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Iodine in PDB 2qch: Crystal Structure of the Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump

Enzymatic activity of Crystal Structure of the Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump

All present enzymatic activity of Crystal Structure of the Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump:
4.1.1.23;

Protein crystallography data

The structure of Crystal Structure of the Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump, PDB code: 2qch was solved by J.Wittmann, M.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.580, 61.998, 70.565, 90.00, 113.27, 90.00
R / Rfree (%) 22.1 / 26.8

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump (pdb code 2qch). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of the Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump, PDB code: 2qch:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 2qch

Go back to Iodine Binding Sites List in 2qch
Iodine binding site 1 out of 4 in the Crystal Structure of the Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump


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 Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I5

b:35.7
occ:0.70
 OD2 A:ASP312 3.2 26.7 1.0
C6 A:5IU1 3.3 26.4 0.3
NZ A:LYS314 3.4 28.3 1.0
C6 A:UMP2 3.5 25.6 0.7
CG A:ASP312 3.6 26.9 1.0
OD1 A:ASN341 3.6 25.9 1.0
OD1 A:ASP312 3.7 29.2 1.0
C5 A:5IU1 3.7 25.6 0.3
I5 A:5IU1 3.8 26.0 0.3
CD A:LYS281 3.9 25.4 1.0
CD1 A:ILE401 3.9 22.3 1.0
CG2 A:ILE401 4.0 25.8 1.0
CG1 A:ILE401 4.0 25.2 1.0
C5 A:UMP2 4.0 25.2 0.7
N1 A:5IU1 4.1 26.5 0.3
CD1 A:ILE448 4.1 20.1 1.0
N1 A:UMP2 4.3 26.1 0.7
C1' A:5IU1 4.3 26.7 0.3
CE A:LYS281 4.3 26.9 1.0
C1' A:UMP2 4.3 26.3 0.7
CZ A:PHE310 4.4 23.1 1.0
CE2 A:PHE310 4.4 24.4 1.0
CG A:PRO417 4.6 23.7 1.0
O4' A:UMP2 4.6 27.5 0.7
CB A:ILE401 4.6 25.5 1.0
CB A:ASP312 4.7 26.1 1.0
CG A:ASN341 4.8 23.8 1.0
NZ A:LYS281 4.9 25.6 1.0
O4' A:5IU1 4.9 27.6 0.3
CE A:LYS314 4.9 27.8 1.0
C4 A:5IU1 4.9 26.3 0.3
CB A:PRO417 5.0 24.3 1.0

Iodine binding site 2 out of 4 in 2qch

Go back to Iodine Binding Sites List in 2qch
Iodine binding site 2 out of 4 in the Crystal Structure of the Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump


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 Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:26.0
occ:0.30
 I5 A:5IU1 0.0 26.0 0.3
C5 A:5IU1 2.1 25.6 0.3
C5 A:UMP2 2.4 25.2 0.7
NZ A:LYS314 2.5 28.3 1.0
CE A:LYS314 2.8 27.8 1.0
C6 A:UMP2 3.0 25.6 0.7
C6 A:5IU1 3.0 26.4 0.3
C4 A:5IU1 3.1 26.3 0.3
O4 A:5IU1 3.3 25.9 0.3
C4 A:UMP2 3.6 25.4 0.7
CE A:MET371 3.7 30.8 1.0
CD1 A:ILE368 3.7 24.0 1.0
CG1 A:ILE368 3.8 23.5 1.0
I A:IOD5 3.8 35.7 0.7
O4 A:UMP2 3.8 25.2 0.7
CG2 A:ILE368 3.9 23.2 1.0
CG2 A:ILE401 4.1 25.8 1.0
CD A:LYS314 4.1 26.3 1.0
N1 A:5IU1 4.3 26.5 0.3
N1 A:UMP2 4.3 26.1 0.7
OD1 B:ASP317 4.4 28.5 1.0
N3 A:5IU1 4.4 25.9 0.3
CG A:LYS314 4.4 26.1 1.0
CB A:ILE368 4.5 24.1 1.0
CG A:MET371 4.6 30.4 1.0
OD1 A:ASN341 4.7 25.9 1.0
N3 A:UMP2 4.8 25.3 0.7
CE1 A:HIS343 4.8 24.8 1.0
OD1 A:ASP312 4.8 29.2 1.0
SD A:MET371 4.8 30.7 1.0
CB A:ILE401 4.8 25.5 1.0
C2 A:5IU1 4.9 26.2 0.3

Iodine binding site 3 out of 4 in 2qch

Go back to Iodine Binding Sites List in 2qch
Iodine binding site 3 out of 4 in the Crystal Structure of the Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump


