Iodine in PDB 3k70: Crystal Structure of the Complete Initiation Complex of Recbcd

All present enzymatic activity of Crystal Structure of the Complete Initiation Complex of Recbcd:
3.1.11.5;

The structure of Crystal Structure of the Complete Initiation Complex of Recbcd, PDB code: 3k70 was solved by K.Saikrishnan, D.B.Wigley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	133.800, 192.900, 334.800, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 29.6

The structure of Crystal Structure of the Complete Initiation Complex of Recbcd also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Complete Initiation Complex of Recbcd (pdb code 3k70). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 18 binding sites of Iodine where determined in the Crystal Structure of the Complete Initiation Complex of Recbcd, PDB code: 3k70:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 18 in the Crystal Structure of the Complete Initiation Complex of Recbcd


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 the Complete Initiation Complex of Recbcd within 5.0Å range: probe atom residue distance (Å) B Occ X:I1 b:0.0 occ:1.00 I5 X:5IU1 0.0 0.0 1.0 C5 X:5IU1 2.0 0.0 1.0 C6 X:5IU1 2.9 0.0 1.0 C4 X:5IU1 3.0 0.0 1.0 O4 X:5IU1 3.2 0.0 1.0 O4 X:5IU3 3.9 0.6 1.0 CG2 C:ILE557 3.9 91.9 1.0 CD1 C:ILE557 4.1 91.9 1.0 N3 X:5IU1 4.3 0.0 1.0 N1 X:5IU1 4.3 0.0 1.0 N C:ILE557 4.5 85.9 1.0 N3 X:5IU3 4.7 0.6 1.0 CB C:LEU556 4.7 0.3 1.0 C4 X:5IU3 4.7 0.6 1.0 CB C:ILE557 4.8 91.9 1.0 C2 X:5IU1 4.8 0.0 1.0 CA C:ILE557 4.9 85.9 1.0

Iodine binding site 2 out of 18 in the Crystal Structure of the Complete Initiation Complex of Recbcd


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 the Complete Initiation Complex of Recbcd within 5.0Å range: probe atom residue distance (Å) B Occ X:I2 b:0.2 occ:1.00 I5 X:5IU2 0.0 0.2 1.0 C5 X:5IU2 2.0 0.2 1.0 C6 X:5IU2 2.9 0.2 1.0 C4 X:5IU2 3.0 0.2 1.0 SD D:MET278 3.2 0.6 1.0 O4 X:5IU2 3.3 0.2 1.0 CB D:PRO204 3.5 0.3 1.0 CE D:MET278 3.5 0.6 1.0 CG D:MET278 3.6 0.6 1.0 CB D:MET278 3.7 0.6 1.0 CD1 D:ILE274 3.7 79.1 1.0 CA D:ILE274 3.7 0.1 1.0 CG D:PRO204 3.8 0.3 1.0 O D:MET273 3.9 0.3 1.0 CD2 D:LEU240 4.0 0.1 1.0 OD1 D:ASP275 4.1 0.2 1.0 CG2 D:ILE274 4.1 79.1 1.0 CA D:PRO204 4.1 95.1 1.0 N1 X:5IU2 4.3 0.2 1.0 N3 X:5IU2 4.3 0.2 1.0 CB D:ILE274 4.3 79.1 1.0 N D:ASP275 4.4 0.8 1.0 CG D:LEU240 4.4 0.1 1.0 N D:ILE274 4.5 0.1 1.0 C D:MET273 4.5 0.3 1.0 CG1 D:ILE274 4.6 79.1 1.0 C D:ILE274 4.6 0.1 1.0 CB D:LEU240 4.8 0.1 1.0 C2 X:5IU2 4.8 0.2 1.0

Iodine binding site 3 out of 18 in the Crystal Structure of the Complete Initiation Complex of Recbcd


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 the Complete Initiation Complex of Recbcd within 5.0Å range: probe atom residue distance (Å) B Occ X:I3 b:0.6 occ:1.00 I5 X:5IU3 0.0 0.6 1.0 C5 X:5IU3 2.0 0.6 1.0 C6 X:5IU3 2.9 0.6 1.0 C4 X:5IU3 3.0 0.6 1.0 O4 X:5IU3 3.3 0.6 1.0 C2' X:5IU1 3.5 0.1 1.0 C3' X:5IU1 4.0 0.1 1.0 C5' X:5IU2 4.1 0.8 1.0 N1 X:5IU3 4.3 0.6 1.0 N3 X:5IU3 4.3 0.6 1.0 O3' X:5IU1 4.4 0.1 1.0 OP2 X:5IU2 4.8 0.9 1.0 C3' X:5IU2 4.8 0.8 1.0 C2 X:5IU3 4.9 0.6 1.0 C1' X:5IU1 5.0 0.1 1.0

