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Manganese in PDB 4nfv: Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2

Enzymatic activity of Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2

All present enzymatic activity of Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2:
3.2.1.17;

Protein crystallography data

The structure of Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2, PDB code: 4nfv was solved by P.Benas, L.Legrand, M.Ries-Kautt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.45 / 1.63
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.607, 79.607, 37.893, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17.9

Other elements in 4nfv:

The structure of Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2 (pdb code 4nfv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2, PDB code: 4nfv:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4nfv

Go back to Manganese Binding Sites List in 4nfv
Manganese binding site 1 out of 4 in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:24.6
occ:0.30
 MN A:MN201 0.0 24.6 0.3
MN A:MN201 2.1 26.3 0.2
O A:HOH305 2.1 32.6 0.9
O A:HOH302 2.3 24.1 0.7
OD2 A:ASP52 2.3 26.9 1.0
MN A:MN201 2.3 22.8 0.3
O A:HOH304 2.5 27.3 0.8
CG A:ASP52 3.2 19.4 1.0
O A:HOH309 3.3 33.2 0.9
MN A:MN202 3.5 29.1 0.5
O A:HOH303 3.7 23.0 1.0
OD1 A:ASP52 3.7 16.1 1.0
O A:HOH301 3.7 30.0 0.7
O A:HOH310 4.0 27.7 0.9
O A:GLN57 4.3 15.0 1.0
CB A:ASP52 4.4 14.4 1.0
OD1 A:ASN46 4.4 30.3 1.0
OE1 A:GLU35 4.4 16.5 1.0
O A:HOH306 4.5 39.3 1.0
CB A:GLN57 4.9 10.3 1.0

Manganese binding site 2 out of 4 in 4nfv

Go back to Manganese Binding Sites List in 4nfv
Manganese binding site 2 out of 4 in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:22.8
occ:0.34
 MN A:MN201 0.0 22.8 0.3
OD1 A:ASN46 2.1 30.3 1.0
O A:HOH301 2.2 30.0 0.7
MN A:MN201 2.2 26.3 0.2
OD2 A:ASP52 2.2 26.9 1.0
MN A:MN201 2.3 24.6 0.3
O A:HOH304 2.9 27.3 0.8
CG A:ASN46 3.1 21.1 1.0
CG A:ASP52 3.3 19.4 1.0
ND2 A:ASN46 3.5 20.6 1.0
OD1 A:ASP52 3.7 16.1 1.0
O A:HOH305 3.8 32.6 0.9
O A:HOH303 4.1 23.0 1.0
CB A:ASN46 4.4 20.1 1.0
CB A:ASP52 4.5 14.4 1.0
O A:HOH302 4.5 24.1 0.7
MN A:MN202 4.6 29.1 0.5

Manganese binding site 3 out of 4 in 4nfv

Go back to Manganese Binding Sites List in 4nfv
Manganese binding site 3 out of 4 in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:26.3
occ:0.24
 MN A:MN201 0.0 26.3 0.2
O A:HOH301 2.0 30.0 0.7
O A:HOH303 2.0 23.0 1.0
OD2 A:ASP52 2.0 26.9 1.0
MN A:MN201 2.1 24.6 0.3
MN A:MN201 2.2 22.8 0.3
O A:HOH305 2.4 32.6 0.9
MN A:MN202 2.6 29.1 0.5
CG A:ASP52 3.2 19.4 1.0
OD1 A:ASN46 3.8 30.3 1.0
O A:HOH302 3.9 24.1 0.7
CB A:ASP52 4.0 14.4 1.0
O A:HOH306 4.0 39.3 1.0
O A:HOH304 4.1 27.3 0.8
OD1 A:ASP52 4.2 16.1 1.0
OE1 A:GLN57 4.3 14.8 1.0
OE1 A:GLU35 4.4 16.5 1.0
O A:HOH307 4.5 28.1 0.9
CB A:ASN44 4.8 17.3 1.0
CG A:ASN46 4.8 21.1 1.0
CB A:GLN57 4.8 10.3 1.0
O A:HOH310 4.9 27.7 0.9

Manganese binding site 4 out of 4 in 4nfv

Go back to Manganese Binding Sites List in 4nfv
Manganese binding site 4 out of 4 in the Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Previously De-Ionized Hew Lysozyme Batch Crystallized in 1.1 M MNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:29.1
occ:0.45
 O A:HOH305 1.6 32.6 0.9
O A:HOH306 1.9 39.3 1.0
O A:HOH303 2.2 23.0 1.0
OE1 A:GLU35 2.3 16.5 1.0
MN A:MN201 2.6 26.3 0.2
O A:HOH307 2.7 28.1 0.9
O A:HOH311 3.3 30.1 1.0
CD A:GLU35 3.4 14.9 1.0
MN A:MN201 3.5 24.6 0.3
O A:HOH310 3.6 27.7 0.9
OE2 A:GLU35 3.9 19.2 1.0
O A:HOH302 4.1 24.1 0.7
O A:HOH301 4.2 30.0 0.7
OD2 A:ASP52 4.3 26.9 1.0
CG A:GLN57 4.4 11.0 1.0
CB A:GLN57 4.4 10.3 1.0
OE1 A:GLN57 4.4 14.8 1.0
O A:GLU35 4.5 14.4 1.0
CA A:GLU35 4.6 9.5 1.0
MN A:MN201 4.6 22.8 0.3
CG A:GLU35 4.6 13.5 1.0
CB A:GLU35 4.8 10.9 1.0
CD A:GLN57 4.9 12.3 1.0

Reference:

P.Benas, N.Auzeil, L.Legrand, F.Brachet, A.Regazzetti, M.Ries-Kautt. Weak Protein-Cationic Co-Ion Interactions Addressed By X-Ray Crystallography and Mass Spectrometry. Acta Crystallogr.,Sect.D V. 70 2217 2014.
ISSN: ISSN 0907-4449
PubMed: 25084340
DOI: 10.1107/S1399004714011304
Page generated: Sat Oct 5 20:30:12 2024

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