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Manganese in PDB 1yny: Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition

Enzymatic activity of Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition

All present enzymatic activity of Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition:
3.5.2.2;

Protein crystallography data

The structure of Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition, PDB code: 1yny was solved by K.V.Radha Kishan, R.M.Vohra, K.Ganeshan, V.Agrawal, V.M.Sharma, R.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 129.540, 129.540, 102.850, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 24.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition (pdb code 1yny). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition, PDB code: 1yny:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1yny

Go back to Manganese Binding Sites List in 1yny
Manganese binding site 1 out of 4 in the Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn471

b:18.0
occ:1.00
 NE2 A:HIS58 2.1 17.5 1.0
O A:HOH1128 2.1 12.1 1.0
NE2 A:HIS60 2.2 21.1 1.0
OD1 A:ASP315 2.3 14.2 1.0
CE1 A:HIS58 3.0 16.3 1.0
CD2 A:HIS58 3.1 16.0 1.0
CE1 A:HIS60 3.2 18.6 1.0
CD2 A:HIS60 3.2 18.4 1.0
CG A:ASP315 3.2 15.3 1.0
NZ A:LYS150 3.3 12.3 1.0
MN A:MN472 3.4 17.8 1.0
OD2 A:ASP315 3.7 12.8 1.0
O A:HOH1112 3.9 18.5 1.0
O A:HOH1093 4.0 22.7 1.0
ND1 A:HIS58 4.2 15.6 1.0
CG A:HIS58 4.2 15.5 1.0
ND1 A:HIS60 4.3 17.5 1.0
CG A:HIS60 4.3 18.4 1.0
CB A:ASP315 4.3 14.7 1.0
CD2 A:HIS239 4.4 15.8 1.0
CE2 A:PHE92 4.5 11.1 1.0
NE2 A:HIS239 4.5 14.7 1.0
CD2 A:PHE92 4.6 11.7 1.0
CA A:ASP315 4.8 15.2 1.0
CE A:LYS150 4.8 15.0 1.0

Manganese binding site 2 out of 4 in 1yny

Go back to Manganese Binding Sites List in 1yny
Manganese binding site 2 out of 4 in the Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn472

b:17.8
occ:1.00
 O A:HOH1128 2.1 12.1 1.0
ND1 A:HIS183 2.3 15.4 1.0
NE2 A:HIS239 2.3 14.7 1.0
O A:HOH1112 2.5 18.5 1.0
CE1 A:HIS183 3.0 16.9 1.0
CD2 A:HIS239 3.2 15.8 1.0
CE1 A:HIS239 3.3 14.9 1.0
CG A:HIS183 3.4 15.1 1.0
NZ A:LYS150 3.4 12.3 1.0
MN A:MN471 3.4 18.0 1.0
CB A:HIS183 3.8 10.6 1.0
O A:SER288 3.9 14.1 1.0
OH A:TYR155 4.1 17.5 1.0
NE2 A:HIS183 4.2 17.0 1.0
CE A:LYS150 4.3 15.0 1.0
CE2 A:PHE152 4.4 15.5 1.0
CD2 A:HIS183 4.4 16.3 1.0
CG A:HIS239 4.4 16.2 1.0
ND1 A:HIS239 4.4 15.9 1.0
CG2 A:VAL238 4.6 11.3 1.0
CE1 A:HIS58 4.6 16.3 1.0
NE2 A:HIS58 4.6 17.5 1.0
OD2 A:ASP315 4.7 12.8 1.0
O A:HOH1093 4.7 22.7 1.0
CA A:HIS183 4.7 10.5 1.0
CE2 A:TYR155 4.8 21.4 1.0
OD1 A:ASP315 4.9 14.2 1.0
CD2 A:PHE152 4.9 14.4 1.0
CZ A:TYR155 5.0 18.9 1.0
C A:SER288 5.0 14.2 1.0

