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Manganese in PDB 4ewt: The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus

Enzymatic activity of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus

All present enzymatic activity of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus:
3.5.1.14;

Protein crystallography data

The structure of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus, PDB code: 4ewt was solved by T.S.Girish, B.Vivek, M.Colaco, S.Misquith, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.32 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.620, 120.110, 132.410, 115.40, 94.64, 96.55
R / Rfree (%) 19.9 / 22.9

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus (pdb code 4ewt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus, PDB code: 4ewt:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4ewt

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Manganese binding site 1 out of 8 in the The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:55.5
occ:1.00
 OE2 A:GLU139 2.2 38.9 1.0
O A:HOH618 2.4 31.9 1.0
SG A:CYS103 2.4 34.0 1.0
NE2 A:HIS362 2.5 43.5 1.0
OE1 A:GLU139 2.8 37.4 1.0
CD A:GLU139 2.8 38.4 1.0
CB A:CYS103 3.3 33.6 1.0
CD2 A:HIS362 3.3 45.0 1.0
O A:HOH600 3.3 36.8 1.0
MN A:MN402 3.4 35.6 1.0
CE1 A:HIS362 3.6 45.0 1.0
O A:HOH546 4.0 29.4 1.0
OE1 A:GLU138 4.2 38.8 1.0
CG A:GLU139 4.3 38.8 1.0
CD1 A:LEU82 4.5 41.6 1.0
NE2 A:HIS105 4.5 31.3 1.0
CG A:HIS362 4.5 47.2 1.0
ND1 A:HIS362 4.6 47.3 1.0
CA A:CYS103 4.7 35.0 1.0
O A:HOH544 4.8 14.5 1.0
CE1 A:HIS105 4.9 31.0 1.0

Manganese binding site 2 out of 8 in 4ewt

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Manganese binding site 2 out of 8 in the The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:35.6
occ:1.00
 O A:HOH617 2.3 36.1 1.0
NE2 A:HIS164 2.3 27.8 1.0
NE2 A:HIS105 2.3 31.3 1.0
O A:HOH618 2.5 31.9 1.0
SG A:CYS103 2.6 34.0 1.0
CD2 A:HIS105 3.1 30.1 1.0
CE1 A:HIS164 3.2 29.9 1.0
CD2 A:HIS164 3.3 25.4 1.0
CE1 A:HIS105 3.4 31.0 1.0
MN A:MN401 3.4 55.5 1.0
CB A:CYS103 3.5 33.6 1.0
OE2 A:GLU139 3.7 38.9 1.0
OE1 A:GLU138 3.8 38.8 1.0
O A:CYS103 3.9 33.0 1.0
OE1 A:GLU333 4.1 37.0 1.0
OD2 A:ASP78 4.1 32.9 1.0
CG A:HIS105 4.3 31.5 1.0
ND1 A:HIS164 4.3 27.4 1.0
ND1 A:HIS105 4.4 31.9 1.0
CD A:GLU138 4.4 37.9 1.0
CG A:HIS164 4.4 26.2 1.0
CD A:GLU139 4.6 38.4 1.0
C A:CYS103 4.6 33.9 1.0
CA A:CYS103 4.6 35.0 1.0
CE1 A:HIS108 4.7 24.9 1.0
OE2 A:GLU138 4.8 36.7 1.0
CG A:ASP78 4.9 31.4 1.0

Manganese binding site 3 out of 8 in 4ewt

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Manganese binding site 3 out of 8 in the The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:49.6
occ:1.00
 OE2 C:GLU139 2.1 45.9 1.0
NE2 C:HIS362 2.5 32.3 1.0
SG C:CYS103 2.5 33.9 1.0
CD C:GLU139 2.8 43.9 1.0
OE1 C:GLU139 2.9 43.7 1.0
MN C:MN402 3.3 35.8 1.0
CB C:CYS103 3.3 31.3 1.0
CD2 C:HIS362 3.4 32.5 1.0
CE1 C:HIS362 3.5 34.2 1.0
OE1 C:GLU138 4.1 42.4 1.0
CG C:GLU139 4.2 44.1 1.0
O C:HOH619 4.3 21.4 1.0
NE2 C:HIS105 4.4 31.6 1.0
CD1 C:LEU82 4.6 35.4 1.0
ND1 C:HIS362 4.6 35.5 1.0
CG C:HIS362 4.6 34.0 1.0
CA C:CYS103 4.7 31.1 1.0
O C:HOH501 4.8 12.3 1.0
CE1 C:HIS105 4.9 31.7 1.0
NE2 C:HIS164 4.9 25.5 1.0

