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Manganese in PDB 8zrl: Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor

Enzymatic activity of Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor

All present enzymatic activity of Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor:
1.1.1.244;

Protein crystallography data

The structure of Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor, PDB code: 8zrl was solved by B.D.Ma, M.J.Zhang, X.D.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.51 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.571, 204.41, 258.145, 90, 90, 90
R / Rfree (%) 19.3 / 24

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor (pdb code 8zrl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor, PDB code: 8zrl:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 8zrl

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Manganese binding site 1 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:23.5
occ:1.00
 NE2 A:HIS200 2.1 26.7 1.0
OD1 A:ASP196 2.2 26.4 1.0
O A:HOH616 2.3 22.2 1.0
NE2 A:HIS265 2.3 23.4 1.0
NE2 A:HIS279 2.4 28.2 1.0
O A:HOH508 2.6 30.7 1.0
CG A:ASP196 2.9 27.2 1.0
CE1 A:HIS200 3.0 24.4 1.0
OD2 A:ASP196 3.0 29.0 1.0
CD2 A:HIS279 3.1 28.0 1.0
CD2 A:HIS265 3.1 24.2 1.0
CD2 A:HIS200 3.2 24.8 1.0
CE1 A:HIS265 3.3 22.4 1.0
CE1 A:HIS279 3.5 29.4 1.0
ND2 A:ASN283 3.8 24.0 1.0
ND1 A:HIS200 4.1 21.8 1.0
O A:HOH561 4.1 24.4 1.0
CG A:HIS200 4.2 24.9 1.0
CG A:HIS279 4.3 26.3 1.0
CG A:HIS265 4.3 24.0 1.0
ND1 A:HIS265 4.4 19.3 1.0
CB A:ASP196 4.4 24.0 1.0
ND1 A:HIS279 4.5 27.9 1.0
O A:ASP196 4.6 25.4 1.0
O1D A:APR402 4.6 23.2 1.0
CG A:ASN283 5.0 30.0 1.0
CA A:ASP196 5.0 25.4 1.0

Manganese binding site 2 out of 10 in 8zrl

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Manganese binding site 2 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:25.2
occ:1.00
 O B:HOH586 2.1 25.2 1.0
NE2 B:HIS200 2.2 26.9 1.0
O B:HOH502 2.3 30.0 1.0
OD1 B:ASP196 2.4 24.8 1.0
NE2 B:HIS265 2.4 21.8 1.0
NE2 B:HIS279 2.4 28.9 1.0
OD2 B:ASP196 2.8 30.1 1.0
CG B:ASP196 3.0 26.6 1.0
CE1 B:HIS200 3.0 23.5 1.0
CD2 B:HIS265 3.1 25.9 1.0
CD2 B:HIS200 3.2 22.6 1.0
CD2 B:HIS279 3.3 23.7 1.0
CE1 B:HIS279 3.4 28.5 1.0
CE1 B:HIS265 3.5 25.0 1.0
ND2 B:ASN283 3.9 18.6 1.0
O B:HOH521 4.1 27.7 1.0
ND1 B:HIS200 4.2 24.5 1.0
O1D B:APR402 4.3 37.8 1.0
CG B:HIS200 4.3 25.1 1.0
CG B:HIS265 4.4 28.3 1.0
CG B:HIS279 4.4 23.3 1.0
ND1 B:HIS279 4.4 30.0 1.0
CB B:ASP196 4.5 26.6 1.0
ND1 B:HIS265 4.5 26.6 1.0
O B:ASP196 4.7 20.6 1.0
CA B:THR144 4.9 25.0 1.0

Manganese binding site 3 out of 10 in 8zrl

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Manganese binding site 3 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor


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 Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:33.4
occ:1.00
 NE2 C:HIS200 2.1 33.6 1.0
NE2 C:HIS279 2.2 34.2 1.0
OD1 C:ASP196 2.2 36.5 1.0
O C:HOH512 2.3 30.5 1.0
NE2 C:HIS265 2.3 33.9 1.0
CE1 C:HIS200 3.0 32.6 1.0
CD2 C:HIS279 3.0 33.4 1.0
CG C:ASP196 3.1 35.7 1.0
CD2 C:HIS200 3.2 29.9 1.0
OD2 C:ASP196 3.2 28.3 1.0
CD2 C:HIS265 3.2 31.7 1.0
CE1 C:HIS279 3.3 33.8 1.0
CE1 C:HIS265 3.3 33.9 1.0
ND2 C:ASN283 3.9 34.6 1.0
ND1 C:HIS200 4.1 29.9 1.0
CG C:HIS200 4.2 31.2 1.0
CG C:HIS279 4.2 30.9 1.0
ND1 C:HIS279 4.3 36.1 1.0
O1D C:APR402 4.3 33.0 1.0
CG C:HIS265 4.4 35.9 1.0
ND1 C:HIS265 4.4 35.2 1.0
CB C:ASP196 4.5 32.5 1.0
O C:ASP196 4.6 27.9 1.0

Manganese binding site 4 out of 10 in 8zrl

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Manganese binding site 4 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor


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 Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:45.0
occ:1.00
 NE2 D:HIS265 2.1 43.7 1.0
NE2 D:HIS200 2.2 40.6 1.0
OD1 D:ASP196 2.2 31.8 1.0
NE2 D:HIS279 2.4 45.2 1.0
CD2 D:HIS265 3.0 36.7 1.0
CG D:ASP196 3.0 36.1 1.0
CE1 D:HIS200 3.1 34.1 1.0
CD2 D:HIS279 3.1 44.6 1.0
OD2 D:ASP196 3.1 38.3 1.0
CE1 D:HIS265 3.2 37.9 1.0
CD2 D:HIS200 3.3 33.4 1.0
CE1 D:HIS279 3.6 43.7 1.0
ND2 D:ASN283 3.8 43.0 1.0
ND1 D:HIS200 4.2 37.5 1.0
CG D:HIS265 4.2 40.7 1.0
ND1 D:HIS265 4.3 37.4 1.0
CG D:HIS200 4.3 34.3 1.0
CG D:HIS279 4.4 48.3 1.0
CB D:ASP196 4.5 35.3 1.0
ND1 D:HIS279 4.6 53.0 1.0
O1D D:APR402 4.7 65.3 1.0
O D:ASP196 4.7 31.9 1.0
CG D:ASN283 4.9 39.9 1.0

Manganese binding site 5 out of 10 in 8zrl

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Manganese binding site 5 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor


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 Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn401

b:42.7
occ:1.00
 OD1 E:ASP196 2.2 43.8 1.0
NE2 E:HIS265 2.2 46.8 1.0
NE2 E:HIS200 2.2 40.1 1.0
NE2 E:HIS279 2.4 48.5 1.0
CG E:ASP196 2.9 41.9 1.0
CE1 E:HIS200 3.0 37.5 1.0
CD2 E:HIS279 3.0 43.7 1.0
OD2 E:ASP196 3.0 41.8 1.0
CE1 E:HIS265 3.1 46.6 1.0
CD2 E:HIS265 3.2 50.2 1.0
CD2 E:HIS200 3.3 38.6 1.0
CE1 E:HIS279 3.5 50.4 1.0
ND2 E:ASN283 3.9 41.7 1.0
ND1 E:HIS200 4.1 42.4 1.0
ND1 E:HIS265 4.2 46.1 1.0
CG E:HIS279 4.3 47.4 1.0
CG E:HIS200 4.3 37.6 1.0
CG E:HIS265 4.3 46.2 1.0
CB E:ASP196 4.4 43.2 1.0
O1D E:APR402 4.5 55.2 1.0
ND1 E:HIS279 4.5 51.5 1.0
O E:ASP196 4.6 30.9 1.0
CA E:THR144 4.9 45.8 1.0

Manganese binding site 6 out of 10 in 8zrl

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Manganese binding site 6 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor


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 Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn401

b:22.2
occ:1.00
 O F:HOH593 2.2 24.1 1.0
NE2 F:HIS265 2.2 26.3 1.0
NE2 F:HIS200 2.2 28.9 1.0
OD1 F:ASP196 2.2 18.3 1.0
O F:HOH513 2.2 31.5 1.0
NE2 F:HIS279 2.5 28.2 1.0
CE1 F:HIS200 2.9 28.3 1.0
CG F:ASP196 3.0 24.6 1.0
CD2 F:HIS265 3.0 22.2 1.0
CD2 F:HIS279 3.1 27.7 1.0
OD2 F:ASP196 3.1 27.5 1.0
CD2 F:HIS200 3.2 23.4 1.0
CE1 F:HIS265 3.3 23.2 1.0
CE1 F:HIS279 3.7 30.3 1.0
ND2 F:ASN283 3.9 19.6 1.0
ND1 F:HIS200 4.0 24.7 1.0
O F:HOH554 4.1 27.7 1.0
CG F:HIS200 4.2 23.6 1.0
CG F:HIS265 4.3 26.3 1.0
ND1 F:HIS265 4.3 22.1 1.0
O F:HOH586 4.4 31.8 1.0
CG F:HIS279 4.4 32.7 1.0
CB F:ASP196 4.5 20.6 1.0
O1D F:APR402 4.5 34.2 1.0
O F:ASP196 4.6 25.2 1.0
ND1 F:HIS279 4.6 30.2 1.0

Manganese binding site 7 out of 10 in 8zrl

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Manganese binding site 7 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor


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 Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn401

b:43.3
occ:1.00
 NE2 G:HIS200 2.0 39.0 1.0
NE2 G:HIS279 2.2 44.3 1.0
OD1 G:ASP196 2.3 43.9 1.0
NE2 G:HIS265 2.4 44.3 1.0
CE1 G:HIS200 2.9 39.2 1.0
CG G:ASP196 3.1 44.7 1.0
CD2 G:HIS200 3.1 37.9 1.0
CE1 G:HIS279 3.1 46.2 1.0
CD2 G:HIS265 3.2 41.0 1.0
OD2 G:ASP196 3.2 45.6 1.0
CD2 G:HIS279 3.3 42.4 1.0
CE1 G:HIS265 3.4 44.3 1.0
ND2 G:ASN283 3.9 40.0 1.0
ND1 G:HIS200 4.0 35.4 1.0
CG G:HIS200 4.2 36.5 1.0
ND1 G:HIS279 4.3 47.8 1.0
CG G:HIS279 4.4 45.0 1.0
CG G:HIS265 4.4 39.2 1.0
ND1 G:HIS265 4.5 34.3 1.0
CB G:ASP196 4.5 38.6 1.0
O G:ASP196 4.6 38.5 1.0
O3D G:APR402 4.9 49.3 1.0
CG G:ASN283 5.0 40.7 1.0

