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Manganese in PDB 6ie2: Crystal Structure of Methyladenine Demethylase

Enzymatic activity of Crystal Structure of Methyladenine Demethylase

All present enzymatic activity of Crystal Structure of Methyladenine Demethylase:
1.14.11.51;

Protein crystallography data

The structure of Crystal Structure of Methyladenine Demethylase, PDB code: 6ie2 was solved by L.F.Tian, Q.Tang, Z.Z.Chen, X.X.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 89.017, 99.170, 126.793, 106.60, 90.42, 93.14
R / Rfree (%) 21.6 / 25.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Methyladenine Demethylase (pdb code 6ie2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Methyladenine Demethylase, PDB code: 6ie2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6ie2

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Manganese binding site 1 out of 8 in the Crystal Structure of Methyladenine Demethylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Methyladenine Demethylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn400

b:19.9
occ:1.00
 OD2 A:ASP233 2.0 21.0 1.0
O5 A:AKG401 2.1 29.1 1.0
NE2 A:HIS287 2.1 22.4 1.0
NE2 A:HIS231 2.1 22.5 1.0
O2 A:AKG401 2.2 30.6 1.0
C2 A:AKG401 2.8 30.3 1.0
C1 A:AKG401 2.9 31.2 1.0
CE1 A:HIS287 3.0 22.7 1.0
CE1 A:HIS231 3.0 22.6 1.0
CG A:ASP233 3.1 21.2 1.0
CD2 A:HIS287 3.1 22.7 1.0
CD2 A:HIS231 3.1 22.5 1.0
OD1 A:ASP233 3.5 20.9 1.0
ND1 A:HIS287 4.1 22.7 1.0
ND1 A:HIS231 4.1 22.2 1.0
O1 A:AKG401 4.1 31.4 1.0
CG A:HIS287 4.2 22.9 1.0
CG A:HIS231 4.2 21.9 1.0
C3 A:AKG401 4.3 29.9 1.0
CB A:ASP233 4.4 21.9 1.0
NH2 A:ARG344 4.6 26.4 1.0
C4 A:AKG401 4.8 29.9 1.0

Manganese binding site 2 out of 8 in 6ie2

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Manganese binding site 2 out of 8 in the Crystal Structure of Methyladenine Demethylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Methyladenine Demethylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn400

b:23.7
occ:1.00
 OD2 B:ASP233 1.8 30.1 1.0
NE2 B:HIS231 2.1 21.2 1.0
NE2 B:HIS287 2.1 23.9 1.0
O5 B:AKG401 2.1 28.9 1.0
O2 B:AKG401 2.2 30.2 1.0
CE1 B:HIS287 2.8 24.1 1.0
C2 B:AKG401 2.8 28.7 1.0
C1 B:AKG401 2.9 28.9 1.0
CG B:ASP233 2.9 30.0 1.0
CD2 B:HIS231 3.0 21.8 1.0
CE1 B:HIS231 3.1 21.5 1.0
CD2 B:HIS287 3.2 23.1 1.0
OD1 B:ASP233 3.4 30.1 1.0
ND1 B:HIS287 4.0 23.5 1.0
O1 B:AKG401 4.1 28.2 1.0
CG B:HIS231 4.1 21.4 1.0
ND1 B:HIS231 4.1 21.3 1.0
CB B:ASP233 4.2 30.1 1.0
CG B:HIS287 4.2 22.7 1.0
C3 B:AKG401 4.3 28.2 1.0
NH2 B:ARG344 4.4 24.4 1.0
CD1 B:LEU243 4.5 33.4 1.0
O B:HOH514 4.7 24.1 1.0
N B:ASP233 4.8 28.5 1.0
C4 B:AKG401 4.9 27.6 1.0