Manganese binding site 4 out of 8 in 4ewt

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Manganese binding site 4 out of 8 in the The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:35.8
occ:1.00
 NE2 C:HIS164 2.2 25.5 1.0
NE2 C:HIS105 2.4 31.6 1.0
O C:HOH627 2.5 17.5 1.0
SG C:CYS103 2.7 33.9 1.0
CD2 C:HIS105 3.1 30.2 1.0
CE1 C:HIS164 3.2 25.6 1.0
CD2 C:HIS164 3.2 26.3 1.0
MN C:MN401 3.3 49.6 1.0
CE1 C:HIS105 3.5 31.7 1.0
CB C:CYS103 3.6 31.3 1.0
OE1 C:GLU138 3.9 42.4 1.0
OE1 C:GLU333 4.0 32.7 1.0
OD1 C:ASP78 4.1 37.2 1.0
O C:CYS103 4.2 30.1 1.0
OE1 C:GLU139 4.2 43.7 1.0
ND1 C:HIS164 4.3 25.6 1.0
CG C:HIS164 4.3 24.8 1.0
CG C:HIS105 4.4 30.7 1.0
ND1 C:HIS105 4.5 32.7 1.0
CD C:GLU138 4.5 40.6 1.0
OE2 C:GLU139 4.6 45.9 1.0
CE1 C:HIS108 4.8 26.2 1.0
CA C:CYS103 4.8 31.1 1.0
C C:CYS103 4.8 30.4 1.0
CD C:GLU139 4.9 43.9 1.0
CG C:ASP78 4.9 34.5 1.0
OD2 C:ASP78 5.0 34.2 1.0

Manganese binding site 5 out of 8 in 4ewt

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Manganese binding site 5 out of 8 in the The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:57.1
occ:1.00
 OE1 D:GLU139 2.4 68.9 1.0
OE2 D:GLU139 2.5 74.5 1.0
NE2 D:HIS362 2.5 42.0 1.0
SG D:CYS103 2.7 68.6 1.0
CD D:GLU139 2.8 69.6 1.0
CE1 D:HIS362 3.2 43.2 1.0
MN D:MN402 3.3 35.3 1.0
CD2 D:HIS362 3.6 41.7 1.0
CB D:CYS103 3.6 64.2 1.0
OE1 D:GLU138 3.9 68.2 1.0
CG D:GLU139 4.3 65.4 1.0
ND1 D:HIS362 4.4 44.0 1.0
NE2 D:HIS105 4.5 53.3 1.0
CD1 D:LEU82 4.6 69.2 1.0
CG D:HIS362 4.6 42.4 1.0
CD D:GLU138 4.8 68.3 1.0
O D:HOH604 4.9 19.8 1.0
NE2 D:HIS164 4.9 53.5 1.0
CE1 D:HIS105 5.0 51.3 1.0

Manganese binding site 6 out of 8 in 4ewt

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Manganese binding site 6 out of 8 in the The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:35.3
occ:1.00
 NE2 D:HIS164 2.1 53.5 1.0
O D:HOH604 2.2 19.8 1.0
NE2 D:HIS105 2.4 53.3 1.0
SG D:CYS103 2.7 68.6 1.0
CE1 D:HIS164 3.1 54.6 1.0
CD2 D:HIS164 3.1 54.4 1.0
CD2 D:HIS105 3.2 48.8 1.0
MN D:MN401 3.3 57.1 1.0
CE1 D:HIS105 3.4 51.3 1.0
OE1 D:GLU139 3.5 68.9 1.0
CB D:CYS103 3.7 64.2 1.0
OE1 D:GLU138 3.9 68.2 1.0
OE1 D:GLU333 4.1 38.3 1.0
O D:CYS103 4.1 60.2 1.0
OD1 D:ASP78 4.1 51.9 1.0
ND1 D:HIS164 4.2 56.1 1.0
CG D:HIS164 4.3 56.1 1.0
CD D:GLU138 4.4 68.3 1.0
CG D:HIS105 4.4 46.3 1.0
ND1 D:HIS105 4.5 48.2 1.0
CD D:GLU139 4.5 69.6 1.0
CE1 D:HIS108 4.8 45.5 1.0
C D:CYS103 4.8 60.0 1.0
CA D:CYS103 4.8 64.0 1.0
OE2 D:GLU138 4.9 70.9 1.0
CG D:GLU138 5.0 63.1 1.0
OE2 D:GLU139 5.0 74.5 1.0
CG D:ASP78 5.0 47.1 1.0