Iodine binding site 4 out of 18 in the Crystal Structure of the Complete Initiation Complex of Recbcd


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 the Complete Initiation Complex of Recbcd within 5.0Å range: probe atom residue distance (Å) B Occ X:I4 b:0.0 occ:1.00 I5 X:5IU4 0.0 0.0 1.0 C5 X:5IU4 2.0 0.0 1.0 C6 X:5IU4 2.9 0.0 1.0 C4 X:5IU4 3.0 0.0 1.0 O4 X:5IU4 3.3 0.0 1.0 N1 X:5IU4 4.3 0.0 1.0 N3 X:5IU4 4.3 0.0 1.0 C2' X:5IU3 4.3 0.9 1.0 OP2 X:5IU4 4.6 0.9 1.0 C6 X:5IU3 4.8 0.6 1.0 C2 X:5IU4 4.8 0.0 1.0 C5 X:5IU3 4.9 0.6 1.0 N1 X:5IU3 4.9 0.6 1.0

Iodine binding site 5 out of 18 in the Crystal Structure of the Complete Initiation Complex of Recbcd


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 the Complete Initiation Complex of Recbcd within 5.0Å range: probe atom residue distance (Å) B Occ X:I5 b:0.0 occ:1.00 I5 X:5IU5 0.0 0.0 1.0 C5 X:5IU5 2.1 0.0 1.0 C6 X:5IU5 3.0 0.0 1.0 C4 X:5IU5 3.1 0.0 1.0 O4 X:5IU5 3.4 0.0 1.0 N1 X:5IU5 4.4 0.0 1.0 N3 X:5IU5 4.4 0.0 1.0 C2 X:5IU5 5.0 0.0 1.0

Iodine binding site 6 out of 18 in the Crystal Structure of the Complete Initiation Complex of Recbcd


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 the Complete Initiation Complex of Recbcd within 5.0Å range: probe atom residue distance (Å) B Occ X:I7 b:0.7 occ:1.00 I5 X:5IU7 0.0 0.7 1.0 C5 X:5IU7 2.0 0.7 1.0 C6 X:5IU7 2.9 0.7 1.0 C4 X:5IU7 3.0 0.7 1.0 O4 X:5IU7 3.3 0.7 1.0 CB C:ARG839 3.6 1.0 1.0 CA C:ARG839 4.0 86.3 1.0 N1 X:5IU7 4.2 0.7 1.0 N3 X:5IU7 4.3 0.7 1.0 O C:ARG839 4.7 86.3 1.0 C2 X:5IU7 4.9 0.7 1.0 C C:ARG839 4.9 86.3 1.0 CG C:ARG839 4.9 1.0 1.0 N C:ARG839 5.0 86.3 1.0

Iodine binding site 7 out of 18 in the Crystal Structure of the Complete Initiation Complex of Recbcd


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 the Complete Initiation Complex of Recbcd within 5.0Å range: probe atom residue distance (Å) B Occ X:I9 b:0.1 occ:1.00 I5 X:5IU9 0.0 0.1 1.0 C5 X:5IU9 2.0 0.1 1.0 OP2 X:DC8 2.8 0.9 1.0 C6 X:5IU9 2.9 0.1 1.0 C4 X:5IU9 3.0 0.1 1.0 O4 X:5IU9 3.2 0.1 1.0 O5' X:DC8 3.7 0.9 1.0 P X:DC8 3.8 0.9 1.0 N6 X:DA10 3.8 92.7 1.0 CD1 C:LEU875 4.2 0.3 1.0 N1 X:5IU9 4.2 0.1 1.0 N3 X:5IU9 4.2 0.1 1.0 C2' X:DC8 4.2 0.9 1.0 CD2 C:LEU875 4.3 0.3 1.0 CG C:LEU875 4.3 0.3 1.0 C6 X:DA10 4.5 92.7 1.0 C6 X:DC8 4.5 0.9 1.0 C3' X:DC8 4.7 0.9 1.0 OP1 X:DC8 4.7 0.9 1.0 C2 X:5IU9 4.8 0.1 1.0 N1 X:DA10 4.9 92.7 1.0 O3' X:5IU7 5.0 0.1 1.0 C5' X:DC8 5.0 0.9 1.0

Iodine binding site 8 out of 18 in the Crystal Structure of the Complete Initiation Complex of Recbcd


