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Iron in PDB 4r7w: Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine

Enzymatic activity of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine

All present enzymatic activity of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine:
3.5.4.1;

Protein crystallography data

The structure of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine, PDB code: 4r7w was solved by A.A.Fedorov, E.V.Fedorov, D.S.Hitchcock, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.78 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.167, 147.808, 185.336, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24.2

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine (pdb code 4r7w). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine, PDB code: 4r7w:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4r7w

Go back to Iron Binding Sites List in 4r7w
Iron binding site 1 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:15.5
occ:0.93
O4 A:O7U502 2.1 7.6 1.0
NE2 A:HIS56 2.3 14.4 1.0
NE2 A:HIS58 2.4 18.7 1.0
OD2 A:ASP308 2.4 16.7 1.0
NE2 A:HIS209 2.4 9.0 1.0
CD2 A:HIS58 3.0 18.5 1.0
CD2 A:HIS56 3.2 10.6 1.0
CG A:ASP308 3.2 22.3 1.0
CD2 A:HIS209 3.3 9.4 1.0
CE1 A:HIS209 3.3 14.9 1.0
CE1 A:HIS56 3.3 11.7 1.0
OD1 A:ASP308 3.4 23.2 1.0
P4 A:O7U502 3.4 10.9 1.0
CE1 A:HIS58 3.6 16.4 1.0
NE2 A:HIS241 3.6 12.6 1.0
C5 A:O7U502 3.7 8.8 1.0
N3 A:O7U502 4.0 8.9 1.0
CG A:HIS58 4.3 11.7 1.0
C6 A:O7U502 4.3 8.2 1.0
CG A:HIS56 4.4 11.1 1.0
ND1 A:HIS209 4.4 13.9 1.0
ND1 A:HIS56 4.4 9.2 1.0
CG A:HIS209 4.4 11.4 1.0
CE1 A:HIS241 4.4 16.5 1.0
CD2 A:HIS241 4.5 13.4 1.0
ND1 A:HIS58 4.5 12.4 1.0
N4 A:O7U502 4.6 8.5 1.0
CB A:ASP308 4.6 7.5 1.0
C2 A:O7U502 4.7 9.4 1.0
N1 A:O7U502 4.8 9.3 1.0
O A:ASP308 4.9 8.6 1.0
CD2 A:HIS117 4.9 8.1 1.0
CA A:ASP308 5.0 7.6 1.0

Iron binding site 2 out of 6 in 4r7w

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Iron binding site 2 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:18.7
occ:1.00
O4 B:O7U502 2.2 15.2 1.0
NE2 B:HIS56 2.3 13.6 1.0
NE2 B:HIS58 2.3 12.7 1.0
OD2 B:ASP308 2.4 16.1 1.0
NE2 B:HIS209 2.5 13.2 1.0
CD2 B:HIS58 3.1 11.5 1.0
CG B:ASP308 3.2 19.5 1.0
CD2 B:HIS56 3.2 9.1 1.0
CD2 B:HIS209 3.3 11.0 1.0
P4 B:O7U502 3.3 13.8 1.0
CE1 B:HIS56 3.3 14.3 1.0
OD1 B:ASP308 3.3 21.0 1.0
CE1 B:HIS58 3.4 11.8 1.0
CE1 B:HIS209 3.5 10.8 1.0
NE2 B:HIS241 3.6 15.1 1.0
C5 B:O7U502 3.7 9.0 1.0
N3 B:O7U502 4.0 12.1 1.0
CG B:HIS58 4.3 16.4 1.0
C6 B:O7U502 4.3 14.0 1.0
ND1 B:HIS56 4.4 11.4 1.0
CG B:HIS56 4.4 12.5 1.0
CE1 B:HIS241 4.4 10.3 1.0
CG B:HIS209 4.4 11.5 1.0
ND1 B:HIS58 4.5 12.6 1.0
N4 B:O7U502 4.5 12.4 1.0
CD2 B:HIS241 4.5 12.5 1.0
ND1 B:HIS209 4.5 10.7 1.0
CB B:ASP308 4.6 14.6 1.0
C2 B:O7U502 4.6 10.5 1.0
N1 B:O7U502 4.8 10.7 1.0
CA B:ASP308 5.0 11.2 1.0

