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Magnesium in PDB 3jyy: Semet Linb Complexed with Ppi

Protein crystallography data

The structure of Semet Linb Complexed with Ppi, PDB code: 3jyy was solved by M.Morar, G.D.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.68 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.994, 96.343, 103.645, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Semet Linb Complexed with Ppi (pdb code 3jyy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Semet Linb Complexed with Ppi, PDB code: 3jyy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3jyy

Go back to Magnesium Binding Sites List in 3jyy
Magnesium binding site 1 out of 5 in the Semet Linb Complexed with Ppi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Semet Linb Complexed with Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:7.1
occ:1.00
O22 A:PPV738 1.9 10.4 1.0
OD1 A:ASP40 2.0 5.0 1.0
O31 A:PPV738 2.1 11.3 1.0
O A:HOH319 2.1 5.4 1.0
O A:HOH274 2.2 15.7 1.0
OE1 A:GLU42 2.2 10.0 1.0
CG A:ASP40 3.0 6.9 1.0
P1 A:PPV738 3.2 10.9 1.0
P2 A:PPV738 3.2 11.1 1.0
CD A:GLU42 3.2 10.2 1.0
OPP A:PPV738 3.5 11.0 1.0
OD2 A:ASP40 3.5 8.2 1.0
O11 A:PPV738 3.6 11.2 1.0
OE2 A:GLU42 3.6 13.2 1.0
MG A:MG304 3.6 27.9 1.0
O A:ASP40 3.8 5.7 1.0
O A:HOH305 3.8 13.9 1.0
OG A:SER29 4.0 9.3 1.0
O32 A:PPV738 4.0 9.8 1.0
O A:HOH346 4.1 23.7 1.0
N A:ASP40 4.2 6.1 1.0
N A:SER29 4.2 8.1 1.0
C A:ASP40 4.3 6.1 1.0
CB A:ASP40 4.3 5.8 1.0
O12 A:PPV738 4.3 11.6 1.0
O A:HOH270 4.4 4.7 1.0
CG A:GLU42 4.4 8.8 1.0
CA A:ASP40 4.5 6.2 1.0
O21 A:PPV738 4.5 11.9 1.0
CA A:GLY28 4.6 8.3 1.0
CB A:SER29 4.7 8.4 1.0
O A:HOH467 4.7 26.1 1.0
C A:GLY28 4.9 7.9 1.0
O A:HOH335 4.9 12.8 1.0

Magnesium binding site 2 out of 5 in 3jyy

Go back to Magnesium Binding Sites List in 3jyy
Magnesium binding site 2 out of 5 in the Semet Linb Complexed with Ppi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Semet Linb Complexed with Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:21.9
occ:1.00
O A:HOH560 1.9 2.4 1.0
O A:HOH559 2.0 9.9 1.0
O A:HOH325 2.1 10.7 1.0
O A:HOH558 2.2 8.8 1.0
OD1 A:ASP63 2.2 12.7 1.0
CG A:ASP63 3.2 12.3 1.0
OD2 A:ASP63 3.5 14.9 1.0
O A:ASN59 4.1 9.8 1.0
O A:HOH380 4.2 15.4 1.0
CB A:ASP63 4.5 10.8 1.0
CD2 A:PHE62 4.5 10.8 1.0
N A:ASP63 4.7 10.0 1.0
CA A:ASP63 4.8 10.6 1.0
C A:ASN59 5.0 10.6 1.0

Magnesium binding site 3 out of 5 in 3jyy

Go back to Magnesium Binding Sites List in 3jyy
Magnesium binding site 3 out of 5 in the Semet Linb Complexed with Ppi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Semet Linb Complexed with Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:27.9
occ:1.00
O A:HOH467 2.0 26.1 1.0
O A:HOH274 2.1 15.7 1.0
OD2 A:ASP40 2.2 8.2 1.0
O A:HOH335 2.3 12.8 1.0
OE2 A:GLU42 2.3 13.2 1.0
OE1 A:GLU89 2.9 20.8 1.0
CG A:ASP40 3.2 6.9 1.0
CD A:GLU42 3.3 10.2 1.0
CD A:GLU89 3.4 17.7 1.0
OD1 A:ASP40 3.4 5.0 1.0
OE1 A:GLU42 3.6 10.0 1.0
MG A:MG301 3.6 7.1 1.0
OE2 A:GLU89 3.7 20.2 1.0
O A:HOH305 3.8 13.9 1.0
O A:HOH588 3.9 35.4 1.0
O A:HOH346 4.1 23.7 1.0
O A:HOH644 4.1 31.2 1.0
CG A:GLU89 4.3 13.2 1.0
O11 A:PPV738 4.5 11.2 1.0
CB A:ASP40 4.6 5.8 1.0
O22 A:PPV738 4.6 10.4 1.0
CG A:GLU42 4.6 8.8 1.0
NH1 A:ARG87 4.7 10.8 1.0
NH2 A:ARG87 4.7 10.6 1.0
O31 A:PPV738 4.7 11.3 1.0
CB A:GLU42 4.9 7.2 1.0
CB A:GLU89 4.9 9.8 1.0

