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Manganese in PDB 8zwd: Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus

Enzymatic activity of Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus

All present enzymatic activity of Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus:
1.1.1.244;

Protein crystallography data

The structure of Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus, PDB code: 8zwd was solved by B.D.Ma, X.D.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.78 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 256.022, 83.578, 220.557, 90, 90, 90
R / Rfree (%) 21.3 / 26

Other elements in 8zwd:

The structure of Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus (pdb code 8zwd). 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 DEHYDROGENASE1 From Bacillus Methanolicus, PDB code: 8zwd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 8zwd

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Manganese binding site 1 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus


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 Methanol DEHYDROGENASE1 From Bacillus Methanolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:41.8
occ:1.00
 NE2 B:HIS197 2.1 39.8 1.0
NE2 B:HIS276 2.3 40.6 1.0
OD1 B:ASP193 2.3 40.7 1.0
NE2 B:HIS262 2.3 40.2 1.0
OD2 B:ASP193 2.4 41.7 1.0
CG B:ASP193 2.7 42.5 1.0
CD2 B:HIS276 3.0 37.1 1.0
CE1 B:HIS197 3.0 36.5 1.0
CD2 B:HIS262 3.0 36.7 1.0
CD2 B:HIS197 3.2 40.6 1.0
CE1 B:HIS276 3.4 40.6 1.0
CE1 B:HIS262 3.5 41.0 1.0
ND2 B:ASN280 4.1 37.4 1.0
ND1 B:HIS197 4.2 39.3 1.0
CG B:HIS276 4.2 41.7 1.0
CB B:ASP193 4.3 31.4 1.0
CG B:HIS262 4.3 35.2 1.0
CG B:HIS197 4.3 39.9 1.0
ND1 B:HIS276 4.4 43.5 1.0
ND1 B:HIS262 4.5 32.4 1.0
O B:ASP193 4.8 41.4 1.0

Manganese binding site 2 out of 10 in 8zwd

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Manganese binding site 2 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus


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 Methanol DEHYDROGENASE1 From Bacillus Methanolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:48.4
occ:1.00
 NE2 D:HIS262 2.0 46.0 1.0
NE2 D:HIS197 2.3 43.5 1.0
NE2 D:HIS276 2.3 45.5 1.0
OD1 D:ASP193 2.4 42.6 1.0
O D:HOH502 2.7 38.3 1.0
OD2 D:ASP193 2.7 47.3 1.0
CD2 D:HIS262 2.9 50.2 1.0
CG D:ASP193 2.9 42.9 1.0
CE1 D:HIS262 3.0 44.0 1.0
CE1 D:HIS197 3.1 46.5 1.0
CD2 D:HIS276 3.2 44.9 1.0
CE1 D:HIS276 3.3 50.0 1.0
CD2 D:HIS197 3.4 42.0 1.0
CG D:HIS262 4.1 46.8 1.0
ND1 D:HIS262 4.1 46.1 1.0
ND1 D:HIS197 4.2 40.9 1.0
ND2 D:ASN280 4.3 47.5 1.0
CG D:HIS276 4.4 51.6 1.0
ND1 D:HIS276 4.4 57.2 1.0
CG D:HIS197 4.4 39.6 1.0
CB D:ASP193 4.5 37.8 1.0
OG D:SER196 4.7 47.4 1.0
O D:ASP193 4.9 46.2 1.0

Manganese binding site 3 out of 10 in 8zwd

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Manganese binding site 3 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus


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 DEHYDROGENASE1 From Bacillus Methanolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn401

b:43.9
occ:1.00
 NE2 H:HIS262 2.1 47.5 1.0
NE2 H:HIS197 2.2 49.2 1.0
NE2 H:HIS276 2.2 38.9 1.0
OD2 H:ASP193 2.3 49.3 1.0
OD1 H:ASP193 2.5 44.6 1.0
CG H:ASP193 2.7 46.9 1.0
CE1 H:HIS197 3.0 50.8 1.0
CD2 H:HIS262 3.0 47.8 1.0
CD2 H:HIS276 3.0 38.7 1.0
CE1 H:HIS262 3.1 51.2 1.0
CE1 H:HIS276 3.2 44.4 1.0
CD2 H:HIS197 3.3 49.4 1.0
ND2 H:ASN280 4.1 48.0 1.0
ND1 H:HIS197 4.2 48.7 1.0
ND1 H:HIS262 4.2 48.9 1.0
CG H:HIS262 4.2 47.7 1.0
CB H:ASP193 4.2 41.9 1.0
CG H:HIS276 4.2 40.0 1.0
ND1 H:HIS276 4.3 44.1 1.0
CG H:HIS197 4.3 50.0 1.0
O H:ASP193 4.7 41.4 1.0
OG H:SER196 4.7 46.6 1.0
CA H:THR141 5.0 61.2 1.0

Manganese binding site 4 out of 10 in 8zwd

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Manganese binding site 4 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus


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 DEHYDROGENASE1 From Bacillus Methanolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn401

b:53.8
occ:1.00
 NE2 J:HIS262 2.1 51.9 1.0
NE2 J:HIS197 2.3 60.5 1.0
OD1 J:ASP193 2.3 66.3 1.0
OD2 J:ASP193 2.4 59.1 1.0
CG J:ASP193 2.7 65.5 1.0
NE2 J:HIS276 2.7 56.1 1.0
CD2 J:HIS262 3.0 56.2 1.0
CE1 J:HIS197 3.1 64.0 1.0
CD2 J:HIS276 3.1 49.5 1.0
CE1 J:HIS262 3.2 53.4 1.0
CD2 J:HIS197 3.3 56.9 1.0
CE1 J:HIS276 3.9 63.8 1.0
CB J:ASP193 4.2 53.2 1.0
CG J:HIS262 4.2 51.9 1.0
ND2 J:ASN280 4.2 59.4 1.0
ND1 J:HIS262 4.3 51.1 1.0
ND1 J:HIS197 4.3 55.4 1.0
CG J:HIS197 4.4 52.9 1.0
CG J:HIS276 4.4 51.5 1.0
O J:ASP193 4.7 55.3 1.0
ND1 J:HIS276 4.8 60.5 1.0
CA J:ASP193 4.9 54.0 1.0

Manganese binding site 5 out of 10 in 8zwd

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Manganese binding site 5 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus


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 DEHYDROGENASE1 From Bacillus Methanolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn401

b:38.6
occ:1.00
 NE2 E:HIS262 1.8 49.4 1.0
OD1 E:ASP193 2.3 56.3 1.0
NE2 E:HIS197 2.3 46.4 1.0
NE2 E:HIS276 2.5 49.8 1.0
OD2 E:ASP193 2.5 52.7 1.0
CG E:ASP193 2.7 57.3 1.0
CD2 E:HIS262 2.8 50.2 1.0
CE1 E:HIS262 2.8 48.2 1.0
CD2 E:HIS276 3.0 45.7 1.0
CE1 E:HIS197 3.2 49.3 1.0
CD2 E:HIS197 3.4 44.9 1.0
CE1 E:HIS276 3.7 53.5 1.0
CG E:HIS262 3.9 48.4 1.0
ND1 E:HIS262 3.9 46.8 1.0
ND2 E:ASN280 4.1 56.6 1.0
CB E:ASP193 4.3 54.8 1.0
CG E:HIS276 4.3 46.1 1.0
ND1 E:HIS197 4.3 48.5 1.0
CG E:HIS197 4.4 47.4 1.0
ND1 E:HIS276 4.6 54.4 1.0
O E:ASP193 4.9 42.8 1.0

Manganese binding site 6 out of 10 in 8zwd

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Manganese binding site 6 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus


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 DEHYDROGENASE1 From Bacillus Methanolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn401

b:42.7
occ:1.00
 NE2 G:HIS276 2.2 47.6 1.0
NE2 G:HIS197 2.2 49.5 1.0
NE2 G:HIS262 2.4 48.9 1.0
OD1 G:ASP193 2.5 42.0 1.0
OD2 G:ASP193 2.7 42.8 1.0
CD2 G:HIS276 2.9 49.8 1.0
CG G:ASP193 3.0 47.2 1.0
CD2 G:HIS262 3.1 43.1 1.0
CE1 G:HIS197 3.1 49.1 1.0
CD2 G:HIS197 3.2 49.0 1.0
CE1 G:HIS276 3.3 50.2 1.0
CE1 G:HIS262 3.6 50.7 1.0
CG G:HIS276 4.1 49.9 1.0
ND1 G:HIS197 4.2 41.5 1.0
ND1 G:HIS276 4.3 55.7 1.0
CG G:HIS262 4.3 41.8 1.0
CG G:HIS197 4.3 44.4 1.0
OD1 G:ASN280 4.5 51.2 1.0
CB G:ASP193 4.5 38.9 1.0
ND1 G:HIS262 4.6 44.3 1.0
O G:ASP193 4.9 46.5 1.0

Manganese binding site 7 out of 10 in 8zwd

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Manganese binding site 7 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus


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 DEHYDROGENASE1 From Bacillus Methanolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn401

b:46.2
occ:1.00
 NE2 F:HIS262 2.1 47.5 1.0
NE2 F:HIS197 2.2 47.4 1.0
OD2 F:ASP193 2.4 41.5 1.0
OD1 F:ASP193 2.7 44.4 1.0
NE2 F:HIS276 2.7 42.0 1.0
CG F:ASP193 2.9 48.6 1.0
CD2 F:HIS262 2.9 43.9 1.0
CE1 F:HIS197 3.1 46.0 1.0
CD2 F:HIS276 3.1 41.2 1.0
CE1 F:HIS262 3.2 46.6 1.0
CD2 F:HIS197 3.3 45.3 1.0
CE1 F:HIS276 3.9 50.0 1.0
CG F:HIS262 4.1 42.2 1.0
ND2 F:ASN280 4.2 36.3 1.0
ND1 F:HIS262 4.2 43.8 1.0
ND1 F:HIS197 4.2 48.7 1.0
CG F:HIS197 4.4 44.9 1.0
CB F:ASP193 4.4 45.0 1.0
CG F:HIS276 4.5 42.8 1.0
ND1 F:HIS276 4.8 47.9 1.0
O F:ASP193 4.9 37.0 1.0