Manganese binding site 3 out of 8 in 6ie2

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Manganese binding site 3 out of 8 in the Crystal Structure of Methyladenine Demethylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Methyladenine Demethylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn400

b:19.8
occ:1.00
 OD2 C:ASP233 1.9 29.7 1.0
O2 C:AKG401 2.0 25.2 1.0
O5 C:AKG401 2.0 27.4 1.0
NE2 C:HIS287 2.1 23.2 1.0
NE2 C:HIS231 2.1 29.2 1.0
C2 C:AKG401 2.5 27.2 1.0
C1 C:AKG401 2.6 26.4 1.0
CE1 C:HIS287 3.0 23.1 1.0
CD2 C:HIS231 3.0 28.2 1.0
CG C:ASP233 3.0 28.2 1.0
CD2 C:HIS287 3.1 23.5 1.0
CE1 C:HIS231 3.2 29.3 1.0
OD1 C:ASP233 3.5 28.9 1.0
C3 C:AKG401 3.8 27.9 1.0
O1 C:AKG401 3.8 24.9 1.0
ND1 C:HIS287 4.1 23.1 1.0
CG C:HIS231 4.2 27.2 1.0
ND1 C:HIS231 4.2 28.6 1.0
CG C:HIS287 4.2 23.0 1.0
CB C:ASP233 4.3 27.6 1.0
NH2 C:ARG344 4.4 29.3 1.0
O C:HOH545 4.7 29.1 1.0
N C:ASP233 4.9 26.5 1.0
CD1 C:LEU243 5.0 36.6 1.0
C4 C:AKG401 5.0 28.2 1.0

Manganese binding site 4 out of 8 in 6ie2

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Manganese binding site 4 out of 8 in the Crystal Structure of Methyladenine Demethylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Methyladenine Demethylase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn400

b:19.1
occ:1.00
 OD2 D:ASP233 2.0 34.7 1.0
NE2 D:HIS231 2.0 23.8 1.0
O2 D:AKG401 2.0 35.4 1.0
NE2 D:HIS287 2.2 23.1 1.0
O5 D:AKG401 2.2 35.9 1.0
C1 D:AKG401 2.8 35.1 1.0
C2 D:AKG401 2.9 35.8 1.0
CE1 D:HIS231 3.0 24.3 1.0
CD2 D:HIS231 3.0 24.6 1.0
CD2 D:HIS287 3.1 22.5 1.0
CG D:ASP233 3.1 34.9 1.0
CE1 D:HIS287 3.1 22.9 1.0
OD1 D:ASP233 3.7 34.0 1.0
O1 D:AKG401 4.0 34.4 1.0
ND1 D:HIS231 4.1 24.4 1.0
CG D:HIS231 4.1 24.6 1.0
ND1 D:HIS287 4.2 22.6 1.0
CG D:HIS287 4.2 22.6 1.0
CB D:ASP233 4.3 35.3 1.0
C3 D:AKG401 4.4 36.4 1.0
NH2 D:ARG344 4.5 32.7 1.0
C4 D:AKG401 5.0 37.1 1.0

Manganese binding site 5 out of 8 in 6ie2

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Manganese binding site 5 out of 8 in the Crystal Structure of Methyladenine Demethylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Methyladenine Demethylase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn400

b:36.3
occ:1.00
 OD2 E:ASP233 1.9 50.0 1.0
O5 E:AKG401 2.0 56.9 1.0
NE2 E:HIS287 2.0 36.0 1.0
O1 E:AKG401 2.2 59.3 1.0
NE2 E:HIS231 2.5 42.8 1.0
C2 E:AKG401 2.7 56.8 1.0
C1 E:AKG401 2.8 59.3 1.0
CG E:ASP233 2.9 49.1 1.0
CD2 E:HIS287 2.9 36.7 1.0
CE1 E:HIS287 3.1 36.0 1.0
CE1 E:HIS231 3.2 44.1 1.0
OD1 E:ASP233 3.3 48.1 1.0
CD2 E:HIS231 3.6 43.0 1.0
O2 E:AKG401 4.0 62.3 1.0
CG E:HIS287 4.1 36.5 1.0
ND1 E:HIS287 4.1 36.5 1.0
C3 E:AKG401 4.1 53.7 1.0
CB E:ASP233 4.2 49.8 1.0
ND1 E:HIS231 4.3 43.1 1.0
CG E:HIS231 4.5 43.0 1.0
O E:HOH512 4.6 31.2 1.0
C4 E:AKG401 4.7 50.7 1.0
NH2 E:ARG344 4.9 53.1 1.0

