Atomistry » Iodine » PDB 1lkr-1pvh » 1m5k
Atomistry »
  Iodine »
    PDB 1lkr-1pvh »
      1m5k »

Iodine in PDB 1m5k: Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation

Protein crystallography data

The structure of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation, PDB code: 1m5k was solved by P.B.Rupert, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.07 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 256.300, 44.100, 102.400, 90.00, 109.00, 90.00
R / Rfree (%) 22.9 / 28.4

Other elements in 1m5k:

The structure of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 33 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation (pdb code 1m5k). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation, PDB code: 1m5k:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 1m5k

Go back to Iodine Binding Sites List in 1m5k
Iodine binding site 1 out of 2 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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 Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I17

b:96.4
occ:0.70
I5 A:IU17 0.0 96.4 0.7
C5 A:IU17 1.6 96.5 1.0
C6 A:IU17 2.6 97.9 1.0
C4 A:IU17 2.7 97.7 1.0
O4 A:IU17 3.0 0.7 1.0
O A:HOH225 3.2 59.7 1.0
O A:HOH219 3.4 52.4 1.0
C5 A:C16 3.6 78.3 1.0
C4 A:C16 3.8 81.2 1.0
C6 A:C16 3.8 83.8 1.0
N1 A:IU17 3.9 95.6 1.0
N3 A:IU17 3.9 94.6 1.0
OP2 A:IU17 4.0 68.1 1.0
N3 A:C16 4.1 81.5 1.0
N1 A:C16 4.1 88.8 1.0
N4 A:C16 4.3 76.4 1.0
C2 A:C16 4.3 87.2 1.0
C2 A:IU17 4.5 96.7 1.0
C2' A:C16 4.6 90.5 1.0
C3' A:C16 4.6 98.3 1.0
N4 A:C18 4.9 83.7 1.0
O4' A:IU17 4.9 91.0 1.0
C1' A:C16 5.0 87.1 1.0

Iodine binding site 2 out of 2 in 1m5k

Go back to Iodine Binding Sites List in 1m5k
Iodine binding site 2 out of 2 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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 Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I17

b:76.3
occ:0.60
I5 D:IU17 0.0 76.3 0.6
C5 D:IU17 1.6 89.4 1.0
C6 D:IU17 2.6 87.8 1.0
C4 D:IU17 2.6 90.8 1.0
O4 D:IU17 3.0 96.6 1.0
O D:HOH228 3.0 54.2 1.0
OP2 D:IU17 3.4 86.9 1.0
C6 D:C16 3.6 81.1 1.0
C5 D:C16 3.6 73.8 1.0
C3' D:C16 3.8 70.1 1.0
N3 D:IU17 3.9 91.5 1.0
N1 D:IU17 3.9 90.4 1.0
N1 D:C16 3.9 82.4 1.0
C4 D:C16 4.1 79.8 1.0
C2 D:C16 4.3 85.1 1.0
C5' D:C16 4.3 81.8 1.0
N3 D:C16 4.4 83.0 1.0
C2' D:C16 4.4 82.5 1.0
C2 D:IU17 4.4 89.2 1.0
OP2 D:C16 4.5 59.6 1.0
P D:IU17 4.5 82.8 1.0
C4' D:C16 4.6 79.6 1.0
C1' D:C16 4.6 78.4 1.0
O3' D:C16 4.7 76.1 1.0
O D:HOH224 4.7 48.2 1.0
O4' D:C16 4.7 87.0 1.0
N4 D:C16 4.8 55.6 1.0
O5' D:IU17 4.8 81.7 1.0
N4 D:C18 4.9 80.1 1.0

Reference:

P.B.Rupert, A.P.Massey, S.T.Sigurdsson, A.R.Ferre-D'amare. Transition State Stabilization By A Catalytic Rna Science V. 298 1421 2002.
ISSN: ISSN 0036-8075
PubMed: 11298439
DOI: 10.1126/SCIENCE.1076093
Page generated: Sun Aug 11 12:28:05 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