Manganese binding site 8 out of 10 in 8zwd

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Manganese binding site 8 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus


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 DEHYDROGENASE1 From Bacillus Methanolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:46.6
occ:1.00
 NE2 C:HIS262 2.2 50.0 1.0
OD1 C:ASP193 2.2 48.7 1.0
NE2 C:HIS197 2.3 45.2 1.0
OD2 C:ASP193 2.4 40.0 1.0
NE2 C:HIS276 2.5 45.4 1.0
CG C:ASP193 2.7 46.1 1.0
CD2 C:HIS262 3.0 46.3 1.0
CD2 C:HIS276 3.1 45.6 1.0
CE1 C:HIS197 3.2 41.4 1.0
CE1 C:HIS262 3.3 51.9 1.0
CD2 C:HIS197 3.3 45.8 1.0
CE1 C:HIS276 3.7 52.2 1.0
ND2 C:ASN280 4.0 49.0 1.0
CB C:ASP193 4.2 42.0 1.0
CG C:HIS262 4.2 45.8 1.0
ND1 C:HIS197 4.3 41.5 1.0
ND1 C:HIS262 4.3 43.4 1.0
CG C:HIS276 4.4 47.5 1.0
CG C:HIS197 4.4 43.5 1.0
ND1 C:HIS276 4.6 49.4 1.0
O C:ASP193 4.8 49.3 1.0
CA C:ASP193 5.0 43.2 1.0

Manganese binding site 9 out of 10 in 8zwd

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Manganese binding site 9 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus


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 DEHYDROGENASE1 From Bacillus Methanolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:47.0
occ:1.00
 NE2 A:HIS262 2.1 50.5 1.0
OD1 A:ASP193 2.2 57.8 1.0
OD2 A:ASP193 2.3 49.4 1.0
NE2 A:HIS197 2.4 42.1 1.0
NE2 A:HIS276 2.4 41.5 1.0
CG A:ASP193 2.5 52.4 1.0
O A:HOH502 2.9 30.1 1.0
CD2 A:HIS262 3.0 49.2 1.0
CD2 A:HIS276 3.1 40.2 1.0
CE1 A:HIS262 3.1 47.5 1.0
CE1 A:HIS197 3.2 50.1 1.0
CD2 A:HIS197 3.5 43.7 1.0
CE1 A:HIS276 3.6 47.3 1.0
ND2 A:ASN280 3.8 46.4 1.0
CB A:ASP193 4.0 39.6 1.0
CG A:HIS262 4.2 44.2 1.0
ND1 A:HIS262 4.2 43.5 1.0
CG A:HIS276 4.4 45.2 1.0
ND1 A:HIS197 4.4 50.1 1.0
OG A:SER196 4.5 48.5 1.0
CG A:HIS197 4.5 45.8 1.0
ND1 A:HIS276 4.5 42.1 1.0
O A:ASP193 4.8 43.1 1.0
CA A:ASP193 4.8 41.4 1.0

Manganese binding site 10 out of 10 in 8zwd

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Manganese binding site 10 out of 10 in the Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus


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 DEHYDROGENASE1 From Bacillus Methanolicus within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn401

b:44.3
occ:1.00
 NE2 I:HIS262 2.3 41.5 1.0
OD1 I:ASP193 2.4 43.5 1.0
NE2 I:HIS276 2.4 44.9 1.0
NE2 I:HIS197 2.4 38.8 1.0
OD2 I:ASP193 2.4 41.9 1.0
CG I:ASP193 2.7 40.3 1.0
CD2 I:HIS262 2.8 40.1 1.0
CD2 I:HIS276 3.1 40.4 1.0
CE1 I:HIS197 3.4 40.3 1.0
CD2 I:HIS197 3.4 41.5 1.0
CE1 I:HIS262 3.5 39.4 1.0
CE1 I:HIS276 3.5 48.9 1.0
CG I:HIS262 4.1 39.4 1.0
ND2 I:ASN280 4.2 45.6 1.0
CB I:ASP193 4.3 40.4 1.0
ND1 I:HIS262 4.4 33.9 1.0
CG I:HIS276 4.4 43.3 1.0
ND1 I:HIS197 4.5 35.2 1.0
ND1 I:HIS276 4.5 52.7 1.0
CG I:HIS197 4.5 39.4 1.0
O I:ASP193 4.8 48.8 1.0

Reference:

B.D.Ma, X.D.Kong. Crystal Structure of Methanol DEHYDROGENASE1 From Bacillus Methanolicus To Be Published.
Page generated: Sun Aug 17 02:06:54 2025

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