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Manganese in PDB 1gq6: Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus

Enzymatic activity of Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus

All present enzymatic activity of Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus:
3.5.3.11;

Protein crystallography data

The structure of Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus, PDB code: 1gq6 was solved by J.M.Elkins, I.J.Clifton, H.Hernandez, C.V.Robinson, C.J.Schofield, K.S.Hewitson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 139.859, 78.931, 93.199, 90.00, 123.90, 90.00
R / Rfree (%) 14.2 / 17

Manganese Binding Sites:

The binding sites of Manganese atom in the Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus (pdb code 1gq6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus, PDB code: 1gq6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1gq6

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Manganese binding site 1 out of 6 in the Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn350

b:9.8
occ:1.00
 OD2 A:ASP148 2.1 6.9 1.0
OD2 A:ASP144 2.2 6.9 1.0
OD2 A:ASP235 2.2 6.5 1.0
O A:HOH2189 2.2 14.2 1.0
ND1 A:HIS121 2.2 6.7 1.0
O A:HOH2190 2.3 13.3 1.0
CG A:ASP148 3.1 6.7 1.0
CG A:ASP144 3.2 5.7 1.0
CG A:ASP235 3.2 6.3 1.0
CE1 A:HIS121 3.2 7.0 1.0
CG A:HIS121 3.2 5.4 1.0
MN A:MN351 3.3 11.0 1.0
OD1 A:ASP144 3.3 7.0 1.0
OD1 A:ASP148 3.4 7.6 1.0
CB A:HIS121 3.5 5.0 1.0
CB A:ASP235 3.5 6.6 1.0
O A:HOH2156 3.9 29.4 1.0
OD1 A:ASP235 4.3 5.3 1.0
NE2 A:HIS121 4.3 6.5 1.0
CD2 A:HIS121 4.4 6.7 1.0
CB A:ASP148 4.4 6.1 1.0
NE2 A:HIS142 4.5 5.7 1.0
O A:HIS160 4.6 6.6 1.0
CB A:ASP144 4.6 5.4 1.0
CG A:GLU279 4.6 6.4 1.0
OE2 A:GLU279 4.7 6.1 1.0
CA A:ASP235 4.8 5.8 1.0
O A:HIS146 4.9 7.3 1.0
OD2 A:ASP237 4.9 6.8 1.0

Manganese binding site 2 out of 6 in 1gq6

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Manganese binding site 2 out of 6 in the Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn351

b:11.0
occ:1.00
 OD2 A:ASP237 2.1 6.8 1.0
O A:HOH2190 2.2 13.3 1.0
OD1 A:ASP144 2.2 7.0 1.0
ND1 A:HIS146 2.2 7.8 1.0
OD2 A:ASP235 2.3 6.5 1.0
OD1 A:ASP237 2.3 7.0 1.0
CG A:ASP237 2.6 5.7 1.0
CE1 A:HIS146 3.1 6.9 1.0
O A:HOH2156 3.1 29.4 1.0
CG A:ASP235 3.1 6.3 1.0
CG A:ASP144 3.2 5.7 1.0
MN A:MN350 3.3 9.8 1.0
CG A:HIS146 3.4 6.8 1.0
OD2 A:ASP144 3.5 6.9 1.0
OD1 A:ASP235 3.6 5.3 1.0
CB A:HIS146 3.8 6.0 1.0
N A:HIS146 3.9 5.1 1.0
CB A:ASP235 4.0 6.6 1.0
N A:ALA145 4.1 5.5 1.0
CB A:ASP237 4.1 5.8 1.0
O A:HOH2189 4.2 14.2 1.0
NE2 A:HIS146 4.2 7.7 1.0
OG1 A:THR249 4.3 6.4 1.0
CD2 A:HIS146 4.4 8.3 1.0
CA A:HIS146 4.5 5.1 1.0
CB A:ASP144 4.5 5.4 1.0
CB A:ALA145 4.6 5.3 1.0
OD1 A:ASP148 4.6 7.6 1.0
O A:HOH2155 4.7 9.9 1.0
CA A:ALA145 4.7 4.8 1.0
C A:ALA145 4.7 4.9 1.0
OD2 A:ASP148 4.7 6.9 1.0
CA A:ASP144 4.8 5.3 1.0
O A:HIS146 4.8 7.3 1.0
C A:ASP144 4.9 5.2 1.0

