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Iodine in PDB 6g33: Crystal Structure of CLK1 in Complex with 5-Iodotubercidin

Enzymatic activity of Crystal Structure of CLK1 in Complex with 5-Iodotubercidin

All present enzymatic activity of Crystal Structure of CLK1 in Complex with 5-Iodotubercidin:
2.7.12.1;

Protein crystallography data

The structure of Crystal Structure of CLK1 in Complex with 5-Iodotubercidin, PDB code: 6g33 was solved by C.Heroven, A.Chaikuad, C.Bountra, C.H.Arrowsmith, A.M.Edwards, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.86 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.181, 116.191, 90.980, 90.00, 98.99, 90.00
R / Rfree (%) 18.8 / 21.8

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of CLK1 in Complex with 5-Iodotubercidin (pdb code 6g33). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of CLK1 in Complex with 5-Iodotubercidin, PDB code: 6g33:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 6g33

Go back to Iodine Binding Sites List in 6g33
Iodine binding site 1 out of 6 in the Crystal Structure of CLK1 in Complex with 5-Iodotubercidin


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 CLK1 in Complex with 5-Iodotubercidin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:28.7
occ:0.75
 IAE A:5ID501 0.0 28.7 0.8
C7 A:5ID501 2.0 21.0 0.2
C7 A:5ID501 2.1 21.1 0.8
C8 A:5ID501 3.0 20.8 0.2
C5 A:5ID501 3.0 19.9 0.2
C8 A:5ID501 3.1 20.2 0.8
C5 A:5ID501 3.1 18.4 0.8
O A:HOH652 3.2 32.4 1.0
N6 A:5ID501 3.4 20.1 0.2
N6 A:5ID501 3.4 19.8 0.8
I A:IOD502 3.5 33.5 0.2
CD2 A:PHE241 3.5 26.3 1.0
C6 A:5ID501 3.6 19.9 0.2
C6 A:5ID501 3.7 19.1 0.8
CE2 A:PHE241 3.8 26.5 1.0
CG A:PHE241 3.9 26.2 1.0
N9 A:5ID501 4.1 21.9 0.2
C4 A:5ID501 4.2 20.5 0.2
CB A:VAL324 4.2 26.2 1.0
N9 A:5ID501 4.2 22.7 0.8
C4 A:5ID501 4.3 19.8 0.8
CZ A:PHE241 4.3 27.1 1.0
CG1 A:VAL324 4.3 26.7 1.0
CD1 A:PHE241 4.3 27.0 1.0
CB A:PHE241 4.4 25.7 1.0
CE1 A:PHE241 4.5 27.1 1.0
CG2 A:VAL324 4.6 26.5 1.0
CG2 A:VAL175 4.8 27.1 1.0
CG1 A:VAL175 4.8 26.9 1.0
N1 A:5ID501 5.0 20.1 0.2
CG2 A:VAL225 5.0 27.5 1.0

Iodine binding site 2 out of 6 in 6g33

Go back to Iodine Binding Sites List in 6g33
Iodine binding site 2 out of 6 in the Crystal Structure of CLK1 in Complex with 5-Iodotubercidin


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 CLK1 in Complex with 5-Iodotubercidin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:33.5
occ:0.25
 O A:HOH652 3.0 32.4 1.0
O5' A:5ID501 3.2 29.0 0.2
NZ A:LYS191 3.2 30.4 1.0
O5' A:5ID501 3.3 36.5 0.8
IAE A:5ID501 3.5 28.7 0.8
O A:HOH620 3.6 32.4 1.0
CB A:ASP325 3.7 27.4 1.0
CE A:LYS191 3.8 29.6 1.0
CD A:LYS191 3.8 29.1 1.0
CA A:ASP325 3.8 26.6 1.0
N A:ASP325 3.9 25.8 1.0
C8 A:5ID501 4.0 20.8 0.2
CG A:ASP325 4.0 29.5 1.0
C8 A:5ID501 4.1 20.2 0.8
OD2 A:ASP325 4.1 33.1 1.0
C7 A:5ID501 4.1 21.0 0.2
C7 A:5ID501 4.2 21.1 0.8
CG2 A:VAL324 4.3 26.5 1.0
CE2 A:PHE172 4.3 35.4 1.0
CZ A:PHE172 4.3 34.9 1.0
CB A:VAL324 4.5 26.2 1.0
OE2 A:GLU206 4.5 30.6 1.0
C5' A:5ID501 4.6 26.9 0.2
CG2 A:VAL175 4.7 27.1 1.0
C5' A:5ID501 4.7 32.6 0.8
OD1 A:ASP325 4.7 30.5 1.0
C A:VAL324 4.9 26.1 1.0
CG A:LYS191 4.9 28.1 1.0