Manganese binding site 7 out of 8 in 4ewt

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Manganese binding site 7 out of 8 in the The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:69.0
occ:1.00
 OE2 B:GLU139 2.3 51.0 1.0
SG B:CYS103 2.7 49.6 1.0
OE1 B:GLU139 2.7 56.5 1.0
NE2 B:HIS362 2.7 46.5 1.0
CD B:GLU139 2.8 53.2 1.0
O B:HOH612 3.1 32.9 1.0
MN B:MN402 3.2 48.0 1.0
CB B:CYS103 3.5 46.5 1.0
CD2 B:HIS362 3.6 45.7 1.0
CE1 B:HIS362 3.7 47.4 1.0
OE1 B:GLU138 3.7 52.2 1.0
NE2 B:HIS105 4.1 38.6 1.0
CG B:GLU139 4.3 51.1 1.0
CE1 B:HIS105 4.5 37.5 1.0
CD1 B:LEU82 4.7 47.1 1.0
NE2 B:HIS164 4.8 39.6 1.0
CG B:HIS362 4.8 46.5 1.0
ND1 B:HIS362 4.8 47.3 1.0
CD B:GLU138 4.8 52.6 1.0
O B:HOH611 4.9 23.9 1.0
O B:HOH589 4.9 20.8 1.0
CA B:CYS103 4.9 46.2 1.0

Manganese binding site 8 out of 8 in 4ewt

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Manganese binding site 8 out of 8 in the The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Crystal Structure of A Putative Aminohydrolase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:48.0
occ:1.00
 NE2 B:HIS164 2.1 39.6 1.0
NE2 B:HIS105 2.2 38.6 1.0
O B:HOH611 2.3 23.9 1.0
SG B:CYS103 2.8 49.6 1.0
CE1 B:HIS164 3.0 40.2 1.0
CD2 B:HIS164 3.1 40.3 1.0
CD2 B:HIS105 3.1 36.7 1.0
CE1 B:HIS105 3.2 37.5 1.0
MN B:MN401 3.2 69.0 1.0
O B:HOH612 3.4 32.9 1.0
OE1 B:GLU138 3.6 52.2 1.0
OE2 B:GLU139 3.8 51.0 1.0
CB B:CYS103 3.8 46.5 1.0
OD1 B:ASP78 3.9 39.1 1.0
OE1 B:GLU333 4.1 42.7 1.0
ND1 B:HIS164 4.1 40.5 1.0
CG B:HIS164 4.2 41.6 1.0
ND1 B:HIS105 4.3 34.8 1.0
CG B:HIS105 4.3 35.3 1.0
CD B:GLU138 4.3 52.6 1.0
O B:CYS103 4.4 44.4 1.0
CD B:GLU139 4.7 53.2 1.0
CE1 B:HIS108 4.8 37.0 1.0
CG B:ASP78 4.8 35.1 1.0
C B:CYS103 5.0 43.7 1.0
CG B:GLU138 5.0 49.2 1.0
CA B:CYS103 5.0 46.2 1.0
OD2 B:ASP78 5.0 33.7 1.0

Reference:

T.S.Girish, B.Vivek, M.Colaco, S.Misquith, B.Gopal. Structure of An Amidohydrolase, SACOL0085, From Methicillin-Resistant Staphylococcus Aureus Col Acta Crystallogr.,Sect.F V. 69 103 2013.
ISSN: ESSN 1744-3091
PubMed: 23385746
DOI: 10.1107/S1744309112049822
Page generated: Sat Oct 5 19:20:52 2024

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