Manganese binding site 6 out of 8 in 6ie2

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Manganese binding site 6 out of 8 in the Crystal Structure of Methyladenine Demethylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Methyladenine Demethylase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn400

b:39.1
occ:1.00
 OD2 F:ASP233 1.8 66.0 1.0
O5 F:AKG401 2.0 70.0 1.0
NE2 F:HIS287 2.2 51.6 1.0
O2 F:AKG401 2.2 62.7 1.0
NE2 F:HIS231 2.4 47.5 1.0
C2 F:AKG401 2.6 67.1 1.0
C1 F:AKG401 2.8 64.6 1.0
CG F:ASP233 2.9 63.2 1.0
CE1 F:HIS231 3.0 48.6 1.0
CE1 F:HIS287 3.1 50.4 1.0
CD2 F:HIS287 3.2 51.1 1.0
OD1 F:ASP233 3.4 62.5 1.0
CD2 F:HIS231 3.6 48.5 1.0
C3 F:AKG401 3.9 67.7 1.0
O1 F:AKG401 4.0 62.9 1.0
CB F:ASP233 4.2 62.7 1.0
ND1 F:HIS287 4.2 49.7 1.0
ND1 F:HIS231 4.3 49.2 1.0
CG F:HIS287 4.3 49.5 1.0
NH2 F:ARG344 4.5 60.1 1.0
CG F:HIS231 4.6 49.0 1.0
C4 F:AKG401 4.8 68.6 1.0

Manganese binding site 7 out of 8 in 6ie2

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Manganese binding site 7 out of 8 in the Crystal Structure of Methyladenine Demethylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Methyladenine Demethylase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn400

b:38.4
occ:1.00
 O5 G:AKG401 1.8 65.7 1.0
NE2 G:HIS287 2.1 47.5 1.0
NE2 G:HIS231 2.2 50.7 1.0
OD2 G:ASP233 2.3 66.1 1.0
O2 G:AKG401 2.3 67.0 1.0
C2 G:AKG401 2.5 66.1 1.0
C1 G:AKG401 2.8 68.7 1.0
CE1 G:HIS287 3.1 47.0 1.0
CE1 G:HIS231 3.1 50.8 1.0
CG G:ASP233 3.1 61.0 1.0
CD2 G:HIS287 3.1 47.2 1.0
CD2 G:HIS231 3.2 51.9 1.0
OD1 G:ASP233 3.3 58.4 1.0
C3 G:AKG401 3.9 65.5 1.0
O1 G:AKG401 4.1 72.3 1.0
ND1 G:HIS287 4.2 46.9 1.0
C4 G:AKG401 4.2 67.8 1.0
NH2 G:ARG344 4.3 52.8 1.0
ND1 G:HIS231 4.3 52.0 1.0
CG G:HIS287 4.3 46.8 1.0
CG G:HIS231 4.3 51.3 1.0
CB G:ASP233 4.6 62.2 1.0

Manganese binding site 8 out of 8 in 6ie2

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Manganese binding site 8 out of 8 in the Crystal Structure of Methyladenine Demethylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Methyladenine Demethylase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn400

b:34.7
occ:1.00
 O5 H:AKG401 2.1 61.2 1.0
NE2 H:HIS287 2.1 46.7 1.0
O2 H:AKG401 2.2 63.8 1.0
OD2 H:ASP233 2.3 67.1 1.0
NE2 H:HIS231 2.4 51.7 1.0
C2 H:AKG401 2.6 62.3 1.0
C1 H:AKG401 2.7 63.9 1.0
OD1 H:ASP233 2.8 62.5 1.0
CE1 H:HIS231 2.9 51.3 1.0
CG H:ASP233 2.9 64.8 1.0
CE1 H:HIS287 3.0 46.2 1.0
CD2 H:HIS287 3.2 46.1 1.0
CD2 H:HIS231 3.5 51.5 1.0
C3 H:AKG401 3.9 59.7 1.0
O1 H:AKG401 4.0 65.1 1.0
ND1 H:HIS231 4.0 52.0 1.0
ND1 H:HIS287 4.1 47.3 1.0
CG H:HIS287 4.2 45.2 1.0
CG H:HIS231 4.3 50.2 1.0
NH2 H:ARG344 4.3 55.5 1.0
CB H:ASP233 4.3 63.8 1.0
C4 H:AKG401 4.9 58.4 1.0

Reference:

L.F.Tian, Q.Tang, Z.Z.Chen, X.X.Yan. Crystal Structure of Methyladenine Demethylase To Be Published.
Page generated: Sun Oct 6 04:52:57 2024

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