Iodine binding site 3 out of 6 in 6g33

Go back to Iodine Binding Sites List in 6g33
Iodine binding site 3 out of 6 in the Crystal Structure of CLK1 in Complex with 5-Iodotubercidin


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 CLK1 in Complex with 5-Iodotubercidin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I501

b:36.6
occ:0.70
 IAE B:5ID501 0.0 36.6 0.7
C7 B:5ID501 2.0 24.1 0.3
C7 B:5ID501 2.1 25.9 0.7
C8 B:5ID501 3.0 23.7 0.3
C8 B:5ID501 3.1 25.2 0.7
C5 B:5ID501 3.1 23.4 0.3
C5 B:5ID501 3.2 24.6 0.7
I B:IOD502 3.4 47.9 0.3
O B:HOH608 3.5 38.9 1.0
N6 B:5ID501 3.5 23.9 0.3
N6 B:5ID501 3.5 26.4 0.7
CD2 B:PHE241 3.6 39.4 1.0
C6 B:5ID501 3.7 23.3 0.3
C6 B:5ID501 3.8 24.2 0.7
CE2 B:PHE241 3.8 39.8 1.0
CG B:PHE241 4.0 38.1 1.0
CB B:VAL324 4.1 35.1 1.0
N9 B:5ID501 4.2 24.9 0.3
C4 B:5ID501 4.2 23.2 0.3
CG1 B:VAL324 4.2 35.3 1.0
N9 B:5ID501 4.2 26.9 0.7
CZ B:PHE241 4.3 40.0 1.0
C4 B:5ID501 4.3 23.3 0.7
CD1 B:PHE241 4.4 39.8 1.0
CB B:PHE241 4.5 37.9 1.0
CE1 B:PHE241 4.6 40.5 1.0
CG2 B:VAL324 4.6 35.0 1.0
CG2 B:VAL175 4.8 37.1 1.0
CG1 B:VAL175 4.8 38.6 1.0
CG2 B:VAL225 5.0 38.4 1.0

Iodine binding site 4 out of 6 in 6g33

Go back to Iodine Binding Sites List in 6g33
Iodine binding site 4 out of 6 in the Crystal Structure of CLK1 in Complex with 5-Iodotubercidin


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 CLK1 in Complex with 5-Iodotubercidin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:47.9
occ:0.30
 NZ B:LYS191 3.1 39.1 1.0
O5' B:5ID501 3.4 29.9 0.3
IAE B:5ID501 3.4 36.6 0.7
O5' B:5ID501 3.4 34.6 0.7
O B:HOH608 3.4 38.9 1.0
CE B:LYS191 3.6 38.0 1.0
CD B:LYS191 3.7 37.6 1.0
O B:HOH609 3.7 40.5 1.0
CB B:ASP325 3.9 39.7 1.0
CA B:ASP325 4.0 39.3 1.0
C8 B:5ID501 4.1 23.7 0.3
C8 B:5ID501 4.1 25.2 0.7
CG B:ASP325 4.1 41.9 1.0
N B:ASP325 4.1 38.5 1.0
OD2 B:ASP325 4.2 44.9 1.0
CZ B:PHE172 4.2 39.2 1.0
C7 B:5ID501 4.2 24.1 0.3
CE2 B:PHE172 4.2 39.4 1.0
C7 B:5ID501 4.3 25.9 0.7
CG2 B:VAL324 4.5 35.0 1.0
CG2 B:VAL175 4.5 37.1 1.0
OE2 B:GLU206 4.5 39.8 1.0
CB B:VAL324 4.6 35.1 1.0
C5' B:5ID501 4.7 28.6 0.3
C5' B:5ID501 4.7 34.0 0.7
CG B:LYS191 4.7 38.2 1.0
OD1 B:ASP325 4.8 40.0 1.0

Iodine binding site 5 out of 6 in 6g33

Go back to Iodine Binding Sites List in 6g33
Iodine binding site 5 out of 6 in the Crystal Structure of CLK1 in Complex with 5-Iodotubercidin