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 the Complete Initiation Complex of Recbcd within 5.0Å range: probe atom residue distance (Å) B Occ X:I46 b:0.3 occ:1.00 I5 X:5IU46 0.0 0.3 1.0 C5 X:5IU46 2.0 0.3 1.0 NE2 B:GLN562 2.8 0.7 1.0 OE1 B:GLN562 2.9 0.7 1.0 C6 X:5IU46 2.9 0.3 1.0 C4 X:5IU46 3.1 0.3 1.0 CD B:GLN562 3.1 0.7 1.0 O4 X:5IU46 3.3 0.3 1.0 C6 X:DT45 3.6 83.7 1.0 C2' X:DT45 3.8 0.3 1.0 C5 X:DT45 4.0 83.7 1.0 C7 X:DT45 4.0 83.7 1.0 N1 X:5IU46 4.2 0.3 1.0 N3 X:5IU46 4.3 0.3 1.0 N1 X:DT45 4.3 83.7 1.0 CG B:GLN562 4.4 0.7 1.0 SD C:MET1079 4.5 87.1 1.0 OP2 X:DT45 4.6 0.9 1.0 C1' X:DT45 4.7 0.3 1.0 O5' X:DT45 4.8 0.3 1.0 C2 X:5IU46 4.8 0.3 1.0 C4 X:DT45 4.9 83.7 1.0 C5' X:5IU46 4.9 0.5 1.0

Iodine binding site 9 out of 18 in the Crystal Structure of the Complete Initiation Complex of Recbcd


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 the Complete Initiation Complex of Recbcd within 5.0Å range: probe atom residue distance (Å) B Occ X:I50 b:0.6 occ:1.00 I5 X:5IU50 0.0 0.6 1.0 C5 X:5IU50 2.0 0.6 1.0 C6 X:5IU50 3.0 0.6 1.0 C4 X:5IU50 3.0 0.6 1.0 O4 X:5IU50 3.2 0.6 1.0 NH2 B:ARG584 3.6 0.4 1.0 N3 X:5IU50 4.3 0.6 1.0 N1 X:5IU50 4.3 0.6 1.0 N6 X:DA51 4.3 0.1 1.0 C4 X:DA49 4.5 0.3 1.0 C5 X:DA49 4.6 0.3 1.0 C2' X:DA49 4.7 0.5 1.0 CZ B:ARG584 4.7 0.4 1.0 N3 X:DA49 4.7 0.3 1.0 N9 X:DA49 4.8 0.3 1.0 C2 X:5IU50 4.8 0.6 1.0 C6 X:DA49 4.9 0.3 1.0 C2 X:DA49 4.9 0.3 1.0 N7 X:DA49 5.0 0.3 1.0

Iodine binding site 10 out of 18 in the Crystal Structure of the Complete Initiation Complex of Recbcd


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 the Complete Initiation Complex of Recbcd within 5.0Å range: probe atom residue distance (Å) B Occ Y:I1 b:0.0 occ:1.00 I5 Y:5IU1 0.0 0.0 1.0 C5 Y:5IU1 2.0 0.0 1.0 C6 Y:5IU1 2.9 0.0 1.0 C4 Y:5IU1 3.0 0.0 1.0 O4 Y:5IU1 3.3 0.0 1.0 CD1 F:ILE557 3.6 75.7 1.0 N F:ILE557 3.7 74.3 1.0 CG2 F:ILE557 3.7 75.7 1.0 CB F:LEU556 3.8 0.8 1.0 C F:LEU556 4.2 0.7 1.0 CA F:ILE557 4.2 74.3 1.0 N1 Y:5IU1 4.3 0.0 1.0 N3 Y:5IU1 4.3 0.0 1.0 CA F:LEU556 4.4 0.7 1.0 CB F:ILE557 4.4 75.7 1.0 O4 Y:5IU3 4.4 0.0 1.0 N F:LEU556 4.4 0.7 1.0 CG F:LEU556 4.5 0.8 1.0 CG1 F:ILE557 4.6 75.7 1.0 C2 Y:5IU1 4.8 0.0 1.0 CD2 F:LEU556 5.0 0.8 1.0 O F:LEU556 5.0 0.7 1.0

K.Saikrishnan, S.P.Griffiths, N.Cook, R.Court, D.B.Wigley. Dna Binding to Recd: Role of the 1B Domain in SF1B Helicase Activity. Embo J. V. 27 2222 2008.
ISSN: ISSN 0261-4189
PubMed: 18668125