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 Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I6

b:35.0
occ:0.70
 C6 B:5IU3 3.2 23.9 0.3
C6 B:UMP4 3.4 23.7 0.7
OD2 B:ASP312 3.4 28.2 1.0
NZ B:LYS314 3.6 23.7 1.0
C5 B:5IU3 3.6 23.8 0.3
OD1 B:ASP312 3.7 26.4 1.0
CG B:ASP312 3.7 27.0 1.0
OD1 B:ASN341 3.8 23.9 1.0
I5 B:5IU3 3.8 23.8 0.3
N1 B:5IU3 4.0 23.9 0.3
CG1 B:ILE401 4.0 22.9 1.0
C5 B:UMP4 4.0 23.3 0.7
CD B:LYS281 4.1 21.4 1.0
CD1 B:ILE448 4.1 20.3 1.0
CG2 B:ILE401 4.2 22.8 1.0
CZ B:PHE310 4.2 22.0 1.0
CD1 B:ILE401 4.2 22.5 1.0
N1 B:UMP4 4.2 23.4 0.7
C1' B:5IU3 4.3 24.4 0.3
C1' B:UMP4 4.3 24.4 0.7
CE B:LYS281 4.3 19.6 1.0
CE2 B:PHE310 4.4 22.3 1.0
NZ B:LYS281 4.5 16.1 1.0
CG B:PRO417 4.6 24.8 1.0
O4' B:5IU3 4.6 24.8 0.3
O4' B:UMP4 4.7 23.4 0.7
CB B:ILE401 4.7 24.2 1.0
C4 B:5IU3 4.7 23.8 0.3
CB B:ASP312 4.8 25.1 1.0
CG B:ASN341 4.9 21.9 1.0
CB B:PRO417 4.9 25.4 1.0
C2 B:5IU3 4.9 24.1 0.3
CE B:LYS314 5.0 24.5 1.0

Iodine binding site 4 out of 4 in 2qch

Go back to Iodine Binding Sites List in 2qch
Iodine binding site 4 out of 4 in the Crystal Structure of the Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump


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 Orotidine-5'-Monophosphate Decarboxylase Domain of Human Ump Synthase Bound to 5-Iodo-Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I3

b:23.8
occ:0.30
 I5 B:5IU3 0.0 23.8 0.3
C5 B:5IU3 2.1 23.8 0.3
NZ B:LYS314 2.4 23.7 1.0
C5 B:UMP4 2.6 23.3 0.7
CE B:LYS314 2.8 24.5 1.0
C6 B:5IU3 3.0 23.9 0.3
C6 B:UMP4 3.1 23.7 0.7
C4 B:5IU3 3.1 23.8 0.3
O4 B:5IU3 3.3 23.8 0.3
CE B:MET371 3.7 27.1 1.0
CD1 B:ILE368 3.7 23.8 1.0
C4 B:UMP4 3.8 24.5 0.7
I B:IOD6 3.8 35.0 0.7
CG1 B:ILE368 3.9 24.1 1.0
CG2 B:ILE368 4.0 25.4 1.0
O4 B:UMP4 4.1 24.0 0.7
CD B:LYS314 4.1 24.4 1.0
CG2 B:ILE401 4.1 22.8 1.0
N1 B:5IU3 4.3 23.9 0.3
N3 B:5IU3 4.4 23.9 0.3
CG B:LYS314 4.4 25.3 1.0
OD1 A:ASP317 4.4 28.5 1.0
N1 B:UMP4 4.5 23.4 0.7
OD1 B:ASN341 4.5 23.9 1.0
CB B:ILE368 4.6 25.6 1.0
SD B:MET371 4.7 27.1 1.0
CG B:MET371 4.7 26.8 1.0
OD1 B:ASP312 4.8 26.4 1.0
C2 B:5IU3 4.8 24.1 0.3
CE1 B:HIS343 4.9 24.3 1.0
CB B:ILE401 4.9 24.2 1.0
NE2 B:HIS343 4.9 23.1 1.0
N3 B:UMP4 4.9 24.9 0.7

Reference:

J.G.Wittmann, D.Heinrich, K.Gasow, A.Frey, U.Diederichsen, M.G.Rudolph. Structures of the Human Orotidine-5'-Monophosphate Decarboxylase Support A Covalent Mechanism and Provide A Framework For Drug Design. Structure V. 16 82 2008.
ISSN: ISSN 0969-2126
PubMed: 18184586
DOI: 10.1016/J.STR.2007.10.020
Page generated: Fri Aug 8 13:33:37 2025

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