: Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin

The structure of Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin, PDB code: 6ptr 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)	42.93 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.950, 93.130, 110.740, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.7

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin (pdb code 6ptr). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin, PDB code: 6ptr:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin


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 A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:27.2 occ:0.63 O A:HOH828 3.4 21.7 1.0 N A:ARG286 3.5 33.2 1.0 N A:ALA287 3.7 24.2 1.0 C A:ARG286 4.0 23.2 1.0 ND2 A:ASN327 4.2 24.0 1.0 CA A:ARG286 4.2 28.4 1.0 CG1 A:VAL371 4.2 17.8 1.0 CA A:ALA287 4.3 20.5 1.0 CB A:ASN327 4.3 14.7 1.0 CG2 X:MVA2 4.3 31.7 1.0 CB A:ALA287 4.4 22.7 1.0 CA A:ASN327 4.4 17.7 1.0 C A:GLY285 4.5 42.7 1.0 CG2 A:VAL371 4.5 21.1 1.0 CB A:ARG286 4.5 31.4 1.0 CG A:ASN327 4.5 18.6 1.0 CA A:GLY285 4.5 39.1 1.0 CB A:VAL371 4.7 19.6 1.0 O A:ARG286 4.7 27.6 1.0 N A:ASN327 5.0 17.5 1.0

Iodine binding site 2 out of 11 in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin


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 A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:39.8 occ:0.76 NE A:ARG372 3.2 51.9 1.0 CD A:ARG372 4.0 40.2 1.0 N X:MP83 4.0 20.7 1.0 CN X:MVA2 4.0 27.2 1.0 CB X:MP83 4.0 22.9 1.0 CD X:MP83 4.1 20.8 1.0 CH3 X:ACE1 4.1 28.7 1.0 N X:MVA2 4.1 26.9 1.0 NH2 A:ARG372 4.1 57.9 1.0 CZ A:ARG372 4.1 55.9 1.0 CA X:MP83 4.2 20.7 1.0 C X:ACE1 4.2 27.4 1.0 CG A:ARG372 4.4 30.8 1.0 C X:MVA2 4.5 28.4 1.0 CG X:MP83 4.5 20.6 1.0 CE X:MP83 4.5 21.7 1.0 O X:ACE1 4.8 24.2 1.0 CA X:MVA2 4.9 22.9 1.0 O X:HOH103 4.9 39.9 1.0 O X:MVA2 5.0 28.2 1.0

Iodine binding site 3 out of 11 in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin


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 A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:35.4 occ:0.48 O A:HOH848 3.1 47.6 1.0 O A:HOH863 3.8 44.6 1.0 CA A:SER226 3.9 23.2 1.0 N A:GLU227 4.0 28.4 1.0 CG A:PRO197 4.1 24.9 1.0 CD A:PRO197 4.1 30.7 1.0 CA A:GLY127 4.2 37.7 1.0 C A:SER226 4.2 17.9 1.0 CG A:GLU227 4.3 37.1 1.0 N A:GLY127 4.4 33.9 1.0 O A:LEU225 4.5 23.7 1.0 CB A:SER226 4.6 23.6 1.0 C A:GLY127 4.8 35.9 1.0 O A:HOH781 4.8 49.0 1.0 CB A:PRO197 4.9 24.5 1.0 N A:SER226 4.9 24.3 1.0

Iodine binding site 4 out of 11 in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin


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 A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:28.2 occ:0.73 O A:HOH931 3.3 33.6 1.0 N A:ILE29 3.5 19.4 1.0 CB A:ILE29 3.7 18.2 1.0 CD A:PRO28 3.9 25.7 1.0 CG2 A:ILE29 3.9 18.1 1.0 O A:HOH913 4.0 56.8 1.0 N A:PRO28 4.0 21.4 1.0 CD1 A:LEU113 4.2 20.3 1.0 CA A:ILE29 4.2 18.6 1.0 CG1 A:VAL27 4.3 22.9 1.0 CB A:PRO28 4.4 27.7 1.0 C A:PRO28 4.5 20.9 1.0 CG A:PRO28 4.5 29.3 1.0 CA A:PRO28 4.6 23.4 1.0 C A:VAL27 4.6 22.7 1.0 CG1 A:ILE29 5.0 19.3 1.0

Iodine binding site 5 out of 11 in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin


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 A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:37.6 occ:0.47 O A:HOH922 3.2 44.2 1.0 N A:SER133 3.5 24.1 1.0 O A:HOH618 3.8 42.2 1.0 CB A:LYS136 3.9 22.2 1.0 OG A:SER133 4.0 28.3 1.0 CG A:LYS136 4.1 27.0 1.0 CB A:SER133 4.1 31.9 1.0 CD2 A:LEU132 4.2 33.3 1.0 CE A:MET187 4.2 26.9 1.0 CA A:LEU132 4.2 20.9 1.0 O A:HOH657 4.3 42.5 1.0 C A:LEU132 4.4 25.9 1.0 CA A:SER133 4.4 22.4 1.0 CB A:LEU132 4.7 26.3 1.0 CD A:LYS136 4.7 40.9 1.0

