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Bromine in PDB 8adq: Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde

Protein crystallography data

The structure of Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde, PDB code: 8adq was solved by I.Justo, S.R.Marsden, U.Hanefeld, I.Bento, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.90 / 1.60
Space group P 42 3 2
Cell size a, b, c (Å), α, β, γ (°) 115.793, 115.793, 115.793, 90, 90, 90
R / Rfree (%) 16.8 / 20.1

Other elements in 8adq:

The structure of Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde also contains other interesting chemical elements:

Potassium (K) 1 atom
Magnesium (Mg) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde (pdb code 8adq). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde, PDB code: 8adq:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in 8adq

Go back to Bromine Binding Sites List in 8adq
Bromine binding site 1 out of 3 in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br310

b:34.7
occ:0.67
O A:HOH404 2.9 38.1 1.0
HG2 A:PRO232 3.0 37.9 1.0
HG11 A:VAL182 3.2 40.1 1.0
O A:HOH466 3.2 42.3 1.0
HD2 A:PRO232 3.2 37.3 1.0
HG21 A:VAL182 3.2 42.4 1.0
HE1 A:PHE210 3.4 40.6 1.0
HA2 A:GLY212 3.5 40.6 1.0
HA3 A:GLY212 3.6 40.6 1.0
HZ A:PHE210 3.8 40.5 1.0
HB A:VAL182 3.8 41.5 1.0
CG A:PRO232 3.8 31.6 1.0
CD A:PRO232 3.8 31.1 1.0
HB2 A:ALA235 3.9 37.5 1.0
HD3 A:PRO232 4.0 37.3 1.0
CA A:GLY212 4.0 33.9 1.0
CG1 A:VAL182 4.0 33.4 1.0
CG2 A:VAL182 4.1 35.3 1.0
HB1 A:ALA235 4.1 37.5 1.0
CE1 A:PHE210 4.1 33.8 1.0
HB3 A:ALA235 4.1 37.5 1.0
HO3 A:3GR303 4.2 63.0 0.9
CB A:VAL182 4.2 34.6 1.0
CB A:ALA235 4.2 31.2 1.0
H31 A:3GR303 4.3 60.7 0.9
CZ A:PHE210 4.3 33.7 1.0
HG3 A:PRO232 4.4 37.9 1.0
HG13 A:VAL182 4.5 40.1 1.0
HG23 A:VAL182 4.5 42.4 1.0
HB1 A:ALA231 4.6 40.5 1.0
HB2 A:PRO232 4.6 36.0 1.0
HG12 A:VAL182 4.7 40.1 1.0
O3 A:3GR303 4.7 52.5 0.9
HG22 A:VAL182 4.7 42.4 1.0
O A:GLY212 4.8 34.7 1.0
CB A:PRO232 4.8 30.0 1.0
N A:GLY212 5.0 32.9 1.0
C A:GLY212 5.0 33.4 1.0

Bromine binding site 2 out of 3 in 8adq

Go back to Bromine Binding Sites List in 8adq
Bromine binding site 2 out of 3 in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br311

b:37.5
occ:0.50
O A:HOH514 2.7 38.6 1.0
HG2 A:ARG242 2.8 44.0 0.4
HH11 A:ARG242 3.2 46.1 0.4
HG2 A:ARG242 3.3 42.7 0.6
HD12 A:ILE245 3.6 38.8 1.0
HG3 A:ARG242 3.7 44.0 0.4
CG A:ARG242 3.7 36.7 0.4
HA A:ARG242 3.7 41.3 0.6
HA A:ARG242 3.7 41.5 0.4
NH1 A:ARG242 3.7 38.4 0.4
HG21 A:ILE245 3.8 43.2 1.0
HH12 A:ARG242 3.8 46.1 0.4
HG22 A:ILE245 4.0 43.2 1.0
HB A:ILE245 4.1 40.7 1.0
HD13 A:ILE245 4.2 38.8 1.0
CG A:ARG242 4.3 35.6 0.6
CG2 A:ILE245 4.3 36.0 1.0
HD3 A:ARG242 4.3 46.2 0.4
CD1 A:ILE245 4.3 32.3 1.0
HD3 A:ARG242 4.4 46.5 0.6
O A:HOH607 4.4 42.7 1.0
CD A:ARG242 4.5 38.5 0.4
CA A:ARG242 4.6 34.6 0.4
CA A:ARG242 4.6 34.4 0.6
HB3 A:ARG242 4.6 42.0 0.6
CB A:ILE245 4.6 33.9 1.0
CZ A:ARG242 4.7 39.7 0.4
CB A:ARG242 4.7 35.6 0.4
CB A:ARG242 4.7 35.0 0.6
HG3 A:ARG242 4.9 42.7 0.6
O A:ARG242 4.9 35.5 0.4
O A:ARG242 4.9 35.4 0.6
CD A:ARG242 4.9 38.7 0.6

Bromine binding site 3 out of 3 in 8adq

Go back to Bromine Binding Sites List in 8adq
Bromine binding site 3 out of 3 in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br312

b:46.0
occ:0.28
O A:HOH637 2.7 34.9 0.5
O A:HOH423 3.1 38.1 1.0
HG3 A:PRO54 3.2 36.6 1.0
HD3 A:PRO54 3.3 35.8 1.0
HB3 A:PRO54 3.3 35.1 1.0
CG A:PRO54 3.8 30.5 1.0
CD A:PRO54 4.0 29.8 1.0
CB A:PRO54 4.0 29.2 1.0
O A:HOH574 4.6 40.9 1.0
HB2 A:PRO54 4.7 35.1 1.0
HD2 A:PRO54 4.7 35.8 1.0
HG2 A:PRO54 4.7 36.6 1.0
O A:GLY50 4.7 33.1 1.0
HB3 A:ALA53 4.8 36.6 1.0
N A:PRO54 4.9 27.1 1.0
CA A:PRO54 5.0 28.7 1.0

Reference:

S.R.Marsden, H.J.Wijma, M.K.F.Mohr, I.Justo, P.L.Hagedoorn, J.Laustsen, C.M.Jeffries, D.Svergun, L.Mestrom, D.G.G.Mcmillan, I.Bento, U.Hanefeld. Substrate Induced Movement of the Metal Cofactor Between Active and Resting State. Angew.Chem.Int.Ed.Engl. V. 61 13338 2022.
ISSN: ESSN 1521-3773
PubMed: 36214476
DOI: 10.1002/ANIE.202213338
Page generated: Thu Jul 11 04:51:32 2024

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