Manganese binding site 8 out of 10 in 8zrl

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Manganese binding site 8 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor


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 Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn401

b:41.4
occ:1.00
 NE2 H:HIS200 2.1 46.6 1.0
NE2 H:HIS265 2.1 52.9 1.0
OD1 H:ASP196 2.2 45.2 1.0
NE2 H:HIS279 2.3 49.7 1.0
CE1 H:HIS265 3.0 47.3 1.0
CE1 H:HIS200 3.0 47.0 1.0
CG H:ASP196 3.0 49.7 1.0
CD2 H:HIS279 3.1 51.0 1.0
OD2 H:ASP196 3.1 41.3 1.0
CD2 H:HIS200 3.1 45.8 1.0
CD2 H:HIS265 3.2 45.9 1.0
CE1 H:HIS279 3.4 48.6 1.0
ND2 H:ASN283 3.9 46.2 1.0
ND1 H:HIS200 4.1 47.4 1.0
ND1 H:HIS265 4.1 46.5 1.0
CG H:HIS200 4.2 44.1 1.0
CG H:HIS265 4.3 48.1 1.0
CG H:HIS279 4.3 50.0 1.0
ND1 H:HIS279 4.4 56.6 1.0
CB H:ASP196 4.5 44.7 1.0
O H:ASP196 4.6 42.3 1.0
O1D H:APR402 4.6 48.8 1.0

Manganese binding site 9 out of 10 in 8zrl

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Manganese binding site 9 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn401

b:33.0
occ:1.00
 NE2 I:HIS265 2.2 28.8 1.0
NE2 I:HIS200 2.3 31.0 1.0
OD1 I:ASP196 2.4 36.2 1.0
NE2 I:HIS279 2.5 35.2 1.0
OD2 I:ASP196 3.0 35.4 1.0
CE1 I:HIS200 3.1 27.7 1.0
CG I:ASP196 3.1 32.5 1.0
CD2 I:HIS279 3.1 30.0 1.0
CD2 I:HIS265 3.2 25.9 1.0
CE1 I:HIS265 3.2 28.9 1.0
CD2 I:HIS200 3.3 27.1 1.0
CE1 I:HIS279 3.6 32.5 1.0
ND2 I:ASN283 3.9 29.7 1.0
ND1 I:HIS200 4.2 31.0 1.0
O1D I:APR402 4.3 36.9 1.0
ND1 I:HIS265 4.3 23.7 1.0
CG I:HIS265 4.4 29.4 1.0
CG I:HIS200 4.4 29.0 1.0
CG I:HIS279 4.4 34.0 1.0
ND1 I:HIS279 4.6 37.5 1.0
CB I:ASP196 4.6 24.1 1.0
O I:ASP196 4.8 25.9 1.0

Manganese binding site 10 out of 10 in 8zrl

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Manganese binding site 10 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn401

b:31.9
occ:1.00
 O J:HOH534 2.0 38.6 1.0
NE2 J:HIS265 2.1 31.8 1.0
NE2 J:HIS200 2.2 32.3 1.0
OD1 J:ASP196 2.2 30.1 1.0
NE2 J:HIS279 2.5 33.4 1.0
CG J:ASP196 3.0 29.0 1.0
CD2 J:HIS265 3.1 29.6 1.0
OD2 J:ASP196 3.1 35.0 1.0
CE1 J:HIS200 3.1 31.5 1.0
CD2 J:HIS200 3.1 26.3 1.0
CE1 J:HIS265 3.2 28.8 1.0
CD2 J:HIS279 3.3 35.6 1.0
CE1 J:HIS279 3.5 36.8 1.0
ND2 J:ASN283 3.7 33.4 1.0
O J:HOH546 4.1 38.5 1.0
ND1 J:HIS200 4.2 27.6 1.0
CG J:HIS200 4.2 28.4 1.0
CG J:HIS265 4.2 35.1 1.0
ND1 J:HIS265 4.2 28.3 1.0
CB J:ASP196 4.5 31.5 1.0
CG J:HIS279 4.5 40.3 1.0
O1D J:APR402 4.5 35.5 1.0
O J:ASP196 4.5 28.3 1.0
ND1 J:HIS279 4.6 42.6 1.0
CG J:ASN283 4.9 31.9 1.0

Reference:

B.D.Ma, X.D.Kong. Crystal Structure of Methanol DEHYDROGENASE2 From Bacillus Methanolicus Complexed with An Inhibitor To Be Published.
Page generated: Sun Aug 17 02:06:26 2025

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