Iodine binding site 6 out of 11 in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin


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 A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:I511 b:89.3 occ:0.46 ND2 A:ASN327 3.5 24.0 1.0 CD A:ARG286 4.0 54.2 1.0 CD A:ARG329 4.2 58.5 1.0 CE1 A:TYR330 4.2 24.8 1.0 OH A:TYR330 4.3 29.7 1.0 OD1 A:ASN327 4.3 20.9 1.0 CG A:ASN327 4.4 18.6 1.0 CZ A:TYR330 4.4 22.2 1.0 CG A:ARG286 4.4 50.3 1.0 NE A:ARG286 4.5 62.9 1.0 CB A:ARG329 4.5 23.7 1.0 NE A:ARG329 4.6 75.2 1.0 CD1 A:TYR330 4.9 21.8 1.0 CG A:ARG329 4.9 27.3 1.0

Iodine binding site 7 out of 11 in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin


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 A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:I512 b:36.5 occ:0.80 O X:HOH102 3.7 31.5 1.0 NE A:ARG154 3.8 26.6 0.5 CB A:TYR156 4.0 15.4 1.0 CD2 X:MLU10 4.0 37.8 1.0 CD A:ARG154 4.0 27.9 0.5 CG A:LEU157 4.0 19.2 1.0 CA A:ARG154 4.1 22.6 0.5 CA A:ARG154 4.1 22.6 0.5 CD A:ARG154 4.2 29.0 0.5 N A:TYR156 4.2 17.3 1.0 CB A:ARG154 4.2 22.1 0.5 CD2 A:TYR156 4.3 24.3 1.0 CB A:ARG154 4.3 22.7 0.5 C A:ARG154 4.3 22.1 1.0 CG A:TYR156 4.4 19.8 1.0 CD2 A:LEU157 4.4 19.3 1.0 N A:LEU157 4.4 17.3 1.0 CA A:TYR156 4.5 14.2 1.0 CD1 A:LEU157 4.6 20.7 1.0 O A:ARG154 4.6 17.3 1.0 C A:TYR156 4.7 16.4 1.0 CG A:ARG154 4.8 26.7 0.5 N A:TYR155 4.8 20.5 1.0 CG A:ARG154 4.8 27.7 0.5 O A:HOH652 4.9 33.0 1.0 CZ A:ARG154 4.9 29.8 0.5

Iodine binding site 8 out of 11 in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin


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 A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:I502 b:45.1 occ:0.57 CA B:SER226 3.9 33.5 1.0 CD B:PRO197 3.9 38.6 1.0 CG B:PRO197 4.0 37.0 1.0 CA B:GLY127 4.1 37.5 1.0 O B:LEU225 4.2 33.9 1.0 C B:SER226 4.3 30.7 1.0 N B:GLU227 4.3 35.7 1.0 N B:GLY127 4.4 39.6 1.0 C B:GLY127 4.5 38.3 1.0 OE2 B:GLU227 4.6 62.2 1.0 CB B:SER226 4.7 34.7 1.0 CG B:GLU227 4.7 49.4 1.0 N B:CYS128 4.7 34.3 1.0 N B:SER226 4.8 30.1 1.0 C B:LEU225 4.8 28.4 1.0 CB B:PRO197 5.0 36.7 1.0 O B:GLY127 5.0 39.3 1.0

Iodine binding site 9 out of 11 in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin


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 A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:I503 b:61.1 occ:0.46 O B:HOH864 3.3 46.3 1.0 CG2 B:ILE116 3.6 42.8 1.0 CA B:ILE116 3.9 23.8 1.0 CE B:LYS115 4.0 31.1 1.0 CG B:LYS115 4.1 27.3 1.0 CD B:LYS115 4.2 27.5 1.0 N B:ILE116 4.3 21.8 1.0 CB B:ILE116 4.3 29.8 1.0 C B:LYS115 4.5 19.6 1.0 O B:LYS115 4.5 21.6 1.0 OE1 B:GLU120 4.7 65.5 1.0 NZ B:LYS115 4.8 31.1 1.0 CB B:LYS115 4.9 23.3 1.0

Iodine binding site 10 out of 11 in the Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin


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 A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:I504 b:46.1 occ:0.46 N B:SER133 3.6 30.7 1.0 OG B:SER133 4.0 39.6 1.0 CD2 B:LEU132 4.1 39.1 1.0 CE B:MET187 4.1 36.5 1.0 CB B:LYS136 4.1 35.1 1.0 CG B:LYS136 4.2 44.4 1.0 CA B:LEU132 4.2 30.1 1.0 CB B:SER133 4.3 30.4 1.0 O B:HOH780 4.4 51.3 1.0 C B:LEU132 4.4 29.7 1.0 CA B:SER133 4.6 28.6 1.0 CB B:LEU132 4.6 30.4 1.0 O B:HOH648 4.8 43.6 1.0

T.E.Edwards, J.Abendroth, P.S.Horanyi, D.D.Lorimer, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of A Dnan Sliding Clamp (Dna Polymerase III Subunit Beta) From Bartonella Birtlesii Bound to Griselimycin To Be Published.