Iron binding site 3 out of 6 in 4r7w

Go back to Iron Binding Sites List in 4r7w
Iron binding site 3 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:21.8
occ:1.00
O4 C:O7U502 2.2 14.4 1.0
NE2 C:HIS56 2.3 9.9 1.0
NE2 C:HIS58 2.3 11.4 1.0
NE2 C:HIS209 2.4 10.5 1.0
OD2 C:ASP308 2.5 11.5 1.0
CD2 C:HIS58 3.1 19.0 1.0
CG C:ASP308 3.2 20.6 1.0
CD2 C:HIS56 3.2 10.1 1.0
OD1 C:ASP308 3.2 22.6 1.0
P4 C:O7U502 3.3 13.2 1.0
CE1 C:HIS56 3.3 9.7 1.0
CD2 C:HIS209 3.4 13.7 1.0
CE1 C:HIS209 3.4 12.3 1.0
CE1 C:HIS58 3.5 11.4 1.0
C5 C:O7U502 3.6 10.3 1.0
NE2 C:HIS241 3.7 14.7 1.0
N3 C:O7U502 4.0 13.0 1.0
C6 C:O7U502 4.3 16.1 1.0
CG C:HIS58 4.3 13.5 1.0
CG C:HIS56 4.4 14.7 1.0
ND1 C:HIS56 4.4 11.1 1.0
ND1 C:HIS209 4.5 13.2 1.0
ND1 C:HIS58 4.5 11.9 1.0
CG C:HIS209 4.5 9.7 1.0
N4 C:O7U502 4.5 12.7 1.0
CE1 C:HIS241 4.6 11.0 1.0
CB C:ASP308 4.6 20.4 1.0
CD2 C:HIS241 4.6 12.1 1.0
C2 C:O7U502 4.6 17.0 1.0
N1 C:O7U502 4.8 18.2 1.0
CD2 C:HIS117 5.0 15.2 1.0
CA C:ASP308 5.0 12.7 1.0

Iron binding site 4 out of 6 in 4r7w

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Iron binding site 4 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:22.7
occ:1.00
O4 D:O7U502 2.2 11.9 1.0
NE2 D:HIS58 2.3 11.5 1.0
NE2 D:HIS56 2.3 16.6 1.0
OD2 D:ASP308 2.4 18.4 1.0
NE2 D:HIS209 2.4 10.4 1.0
CD2 D:HIS58 3.0 11.6 1.0
CG D:ASP308 3.1 20.8 1.0
OD1 D:ASP308 3.1 26.9 1.0
CD2 D:HIS56 3.1 11.8 1.0
P4 D:O7U502 3.2 13.8 1.0
CD2 D:HIS209 3.3 15.0 1.0
CE1 D:HIS56 3.4 8.8 1.0
C5 D:O7U502 3.4 18.2 1.0
CE1 D:HIS58 3.4 11.1 1.0
CE1 D:HIS209 3.4 9.0 1.0
NE2 D:HIS241 3.6 10.5 1.0
N3 D:O7U502 4.0 15.5 1.0
C6 D:O7U502 4.1 15.0 1.0
CG D:HIS58 4.3 10.5 1.0
CG D:HIS56 4.3 12.5 1.0
CE1 D:HIS241 4.4 14.4 1.0
N4 D:O7U502 4.4 9.7 1.0
ND1 D:HIS56 4.4 14.8 1.0
ND1 D:HIS58 4.4 10.5 1.0
CG D:HIS209 4.5 15.7 1.0
CB D:ASP308 4.5 12.4 1.0
ND1 D:HIS209 4.5 13.7 1.0
CD2 D:HIS241 4.6 8.2 1.0
C2 D:O7U502 4.7 16.4 1.0
N1 D:O7U502 4.7 9.8 1.0
CA D:ASP308 5.0 15.4 1.0