Manganese binding site 3 out of 6 in 1gq6

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Manganese binding site 3 out of 6 in the Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn350

b:8.9
occ:1.00
 OD2 B:ASP148 2.1 4.8 1.0
OD2 B:ASP144 2.2 6.5 1.0
OD2 B:ASP235 2.2 4.8 1.0
O B:HOH2173 2.2 9.6 1.0
ND1 B:HIS121 2.2 6.3 1.0
O B:HOH2174 2.2 11.4 1.0
CG B:ASP148 3.1 6.5 1.0
CG B:ASP235 3.1 4.9 1.0
CE1 B:HIS121 3.1 5.9 1.0
CG B:ASP144 3.2 6.1 1.0
CG B:HIS121 3.2 6.1 1.0
MN B:MN351 3.3 9.9 1.0
OD1 B:ASP148 3.4 6.7 1.0
OD1 B:ASP144 3.4 5.7 1.0
CB B:ASP235 3.5 6.2 1.0
CB B:HIS121 3.5 5.8 1.0
O B:HOH2137 4.1 27.9 1.0
OD1 B:ASP235 4.2 5.2 1.0
NE2 B:HIS121 4.3 5.0 1.0
CD2 B:HIS121 4.3 7.5 1.0
CB B:ASP148 4.4 4.8 1.0
O B:HIS160 4.4 6.8 1.0
CB B:ASP144 4.6 4.5 1.0
NE2 B:HIS142 4.6 5.7 1.0
OE2 B:GLU279 4.6 6.0 1.0
CG B:GLU279 4.6 6.6 1.0
CA B:ASP235 4.8 5.3 1.0
OD2 B:ASP237 4.9 7.1 1.0
O B:HIS146 4.9 6.2 1.0

Manganese binding site 4 out of 6 in 1gq6

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Manganese binding site 4 out of 6 in the Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn351

b:9.9
occ:1.00
 OD2 B:ASP237 2.2 7.1 1.0
OD1 B:ASP144 2.2 5.7 1.0
O B:HOH2174 2.2 11.4 1.0
ND1 B:HIS146 2.2 6.4 1.0
OD2 B:ASP235 2.3 4.8 1.0
OD1 B:ASP237 2.4 6.0 1.0
CG B:ASP237 2.6 7.2 1.0
CE1 B:HIS146 3.1 6.4 1.0
CG B:ASP235 3.1 4.9 1.0
CG B:ASP144 3.2 6.1 1.0
CG B:HIS146 3.3 6.8 1.0
MN B:MN350 3.3 8.9 1.0
O B:HOH2137 3.3 27.9 1.0
OD2 B:ASP144 3.5 6.5 1.0
OD1 B:ASP235 3.6 5.2 1.0
CB B:HIS146 3.7 6.4 1.0
N B:HIS146 3.9 4.4 1.0
CB B:ASP235 4.1 6.2 1.0
N B:ALA145 4.1 4.7 1.0
CB B:ASP237 4.1 5.7 1.0
O B:HOH2173 4.2 9.6 1.0
NE2 B:HIS146 4.3 7.0 1.0
OG1 B:THR249 4.3 7.1 1.0
CD2 B:HIS146 4.4 6.9 1.0
CA B:HIS146 4.4 5.8 1.0
CB B:ASP144 4.5 4.5 1.0
OD1 B:ASP148 4.6 6.7 1.0
CB B:ALA145 4.6 5.4 1.0
O B:HOH2136 4.6 9.1 1.0
CA B:ALA145 4.7 4.2 1.0
C B:ALA145 4.7 4.7 1.0
CA B:ASP144 4.8 4.8 1.0
OD2 B:ASP148 4.8 4.8 1.0
O B:HIS146 4.8 6.2 1.0
C B:ASP144 4.9 3.8 1.0