Manganese binding site 3 out of 4 in 1yny

Go back to Manganese Binding Sites List in 1yny
Manganese binding site 3 out of 4 in the Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn471

b:17.1
occ:1.00
 O B:HOH5110 2.1 19.3 1.0
NE2 B:HIS58 2.2 18.2 1.0
NE2 B:HIS60 2.2 17.1 1.0
OD1 B:ASP315 2.3 14.2 1.0
CD2 B:HIS58 3.1 17.9 1.0
CD2 B:HIS60 3.1 15.2 1.0
NZ B:LYS150 3.2 11.6 1.0
CE1 B:HIS58 3.3 17.4 1.0
CE1 B:HIS60 3.3 16.9 1.0
CG B:ASP315 3.3 14.0 1.0
MN B:MN472 3.5 15.3 1.0
OD2 B:ASP315 3.8 14.6 1.0
O B:HOH5109 4.0 31.0 1.0
O B:HOH5084 4.0 20.2 1.0
CG B:HIS58 4.3 14.6 1.0
CG B:HIS60 4.3 16.4 1.0
ND1 B:HIS58 4.3 15.6 1.0
ND1 B:HIS60 4.3 18.0 1.0
CE2 B:PHE92 4.4 10.8 1.0
CB B:ASP315 4.4 13.3 1.0
CD2 B:HIS239 4.4 12.1 1.0
CD2 B:PHE92 4.5 12.2 1.0
NE2 B:HIS239 4.6 10.1 1.0
CA B:ASP315 4.7 14.1 1.0
CE B:LYS150 4.7 16.6 1.0

Manganese binding site 4 out of 4 in 1yny

Go back to Manganese Binding Sites List in 1yny
Manganese binding site 4 out of 4 in the Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Molecular Structure of D-Hydantoinase From A Bacillus Sp. AR9: Evidence For Mercury Inhibition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn472

b:15.3
occ:1.00
 O B:HOH5110 2.1 19.3 1.0
ND1 B:HIS183 2.3 11.9 1.0
O B:HOH5109 2.3 31.0 1.0
NE2 B:HIS239 2.3 10.1 1.0
CE1 B:HIS183 3.1 11.4 1.0
CD2 B:HIS239 3.3 12.1 1.0
CE1 B:HIS239 3.3 10.6 1.0
NZ B:LYS150 3.4 11.6 1.0
CG B:HIS183 3.4 12.7 1.0
MN B:MN471 3.5 17.1 1.0
CB B:HIS183 3.8 11.6 1.0
O B:SER288 3.9 15.7 1.0
CE2 B:PHE152 4.2 14.5 1.0
NE2 B:HIS183 4.3 11.6 1.0
OH B:TYR155 4.3 21.5 1.0
CE B:LYS150 4.3 16.6 1.0
CD2 B:HIS183 4.4 13.3 1.0
CG B:HIS239 4.4 13.1 1.0
ND1 B:HIS239 4.4 13.1 1.0
CG2 B:VAL238 4.5 9.5 1.0
NE2 B:HIS58 4.6 18.2 1.0
CE1 B:HIS58 4.7 17.4 1.0
OD2 B:ASP315 4.7 14.6 1.0
CA B:HIS183 4.8 10.5 1.0
O B:HOH5084 4.8 20.2 1.0
OD1 B:ASP315 4.8 14.2 1.0
CE2 B:TYR155 4.9 23.6 1.0
CD2 B:PHE152 4.9 15.7 1.0

Reference:

K.V.Radha Kishan, R.M.Vohra, K.Ganesan, V.Agrawal, V.M.Sharma, R.Sharma. Molecular Structure of D-Hydantoinase From Bacillus Sp. AR9: Evidence For Mercury Inhibition. J.Mol.Biol. V. 347 95 2005.
ISSN: ISSN 0022-2836
PubMed: 15733920
DOI: 10.1016/J.JMB.2005.01.025
Page generated: Sat Oct 5 13:13:17 2024

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