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Iron in PDB 8jk9: SP1746 in Complex with Gdp

Enzymatic activity of SP1746 in Complex with Gdp

All present enzymatic activity of SP1746 in Complex with Gdp:
3.6.1.41;

Protein crystallography data

The structure of SP1746 in Complex with Gdp, PDB code: 8jk9 was solved by Y.Jin, J.Ke, L.Niu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.63 / 1.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.302, 69.302, 88.561, 90, 90, 120
R / Rfree (%) 18.1 / 21.1

Other elements in 8jk9:

The structure of SP1746 in Complex with Gdp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the SP1746 in Complex with Gdp (pdb code 8jk9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the SP1746 in Complex with Gdp, PDB code: 8jk9:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 8jk9

Go back to Iron Binding Sites List in 8jk9
Iron binding site 1 out of 2 in the SP1746 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of SP1746 in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:18.1
occ:1.00
O A:HOH440 2.0 18.8 1.0
NE2 A:HIS29 2.1 18.4 1.0
O1B A:GDP304 2.1 20.4 1.0
NE2 A:HIS58 2.2 17.3 1.0
OD2 A:ASP59 2.2 19.1 1.0
OD1 A:ASP135 2.2 18.1 1.0
CG A:ASP59 3.0 18.7 1.0
CD2 A:HIS58 3.0 17.5 1.0
CE1 A:HIS29 3.1 18.5 1.0
CG A:ASP135 3.1 18.6 1.0
CD2 A:HIS29 3.1 18.7 1.0
CE1 A:HIS58 3.2 17.7 1.0
PB A:GDP304 3.2 21.8 1.0
OD2 A:ASP135 3.4 19.2 1.0
OD1 A:ASP59 3.4 18.6 1.0
O3B A:GDP304 3.5 20.4 1.0
FE A:FE303 3.6 16.1 1.0
NH1 A:ARG141 3.7 32.3 1.0
O3A A:GDP304 3.8 20.3 1.0
NH2 A:ARG26 4.0 28.7 1.0
ND1 A:HIS29 4.2 18.4 1.0
CB A:ASP59 4.2 18.3 1.0
CG A:HIS58 4.2 17.3 1.0
CG A:HIS29 4.2 18.7 1.0
ND1 A:HIS58 4.3 17.2 1.0
CB A:ASP135 4.4 18.2 1.0
O2B A:GDP304 4.6 22.6 1.0
NE2 A:HIS117 4.6 15.7 1.0
CZ A:ARG141 4.7 32.9 1.0
O1A A:GDP304 4.7 19.2 1.0
CD2 A:HIS117 4.7 15.7 1.0
CG2 A:VAL33 4.8 17.2 1.0
PA A:GDP304 4.8 19.0 1.0
CA A:ASP135 4.9 18.0 1.0
O A:ASP135 5.0 18.1 1.0

Iron binding site 2 out of 2 in 8jk9

Go back to Iron Binding Sites List in 8jk9
Iron binding site 2 out of 2 in the SP1746 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of SP1746 in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:16.1
occ:1.00
O A:HOH440 1.9 18.8 1.0
OD1 A:ASP59 2.1 18.6 1.0
NE2 A:HIS91 2.1 17.3 1.0
O3B A:GDP304 2.1 20.4 1.0
NE2 A:HIS117 2.2 15.7 1.0
O1A A:GDP304 2.2 19.2 1.0
CG A:ASP59 3.1 18.7 1.0
CE1 A:HIS91 3.1 17.6 1.0
CD2 A:HIS91 3.1 17.4 1.0
CD2 A:HIS117 3.1 15.7 1.0
CE1 A:HIS117 3.2 15.7 1.0
PB A:GDP304 3.2 21.8 1.0
PA A:GDP304 3.3 19.0 1.0
OD2 A:ASP59 3.3 19.1 1.0
O3A A:GDP304 3.5 20.3 1.0
FE A:FE302 3.6 18.1 1.0
O1B A:GDP304 3.8 20.4 1.0
OG1 A:THR118 3.8 16.1 1.0
CD2 A:HIS58 4.0 17.5 1.0
ND1 A:HIS91 4.2 17.6 1.0
CG A:HIS91 4.2 17.3 1.0
CG A:HIS117 4.3 15.9 1.0
ND1 A:HIS117 4.3 16.1 1.0
OD2 A:ASP135 4.3 19.2 1.0
NE2 A:HIS58 4.4 17.3 1.0
O2A A:GDP304 4.4 20.5 1.0
NZ A:LYS62 4.4 23.8 1.0
O5' A:GDP304 4.4 20.3 1.0
CB A:ASP59 4.5 18.3 1.0
O2B A:GDP304 4.5 22.6 1.0
C5' A:GDP304 4.7 21.7 1.0
CD A:LYS62 4.7 22.8 1.0
CA A:ASP59 4.8 17.9 1.0
OD1 A:ASP135 4.9 18.1 1.0
O A:HIS58 4.9 17.9 1.0
CG A:ASP135 5.0 18.6 1.0

Reference:

Y.Jin, J.Ke, L.Niu. Structural and Biochemical Characterization of A Novel Hydrolase From Streptococcus Pneumoniae To Be Published.
Page generated: Sat Aug 10 07:19:30 2024

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