Manganese binding site 5 out of 6 in 1gq6

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Manganese binding site 5 out of 6 in the Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn350

b:8.7
occ:1.00
 OD2 C:ASP148 2.1 6.5 1.0
OD2 C:ASP235 2.1 5.0 1.0
OD2 C:ASP144 2.2 7.8 1.0
ND1 C:HIS121 2.2 4.2 1.0
O C:HOH2207 2.2 12.4 1.0
O C:HOH2208 2.4 12.4 1.0
CG C:ASP235 3.1 5.4 1.0
CG C:ASP148 3.1 6.2 1.0
CG C:ASP144 3.2 5.3 1.0
CE1 C:HIS121 3.2 6.7 1.0
CG C:HIS121 3.2 6.4 1.0
MN C:MN351 3.3 9.7 1.0
OD1 C:ASP144 3.3 4.8 1.0
OD1 C:ASP148 3.5 7.8 1.0
CB C:HIS121 3.5 5.9 1.0
CB C:ASP235 3.5 7.0 1.0
OD1 C:ASP235 4.2 5.3 1.0
O C:HOH2170 4.3 29.0 1.0
NE2 C:HIS121 4.3 6.9 1.0
CD2 C:HIS121 4.3 5.2 1.0
CB C:ASP148 4.4 5.1 1.0
NE2 C:HIS142 4.5 4.7 1.0
O C:HIS160 4.5 6.9 1.0
CB C:ASP144 4.6 5.4 1.0
CG C:GLU279 4.6 5.8 1.0
OE2 C:GLU279 4.6 6.1 1.0
CA C:ASP235 4.8 6.2 1.0
OD2 C:ASP237 4.8 5.2 1.0
O C:HIS146 4.9 5.7 1.0

Manganese binding site 6 out of 6 in 1gq6

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Manganese binding site 6 out of 6 in the Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Proclavaminate Amidino Hydrolase From Streptomyces Clavuligerus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn351

b:9.7
occ:1.00
 O C:HOH2208 2.1 12.4 1.0
OD2 C:ASP237 2.1 5.2 1.0
OD1 C:ASP144 2.1 4.8 1.0
ND1 C:HIS146 2.2 5.6 1.0
OD1 C:ASP237 2.3 6.4 1.0
OD2 C:ASP235 2.3 5.0 1.0
CG C:ASP237 2.6 6.3 1.0
CE1 C:HIS146 3.0 7.7 1.0
CG C:ASP235 3.1 5.4 1.0
CG C:ASP144 3.2 5.3 1.0
MN C:MN350 3.3 8.7 1.0
CG C:HIS146 3.3 6.1 1.0
O C:HOH2170 3.5 29.0 1.0
OD2 C:ASP144 3.5 7.8 1.0
OD1 C:ASP235 3.6 5.3 1.0
CB C:HIS146 3.8 5.8 1.0
N C:HIS146 4.0 5.4 1.0
CB C:ASP235 4.0 7.0 1.0
N C:ALA145 4.1 5.6 1.0
CB C:ASP237 4.1 5.5 1.0
O C:HOH2207 4.1 12.4 1.0
NE2 C:HIS146 4.2 6.4 1.0
OG1 C:THR249 4.3 7.2 1.0
CD2 C:HIS146 4.4 9.0 1.0
CA C:HIS146 4.5 5.6 1.0
CB C:ASP144 4.5 5.4 1.0
CB C:ALA145 4.6 6.3 1.0
O C:HOH2169 4.6 10.8 1.0
OD1 C:ASP148 4.6 7.8 1.0
CA C:ALA145 4.7 5.5 1.0
OD2 C:ASP148 4.7 6.5 1.0
C C:ALA145 4.7 5.8 1.0
CA C:ASP144 4.8 4.9 1.0
O C:HIS146 4.9 5.7 1.0
C C:ASP144 4.9 5.5 1.0
O C:THR249 5.0 5.7 1.0

Reference:

J.M.Elkins, I.J.Clifton, H.Hernandez, L.X.Doan, C.V.Robinson, C.J.Schofield, K.S.Hewitson. Oligomeric Structure of Proclavaminic Acid Amidino Hydrolase: Evolution of A Hydrolytic Enzyme in Clavulanic Acid Biosynthesis Biochem.J. V. 366 423 2002.
ISSN: ISSN 0264-6021
PubMed: 12020346
DOI: 10.1042/BJ20020125
Page generated: Sat Oct 5 10:45:33 2024

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