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 CLK1 in Complex with 5-Iodotubercidin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I501

b:34.9
occ:0.75
 IAE C:5ID501 0.0 34.9 0.8
C7 C:5ID501 2.0 24.3 0.2
C7 C:5ID501 2.1 22.2 0.8
C8 C:5ID501 2.9 25.4 0.2
C8 C:5ID501 3.1 24.4 0.8
C5 C:5ID501 3.1 24.5 0.2
C5 C:5ID501 3.1 23.2 0.8
O C:HOH624 3.3 35.7 1.0
I C:IOD502 3.4 49.2 0.2
N6 C:5ID501 3.6 25.6 0.2
N6 C:5ID501 3.6 26.9 0.8
CD2 C:PHE241 3.6 34.9 1.0
C6 C:5ID501 3.8 25.0 0.2
CE2 C:PHE241 3.8 34.8 1.0
C6 C:5ID501 3.8 25.1 0.8
CG C:PHE241 3.9 34.4 1.0
N9 C:5ID501 4.1 26.6 0.2
CB C:VAL324 4.1 33.9 1.0
CG1 C:VAL324 4.2 34.2 1.0
C4 C:5ID501 4.2 25.2 0.2
CZ C:PHE241 4.2 33.9 1.0
N9 C:5ID501 4.2 27.0 0.8
C4 C:5ID501 4.3 24.6 0.8
CD1 C:PHE241 4.4 34.3 1.0
CE1 C:PHE241 4.5 34.0 1.0
CB C:PHE241 4.5 35.3 1.0
CG2 C:VAL324 4.7 34.2 1.0
CG2 C:VAL175 4.9 34.5 1.0
CG2 C:VAL225 4.9 37.7 1.0
CG1 C:VAL175 4.9 34.5 1.0
CG1 C:VAL225 4.9 37.5 1.0

Iodine binding site 6 out of 6 in 6g33

Go back to Iodine Binding Sites List in 6g33
Iodine binding site 6 out of 6 in the Crystal Structure of CLK1 in Complex with 5-Iodotubercidin


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 CLK1 in Complex with 5-Iodotubercidin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I502

b:49.2
occ:0.25
 O C:HOH624 2.9 35.7 1.0
NZ C:LYS191 3.0 38.2 1.0
IAE C:5ID501 3.4 34.9 0.8
O5' C:5ID501 3.4 34.8 0.2
O5' C:5ID501 3.5 37.8 0.8
CE C:LYS191 3.6 38.1 1.0
O C:HOH620 3.6 38.3 1.0
CD C:LYS191 3.6 37.5 1.0
CB C:ASP325 4.0 34.1 1.0
CA C:ASP325 4.0 33.2 1.0
N C:ASP325 4.0 32.1 1.0
C8 C:5ID501 4.1 25.4 0.2
C8 C:5ID501 4.2 24.4 0.8
CG C:ASP325 4.2 35.9 1.0
C7 C:5ID501 4.3 24.3 0.2
OD2 C:ASP325 4.3 38.6 1.0
C7 C:5ID501 4.3 22.2 0.8
OE2 C:GLU206 4.3 36.2 1.0
CZ C:PHE172 4.4 42.8 1.0
CE2 C:PHE172 4.4 43.4 1.0
CG2 C:VAL324 4.4 34.2 1.0
CB C:VAL324 4.5 33.9 1.0
CG2 C:VAL175 4.8 34.5 1.0
C5' C:5ID501 4.8 32.3 0.2
OD1 C:ASP325 4.8 37.2 1.0
CG C:LYS191 4.8 36.1 1.0
C5' C:5ID501 4.8 36.1 0.8
OE1 C:GLU206 4.9 36.2 1.0
C C:VAL324 5.0 31.8 1.0
CE2 C:PHE241 5.0 34.8 1.0

Reference:

C.Heroven, V.Georgi, G.K.Ganotra, P.Brennan, F.Wolfreys, R.C.Wade, A.E.Fernandez-Montalvan, A.Chaikuad, S.Knapp. Halogen-Aromatic Pi Interactions Modulate Inhibitor Residence Times. Angew. Chem. Int. Ed. Engl. V. 57 7220 2018.
ISSN: ESSN 1521-3773
PubMed: 29601130
DOI: 10.1002/ANIE.201801666
Page generated: Sun Aug 11 23:12:45 2024

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