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Zinc in PDB 3neh: Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala

Enzymatic activity of Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala

All present enzymatic activity of Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala:
4.99.1.1;

Protein crystallography data

The structure of Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala, PDB code: 3neh was solved by A.A.Fedorov, E.V.Fedorov, J.Cummings, F.M.Raushel, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.73 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.834, 79.453, 152.014, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala (pdb code 3neh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala, PDB code: 3neh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3neh

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Zinc binding site 1 out of 4 in the Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn320

b:30.1
occ:0.33
 OE1 A:GLU107 2.0 33.7 1.0
OD2 A:ASP11 2.2 31.0 1.0
NE2 A:HIS9 2.2 27.7 1.0
O31 A:L3A319 2.4 36.7 1.0
OD1 A:ASP11 2.4 30.3 1.0
CG A:ASP11 2.6 29.2 1.0
N1 A:L3A319 2.7 35.7 1.0
CD A:GLU107 2.9 30.6 1.0
OE2 A:GLU107 3.1 33.2 1.0
CE1 A:HIS9 3.1 26.0 1.0
CD2 A:HIS9 3.3 28.6 1.0
C2 A:L3A319 3.4 35.2 1.0
P A:L3A319 3.6 35.4 0.5
OD1 A:ASP263 3.7 36.4 1.0
ZN A:ZN321 3.7 30.3 0.4
CB A:ALA49 4.1 25.9 1.0
CB A:ASP11 4.1 26.7 1.0
ND1 A:HIS9 4.2 25.3 1.0
CG A:GLU107 4.3 25.2 1.0
CG A:HIS9 4.4 21.0 1.0
NE2 A:HIS194 4.4 23.6 1.0
O32 A:L3A319 4.4 35.5 1.0
CB A:GLU107 4.7 25.4 1.0
CB A:PHE51 4.7 24.9 1.0
CG A:ASP263 4.8 31.5 1.0
CG A:PHE51 4.8 27.9 1.0
CE1 A:HIS194 4.8 24.9 1.0
CA A:ASP11 4.8 25.8 1.0
C1 A:L3A319 4.9 38.9 1.0
N A:ASP11 5.0 24.3 1.0

Zinc binding site 2 out of 4 in 3neh

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Zinc binding site 2 out of 4 in the Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn321

b:30.3
occ:0.36
 NE2 A:HIS174 2.0 25.6 1.0
OE2 A:GLU107 2.2 33.2 1.0
O31 A:L3A319 2.2 36.7 1.0
NE2 A:HIS194 2.3 23.6 1.0
O32 A:L3A319 2.6 35.5 1.0
O62 A:L3A319 2.6 30.2 1.0
CE1 A:HIS174 2.8 26.2 1.0
P A:L3A319 2.9 35.4 0.5
CD2 A:HIS174 3.1 24.6 1.0
CD2 A:HIS194 3.2 22.9 1.0
CE1 A:HIS194 3.3 24.9 1.0
CD A:GLU107 3.3 30.6 1.0
C6 A:L3A319 3.4 35.0 1.0
ZN A:ZN320 3.7 30.1 0.3
NH2 A:ARG205 3.8 22.3 1.0
OE1 A:GLU107 3.9 33.7 1.0
C4 A:L3A319 4.0 32.1 1.0
O61 A:L3A319 4.0 29.6 1.0
ND1 A:HIS174 4.0 26.4 1.0
NE1 A:TRP134 4.1 25.5 1.0
NE2 A:HIS9 4.1 27.7 1.0
CG A:HIS174 4.2 23.6 1.0
N1 A:L3A319 4.2 35.7 1.0
C5 A:L3A319 4.2 31.8 1.0
CD1 A:TRP134 4.2 22.3 1.0
C2 A:L3A319 4.3 35.2 1.0
OD2 A:ASP263 4.3 42.4 1.0
ND1 A:HIS194 4.4 23.4 1.0
CG A:HIS194 4.4 23.1 1.0
CG A:GLU107 4.5 25.2 1.0
OD1 A:ASP263 4.6 36.4 1.0
CE1 A:HIS9 4.6 26.0 1.0
CZ A:ARG205 4.7 25.8 1.0
NE A:ARG205 4.7 23.6 1.0
CG A:ASP263 4.8 31.5 1.0
CD2 A:HIS9 4.8 28.6 1.0