Magnesium binding site 4 out of 5 in 3jyy

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Magnesium binding site 4 out of 5 in the Semet Linb Complexed with Ppi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Semet Linb Complexed with Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg300

b:11.1
occ:1.00
O B:HOH280 1.9 3.2 1.0
O12 B:PPV738 2.0 11.2 1.0
O11 B:PPV738 2.0 10.0 1.0
OD1 B:ASP40 2.0 4.3 1.0
OE1 B:GLU42 2.1 7.8 1.0
O B:HOH274 2.2 10.6 1.0
P2 B:PPV738 3.0 11.6 1.0
CG B:ASP40 3.1 4.9 1.0
CD B:GLU42 3.1 10.7 1.0
P1 B:PPV738 3.3 10.1 1.0
O22 B:PPV738 3.4 11.9 1.0
OPP B:PPV738 3.4 10.8 1.0
OD2 B:ASP40 3.5 7.0 1.0
OE2 B:GLU42 3.6 11.7 1.0
MG B:MG302 3.7 24.5 1.0
O B:HOH278 3.8 11.6 1.0
O B:ASP40 4.0 6.1 1.0
OG B:SER29 4.0 8.3 1.0
O B:HOH557 4.1 24.0 1.0
N B:SER29 4.1 8.2 1.0
O21 B:PPV738 4.1 9.8 1.0
N B:ASP40 4.2 5.1 1.0
O B:HOH380 4.3 9.5 1.0
CG B:GLU42 4.3 8.1 1.0
O31 B:PPV738 4.3 10.8 1.0
C B:ASP40 4.4 5.4 1.0
CB B:ASP40 4.4 4.9 1.0
O32 B:PPV738 4.4 11.5 1.0
CA B:ASP40 4.5 5.0 1.0
O B:HOH283 4.5 11.8 1.0
CA B:GLY28 4.6 8.2 1.0
CB B:SER29 4.6 7.9 1.0
C B:GLY28 4.8 8.1 1.0
O B:HOH643 4.9 46.4 1.0
O B:HOH399 5.0 9.0 1.0

Magnesium binding site 5 out of 5 in 3jyy

Go back to Magnesium Binding Sites List in 3jyy
Magnesium binding site 5 out of 5 in the Semet Linb Complexed with Ppi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Semet Linb Complexed with Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:24.5
occ:1.00
O B:HOH283 2.0 11.8 1.0
O B:HOH274 2.1 10.6 1.0
OE1 B:GLU89 2.1 19.7 1.0
O B:HOH399 2.1 9.0 1.0
OD2 B:ASP40 2.2 7.0 1.0
OE2 B:GLU42 2.2 11.7 1.0
CG B:ASP40 3.1 4.9 1.0
CD B:GLU42 3.2 10.7 1.0
CD B:GLU89 3.3 17.1 1.0
OD1 B:ASP40 3.4 4.3 1.0
OE1 B:GLU42 3.5 7.8 1.0
O B:HOH605 3.6 36.9 1.0
MG B:MG300 3.7 11.1 1.0
O B:HOH278 3.7 11.6 1.0
O B:HOH643 3.8 46.4 1.0
O B:HOH557 4.1 24.0 1.0
CG B:GLU89 4.2 12.1 1.0
OE2 B:GLU89 4.2 18.4 1.0
O22 B:PPV738 4.5 11.9 1.0
CG B:GLU42 4.5 8.1 1.0
CB B:ASP40 4.5 4.9 1.0
NH1 B:ARG87 4.6 11.2 1.0
CB B:GLU42 4.7 6.9 1.0
NH2 B:ARG87 4.7 11.6 1.0
O12 B:PPV738 4.8 11.2 1.0
O11 B:PPV738 4.8 10.0 1.0
CB B:GLU89 5.0 9.4 1.0

Reference:

M.Morar, K.Bhullar, D.W.Hughes, M.Junop, G.D.Wright. Structure and Mechanism of the Lincosamide Antibiotic Adenylyltransferase Linb. Structure V. 17 1649 2009.
ISSN: ISSN 0969-2126
PubMed: 20004168
DOI: 10.1016/J.STR.2009.10.013
Page generated: Mon Dec 14 08:20:57 2020

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