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Iron in PDB 6l5a: The Structure of the Udgx Mutant H109E at A Pre-Excision State

Protein crystallography data

The structure of The Structure of the Udgx Mutant H109E at A Pre-Excision State, PDB code: 6l5a was solved by W.Xie, J.Tu, H.Zeng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.56 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.698, 48.316, 86.222, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 19.3

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of the Udgx Mutant H109E at A Pre-Excision State (pdb code 6l5a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Structure of the Udgx Mutant H109E at A Pre-Excision State, PDB code: 6l5a:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6l5a

Go back to Iron Binding Sites List in 6l5a
Iron binding site 1 out of 4 in the The Structure of the Udgx Mutant H109E at A Pre-Excision State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of the Udgx Mutant H109E at A Pre-Excision State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:5.8
occ:1.00
 FE1 A:SF4301 0.0 5.8 1.0
S4 A:SF4301 2.2 5.8 1.0
S3 A:SF4301 2.2 5.1 1.0
S2 A:SF4301 2.2 5.7 1.0
SG A:CYS120 2.3 3.5 1.0
FE2 A:SF4301 2.7 6.1 1.0
FE3 A:SF4301 2.8 6.3 1.0
FE4 A:SF4301 2.8 6.2 1.0
CB A:CYS120 3.2 3.8 1.0
S1 A:SF4301 3.8 5.1 1.0
CA A:CYS120 3.8 3.6 1.0
N A:LYS94 4.1 4.7 1.0
CD1 A:TRP123 4.2 4.8 1.0
CB A:LYS94 4.5 7.7 1.0
NE1 A:TRP123 4.5 4.8 1.0
N A:CYS120 4.6 3.9 1.0
ND1 A:HIS95 4.6 6.6 1.0
SG A:CYS27 4.7 7.0 1.0
SG A:CYS24 4.7 4.2 1.0
CA A:LYS94 4.8 7.8 1.0
N A:HIS95 4.9 4.8 1.0
C A:CYS120 5.0 4.5 1.0
O A:CYS120 5.0 4.8 1.0

Iron binding site 2 out of 4 in 6l5a

Go back to Iron Binding Sites List in 6l5a
Iron binding site 2 out of 4 in the The Structure of the Udgx Mutant H109E at A Pre-Excision State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of the Udgx Mutant H109E at A Pre-Excision State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:6.1
occ:1.00
 FE2 A:SF4301 0.0 6.1 1.0
S3 A:SF4301 2.2 5.1 1.0
S4 A:SF4301 2.2 5.8 1.0
S1 A:SF4301 2.2 5.1 1.0
SG A:CYS24 2.3 4.2 1.0
FE3 A:SF4301 2.7 6.3 1.0
FE1 A:SF4301 2.7 5.8 1.0
FE4 A:SF4301 2.8 6.2 1.0
CB A:CYS24 3.2 5.5 1.0
N A:GLY26 3.7 3.7 1.0
S2 A:SF4301 3.8 5.7 1.0
NE1 A:TRP123 4.0 4.8 1.0
C A:CYS24 4.1 4.6 1.0
CA A:GLY26 4.1 5.9 1.0
O A:CYS24 4.2 6.5 1.0
CA A:CYS24 4.3 6.0 1.0
N A:CYS27 4.3 7.0 1.0
CB A:ALA4 4.4 5.4 1.0
ND1 A:HIS95 4.5 6.6 1.0
N A:ARG25 4.6 4.7 1.0
C A:GLY26 4.6 6.9 1.0
CD1 A:TRP123 4.6 4.8 1.0
SG A:CYS120 4.7 3.5 1.0
C A:ARG25 4.8 4.8 1.0
CE1 A:HIS95 4.8 7.8 1.0
SG A:CYS27 4.9 7.0 1.0
CA A:ARG25 5.0 6.0 1.0

Iron binding site 3 out of 4 in 6l5a

Go back to Iron Binding Sites List in 6l5a
Iron binding site 3 out of 4 in the The Structure of the Udgx Mutant H109E at A Pre-Excision State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of the Udgx Mutant H109E at A Pre-Excision State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:6.3
occ:1.00
 FE3 A:SF4301 0.0 6.3 1.0
ND1 A:HIS95 2.1 6.6 1.0
S2 A:SF4301 2.2 5.7 1.0
S4 A:SF4301 2.2 5.8 1.0
S1 A:SF4301 2.2 5.1 1.0
FE2 A:SF4301 2.7 6.1 1.0
FE4 A:SF4301 2.8 6.2 1.0
FE1 A:SF4301 2.8 5.8 1.0
CE1 A:HIS95 2.9 7.8 1.0
CG A:HIS95 3.2 7.7 1.0
CB A:HIS95 3.6 4.3 1.0
S3 A:SF4301 3.8 5.1 1.0
NE2 A:HIS95 4.1 8.0 1.0
N A:HIS95 4.1 4.8 1.0
CD2 A:HIS95 4.2 6.5 1.0
N A:TYR30 4.4 8.5 1.0
CA A:HIS95 4.5 5.7 1.0
C A:LYS94 4.6 5.2 1.0
SG A:CYS27 4.6 7.0 1.0
CB A:TYR30 4.7 6.1 1.0
CA A:TYR30 4.7 8.0 1.0
SG A:CYS24 4.7 4.2 1.0
CB A:CYS24 4.8 5.5 1.0
SG A:CYS120 4.8 3.5 1.0
CB A:LEU29 4.8 5.8 1.0
O A:CYS24 4.8 6.5 1.0
CB A:LYS94 4.9 7.7 1.0
C A:LEU29 4.9 6.2 1.0
N A:LYS94 5.0 4.7 1.0

Iron binding site 4 out of 4 in 6l5a

Go back to Iron Binding Sites List in 6l5a
Iron binding site 4 out of 4 in the The Structure of the Udgx Mutant H109E at A Pre-Excision State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of the Udgx Mutant H109E at A Pre-Excision State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:6.2
occ:1.00
 FE4 A:SF4301 0.0 6.2 1.0
S1 A:SF4301 2.2 5.1 1.0
S3 A:SF4301 2.2 5.1 1.0
S2 A:SF4301 2.2 5.7 1.0
SG A:CYS27 2.2 7.0 1.0
FE3 A:SF4301 2.8 6.3 1.0
FE2 A:SF4301 2.8 6.1 1.0
FE1 A:SF4301 2.8 5.8 1.0
CB A:CYS27 3.3 4.7 1.0
N A:CYS27 3.4 7.0 1.0
CA A:CYS27 3.8 5.8 1.0
S4 A:SF4301 3.8 5.8 1.0
C A:CYS27 4.1 6.7 1.0
C A:GLY26 4.2 6.9 1.0
O A:CYS27 4.3 9.0 1.0
CB A:LEU29 4.5 5.8 1.0
N A:LEU29 4.6 5.2 1.0
ND1 A:HIS95 4.7 6.6 1.0
N A:GLY26 4.7 3.7 1.0
CA A:GLY26 4.7 5.9 1.0
SG A:CYS120 4.8 3.5 1.0
N A:GLY28 4.8 4.5 1.0
SG A:CYS24 4.9 4.2 1.0
O A:GLY26 4.9 8.8 1.0
CB A:CYS120 5.0 3.8 1.0
N A:TYR30 5.0 8.5 1.0
CG A:LEU29 5.0 3.2 1.0

Reference:

W.Xie, J.Tu, H.Zeng. Structure of An Covalent Complex-Forming Udgx Mutant To Be Published.
Page generated: Wed Aug 7 00:39:57 2024

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