Zinc binding site 3 out of 4 in 3neh

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Zinc binding site 3 out of 4 in the Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn320

b:31.7
occ:0.36
 OE1 B:GLU107 2.0 33.7 1.0
NE2 B:HIS9 2.2 25.6 1.0
OD2 B:ASP11 2.3 32.1 1.0
O31 B:L3A319 2.4 35.5 1.0
OD1 B:ASP11 2.5 28.3 1.0
N1 B:L3A319 2.7 32.7 1.0
CD B:GLU107 2.7 31.4 1.0
CG B:ASP11 2.7 26.8 1.0
OE2 B:GLU107 2.8 33.1 1.0
CE1 B:HIS9 3.0 27.0 1.0
CD2 B:HIS9 3.3 26.2 1.0
C2 B:L3A319 3.5 35.7 1.0
P B:L3A319 3.5 34.7 0.4
ZN B:ZN321 3.6 29.0 0.3
OD1 B:ASP263 4.0 31.8 1.0
CG B:GLU107 4.1 27.1 1.0
CB B:ALA49 4.2 23.3 1.0
ND1 B:HIS9 4.2 25.9 1.0
O32 B:L3A319 4.2 35.3 1.0
CB B:ASP11 4.3 25.2 1.0
NE2 B:HIS194 4.3 24.2 1.0
CG B:HIS9 4.3 22.4 1.0
CB B:GLU107 4.6 25.2 1.0
CB B:PHE51 4.6 22.9 1.0
CE1 B:HIS194 4.8 24.6 1.0
CG B:PHE51 4.8 25.2 1.0
C1 B:L3A319 4.9 38.8 1.0
CA B:ASP11 4.9 25.9 1.0

Zinc binding site 4 out of 4 in 3neh

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Zinc binding site 4 out of 4 in the Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn321

b:29.0
occ:0.26
 NE2 B:HIS174 2.1 25.0 1.0
OE2 B:GLU107 2.2 33.1 1.0
O31 B:L3A319 2.3 35.5 1.0
NE2 B:HIS194 2.3 24.2 1.0
O32 B:L3A319 2.4 35.3 1.0
O62 B:L3A319 2.8 29.8 1.0
P B:L3A319 2.8 34.7 0.4
CE1 B:HIS174 2.9 26.8 1.0
CD2 B:HIS174 3.2 21.8 1.0
CD2 B:HIS194 3.2 25.3 1.0
CE1 B:HIS194 3.2 24.6 1.0
CD B:GLU107 3.3 31.4 1.0
C6 B:L3A319 3.4 33.1 1.0
ZN B:ZN320 3.6 31.7 0.4
C4 B:L3A319 3.9 30.8 1.0
O61 B:L3A319 4.0 33.5 1.0
OE1 B:GLU107 4.0 33.7 1.0
NE2 B:HIS9 4.0 25.6 1.0
NE1 B:TRP134 4.1 30.1 1.0
ND1 B:HIS174 4.1 23.9 1.0
CD1 B:TRP134 4.1 23.9 1.0
NH2 B:ARG205 4.1 23.2 1.0
C5 B:L3A319 4.2 34.2 1.0
N1 B:L3A319 4.2 32.7 1.0
CG B:HIS174 4.2 21.3 1.0
C2 B:L3A319 4.2 35.7 1.0
ND1 B:HIS194 4.4 23.1 1.0
CG B:HIS194 4.4 23.8 1.0
CG B:GLU107 4.4 27.1 1.0
OD1 B:ASP263 4.5 31.8 1.0
CE1 B:HIS9 4.5 27.0 1.0
OD2 B:ASP263 4.6 37.9 1.0
CD2 B:HIS9 4.8 26.2 1.0
CG B:ASP263 4.8 34.7 1.0
CZ B:ARG205 4.9 23.3 1.0
NE B:ARG205 4.9 24.4 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, J.Cummings, F.M.Raushel, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of the Protein LMO2462 From Listeria Monocytogenes Complexed with Zn and Phosphonate Mimic of Dipeptide L-Leu-D-Ala To Be Published.
Page generated: Sat Oct 26 10:12:53 2024

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