Iron binding site 5 out of 6 in 4r7w

Go back to Iron Binding Sites List in 4r7w
Iron binding site 5 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:18.9
occ:1.00
O4 E:O7U502 2.3 11.2 1.0
NE2 E:HIS56 2.3 8.2 1.0
NE2 E:HIS58 2.4 11.8 1.0
NE2 E:HIS209 2.5 11.5 1.0
OD2 E:ASP308 2.5 14.2 1.0
CD2 E:HIS58 3.1 11.4 1.0
CD2 E:HIS56 3.2 10.0 1.0
CG E:ASP308 3.2 19.9 1.0
OD1 E:ASP308 3.2 20.0 1.0
CD2 E:HIS209 3.3 14.3 1.0
CE1 E:HIS56 3.3 14.2 1.0
P4 E:O7U502 3.3 13.1 1.0
CE1 E:HIS209 3.4 11.0 1.0
CE1 E:HIS58 3.5 10.3 1.0
C5 E:O7U502 3.6 18.2 1.0
NE2 E:HIS241 3.7 10.7 1.0
N3 E:O7U502 4.2 9.2 1.0
C6 E:O7U502 4.3 15.1 1.0
CG E:HIS58 4.4 9.7 1.0
CG E:HIS56 4.4 10.3 1.0
ND1 E:HIS56 4.4 10.4 1.0
CG E:HIS209 4.5 16.1 1.0
ND1 E:HIS209 4.5 10.7 1.0
ND1 E:HIS58 4.5 10.4 1.0
N4 E:O7U502 4.5 12.1 1.0
CE1 E:HIS241 4.5 17.4 1.0
CD2 E:HIS241 4.6 10.3 1.0
CB E:ASP308 4.6 8.3 1.0
C2 E:O7U502 4.8 12.6 1.0
N1 E:O7U502 4.9 14.0 1.0
CD2 E:HIS117 4.9 10.5 1.0
CA E:ASP308 5.0 9.2 1.0

Iron binding site 6 out of 6 in 4r7w

Go back to Iron Binding Sites List in 4r7w
Iron binding site 6 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:16.9
occ:0.79
O4 F:O7U502 2.2 12.4 1.0
NE2 F:HIS56 2.3 16.2 1.0
NE2 F:HIS58 2.4 21.9 1.0
NE2 F:HIS209 2.5 14.6 1.0
OD2 F:ASP308 2.6 26.1 1.0
CD2 F:HIS58 3.0 23.4 1.0
P4 F:O7U502 3.2 14.8 1.0
CD2 F:HIS56 3.2 21.9 1.0
CG F:ASP308 3.3 26.7 1.0
C5 F:O7U502 3.3 16.6 1.0
OD1 F:ASP308 3.3 32.0 1.0
CD2 F:HIS209 3.3 12.9 1.0
CE1 F:HIS56 3.3 16.1 1.0
CE1 F:HIS209 3.5 12.9 1.0
CE1 F:HIS58 3.6 22.6 1.0
NE2 F:HIS241 3.7 16.7 1.0
C6 F:O7U502 4.0 18.9 1.0
N3 F:O7U502 4.1 14.8 1.0
CG F:HIS58 4.3 13.4 1.0
CG F:HIS56 4.4 12.2 1.0
N4 F:O7U502 4.4 14.4 1.0
ND1 F:HIS56 4.4 15.5 1.0
CG F:HIS209 4.5 13.1 1.0
ND1 F:HIS58 4.5 14.8 1.0
CD2 F:HIS241 4.5 14.1 1.0
CE1 F:HIS241 4.5 15.5 1.0
ND1 F:HIS209 4.5 11.8 1.0
N1 F:O7U502 4.6 16.9 1.0
CB F:ASP308 4.6 18.5 1.0
C2 F:O7U502 4.7 11.9 1.0
CD2 F:HIS117 5.0 13.2 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, D.S.Hitchcock, F.M.Raushel, S.C.Almo. Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with Phosphonocytosine To Be Published.
Page generated: Mon Aug 5 09:09:59 2024

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