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Iron in PDB 1gup: Structure of Nucleotidyltransferase Complexed with Udp- Galactose

Enzymatic activity of Structure of Nucleotidyltransferase Complexed with Udp- Galactose

All present enzymatic activity of Structure of Nucleotidyltransferase Complexed with Udp- Galactose:
2.7.7.10;

Protein crystallography data

The structure of Structure of Nucleotidyltransferase Complexed with Udp- Galactose, PDB code: 1gup was solved by J.B.Thoden, I.Rayment, H.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.700, 57.700, 188.700, 90.00, 100.08, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1gup:

The structure of Structure of Nucleotidyltransferase Complexed with Udp- Galactose also contains other interesting chemical elements:

Potassium (K) 4 atoms
Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Nucleotidyltransferase Complexed with Udp- Galactose (pdb code 1gup). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Nucleotidyltransferase Complexed with Udp- Galactose, PDB code: 1gup:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1gup

Go back to Iron Binding Sites List in 1gup
Iron binding site 1 out of 4 in the Structure of Nucleotidyltransferase Complexed with Udp- Galactose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Nucleotidyltransferase Complexed with Udp- Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe351

b:17.9
occ:1.00
OE2 A:GLU182 1.9 18.2 1.0
OE1 A:GLU182 2.0 20.8 1.0
NE2 A:HIS296 2.1 13.5 1.0
NE2 A:HIS298 2.2 14.4 1.0
CD A:GLU182 2.3 12.6 1.0
ND1 A:HIS281 2.3 19.0 1.0
CD2 A:HIS296 3.0 12.8 1.0
CE1 A:HIS296 3.1 18.8 1.0
CE1 A:HIS298 3.1 13.7 1.0
CD2 A:HIS298 3.2 11.7 1.0
CE1 A:HIS281 3.2 29.2 1.0
CG A:HIS281 3.3 32.1 1.0
CB A:HIS281 3.5 13.9 1.0
CG A:GLU182 3.8 21.0 1.0
CD1 A:LEU17 3.9 18.7 1.0
O A:HOH656 4.0 47.4 1.0
CG A:HIS296 4.1 11.9 1.0
ND1 A:HIS296 4.2 13.3 1.0
ND1 A:HIS298 4.3 11.6 1.0
CG A:HIS298 4.3 13.1 1.0
NE2 A:HIS281 4.4 12.6 1.0
CD2 A:HIS281 4.5 11.2 1.0
O A:HOH527 4.6 36.8 1.0
CB A:GLU182 4.7 17.6 1.0
CG A:LEU17 4.9 11.2 1.0
CD2 A:LEU17 4.9 10.6 1.0

Iron binding site 2 out of 4 in 1gup

Go back to Iron Binding Sites List in 1gup
Iron binding site 2 out of 4 in the Structure of Nucleotidyltransferase Complexed with Udp- Galactose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Nucleotidyltransferase Complexed with Udp- Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe351

b:18.8
occ:1.00
OE2 B:GLU182 1.8 18.0 1.0
OE1 B:GLU182 2.1 16.0 1.0
ND1 B:HIS281 2.2 25.5 1.0
NE2 B:HIS296 2.2 20.4 1.0
NE2 B:HIS298 2.2 19.6 1.0
CD B:GLU182 2.3 14.4 1.0
CE1 B:HIS298 3.1 13.3 1.0
CG B:HIS281 3.1 23.1 1.0
CD2 B:HIS296 3.1 18.4 1.0
CE1 B:HIS281 3.2 18.2 1.0
CE1 B:HIS296 3.2 21.9 1.0
CD2 B:HIS298 3.3 19.8 1.0
CB B:HIS281 3.4 14.6 1.0
CG B:GLU182 3.7 11.9 1.0
CD1 B:LEU17 3.9 17.7 1.0
O B:HOH546 4.2 30.8 1.0
ND1 B:HIS298 4.3 13.4 1.0
NE2 B:HIS281 4.3 32.1 1.0
CG B:HIS296 4.3 15.1 1.0
CD2 B:HIS281 4.3 21.4 1.0
ND1 B:HIS296 4.3 15.2 1.0
CG B:HIS298 4.4 14.9 1.0
O B:HOH417 4.4 28.8 1.0
CD2 B:LEU17 4.6 20.8 1.0
CB B:GLU182 4.7 19.3 1.0
O B:HOH370 4.8 13.3 1.0
CG B:LEU17 4.8 16.4 1.0
CA B:HIS281 4.9 9.4 1.0

Iron binding site 3 out of 4 in 1gup

Go back to Iron Binding Sites List in 1gup
Iron binding site 3 out of 4 in the Structure of Nucleotidyltransferase Complexed with Udp- Galactose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Nucleotidyltransferase Complexed with Udp- Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe351

b:19.9
occ:1.00
OE2 C:GLU182 1.8 16.2 1.0
ND1 C:HIS281 2.0 33.7 1.0
NE2 C:HIS296 2.0 19.0 1.0
NE2 C:HIS298 2.2 19.6 1.0
CD C:GLU182 2.5 24.4 1.0
OE1 C:GLU182 2.6 29.9 1.0
CE1 C:HIS296 2.7 17.6 1.0
CE1 C:HIS281 2.9 37.2 1.0
CG C:HIS281 3.0 39.8 1.0
CE1 C:HIS298 3.2 19.6 1.0
CD2 C:HIS298 3.2 15.8 1.0
CD2 C:HIS296 3.2 14.3 1.0
CB C:HIS281 3.3 21.6 1.0
CG C:GLU182 3.9 17.4 1.0
ND1 C:HIS296 4.0 22.6 1.0
CD1 C:LEU17 4.0 23.7 1.0
NE2 C:HIS281 4.1 23.6 1.0
CD2 C:HIS281 4.1 25.9 1.0
CG C:HIS296 4.2 12.7 1.0
ND1 C:HIS298 4.3 18.2 1.0
CG C:HIS298 4.3 31.6 1.0
O C:HOH827 4.5 29.9 1.0
CD2 C:LEU17 4.7 22.3 1.0
CB C:GLU182 4.8 14.1 1.0
CA C:HIS281 4.8 31.1 1.0
O C:HOH818 4.9 36.8 1.0
CG C:LEU17 4.9 28.3 1.0

Iron binding site 4 out of 4 in 1gup

Go back to Iron Binding Sites List in 1gup
Iron binding site 4 out of 4 in the Structure of Nucleotidyltransferase Complexed with Udp- Galactose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Nucleotidyltransferase Complexed with Udp- Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe351

b:23.6
occ:1.00
NE2 D:HIS296 1.9 19.9 1.0
OE2 D:GLU182 2.1 25.7 1.0
ND1 D:HIS281 2.1 11.2 1.0
NE2 D:HIS298 2.3 14.8 1.0
OE1 D:GLU182 2.4 20.1 1.0
CD D:GLU182 2.5 0.0 1.0
CD2 D:HIS296 2.8 17.6 1.0
CE1 D:HIS296 3.0 20.4 1.0
CE1 D:HIS298 3.1 0.0 1.0
CG D:HIS281 3.1 10.7 1.0
CE1 D:HIS281 3.1 13.2 1.0
CD2 D:HIS298 3.4 27.4 1.0
CB D:HIS281 3.4 14.3 1.0
CG D:HIS296 4.0 22.9 1.0
CG D:GLU182 4.0 21.2 1.0
O D:HOH919 4.1 35.1 1.0
ND1 D:HIS296 4.1 22.8 1.0
CD1 D:LEU17 4.1 61.3 1.0
NE2 D:HIS281 4.2 12.9 1.0
CD2 D:HIS281 4.3 11.0 1.0
ND1 D:HIS298 4.3 19.3 1.0
CG D:HIS298 4.4 27.7 1.0
CD2 D:LEU17 4.7 36.1 1.0
CA D:HIS281 4.9 29.9 1.0
CB D:GLU182 4.9 29.4 1.0

Reference:

J.B.Thoden, F.J.Ruzicka, P.A.Frey, I.Rayment, H.M.Holden. Structural Analysis of the H166G Site-Directed Mutant of Galactose-1-Phosphate Uridylyltransferase Complexed with Either Udp-Glucose or Udp-Galactose: Detailed Description of the Nucleotide Sugar Binding Site. Biochemistry V. 36 1212 1997.
ISSN: ISSN 0006-2960
PubMed: 9063869
DOI: 10.1021/BI9626517
Page generated: Sun Dec 13 14:16:06 2020

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