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Magnesium in PDB 7zrn: Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate

Enzymatic activity of Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate

All present enzymatic activity of Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate:
4.2.3.175;

Protein crystallography data

The structure of Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate, PDB code: 7zrn was solved by C.W.Levy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.92 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.315, 89.644, 100.563, 90, 90, 90
R / Rfree (%) 17.5 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate (pdb code 7zrn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate, PDB code: 7zrn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7zrn

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Magnesium binding site 1 out of 6 in the Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:43.4
occ:1.00
 O11 A:PPV401 2.1 33.6 0.7
O32 A:PPV401 2.1 40.9 0.7
O A:HOH509 2.2 36.0 1.0
OD1 A:ASN248 2.3 37.6 1.0
OE2 A:GLU256 2.3 45.0 1.0
OG A:SER252 2.7 44.4 1.0
HG A:SER252 2.9 53.3 1.0
HD21 A:ASN248 3.0 51.5 1.0
CG A:ASN248 3.2 38.8 1.0
HH22 A:ARG202 3.2 33.4 1.0
P2 A:PPV401 3.2 41.4 0.7
P1 A:PPV401 3.3 36.3 0.7
CD A:GLU256 3.3 54.8 1.0
OPP A:PPV401 3.4 36.8 0.7
ND2 A:ASN248 3.4 42.9 1.0
NH2 A:ARG202 3.6 27.8 1.0
HH21 A:ARG202 3.6 33.4 1.0
OE1 A:GLU256 3.7 41.6 1.0
CB A:SER252 3.8 45.3 1.0
HB2 A:SER252 3.8 54.4 1.0
HB3 A:SER252 3.9 54.4 1.0
O12 A:PPV401 3.9 33.6 0.7
HA A:ASP249 3.9 31.8 1.0
OD1 A:ASP249 4.0 29.0 1.0
O A:HOH587 4.0 38.3 1.0
O31 A:PPV401 4.3 35.5 0.7
O A:ASN248 4.3 27.0 1.0
HD22 A:ASN248 4.3 51.5 1.0
O21 A:PPV401 4.3 26.7 0.7
O A:HOH619 4.4 43.3 1.0
O22 A:PPV401 4.5 37.8 0.7
CZ A:ARG202 4.5 25.5 1.0
C A:ASN248 4.5 28.2 1.0
HE3 A:LYS255 4.5 78.6 1.0
HG3 A:GLU256 4.6 62.6 1.0
HH12 A:ARG202 4.6 32.0 1.0
CB A:ASN248 4.6 27.5 1.0
CG A:GLU256 4.6 52.2 1.0
HZ2 A:LYS255 4.6 67.8 1.0
HZ1 A:LYS255 4.6 67.8 1.0
N A:ASP249 4.7 26.8 1.0
MG A:MG403 4.7 43.9 1.0
HD22 A:ASN264 4.7 31.6 1.0
CA A:ASP249 4.7 26.5 1.0
HB3 A:ASN248 4.8 33.0 1.0
HE2 A:TYR337 4.8 66.2 1.0
NH1 A:ARG202 4.9 26.7 1.0
O A:SER252 4.9 52.9 1.0
HH A:TYR337 4.9 57.7 1.0
NZ A:LYS255 5.0 56.5 1.0

Magnesium binding site 2 out of 6 in 7zrn

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Magnesium binding site 2 out of 6 in the Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:43.9
occ:1.00
 O31 A:PPV401 2.1 35.5 0.7
O A:HOH619 2.1 43.3 1.0
O12 A:PPV401 2.1 33.6 0.7
OE2 A:GLU111 2.2 35.7 1.0
O A:HOH516 2.2 38.2 1.0
HZ1 A:LYS255 3.0 67.8 1.0
P1 A:PPV401 3.1 36.3 0.7
CD A:GLU111 3.1 43.9 1.0
P2 A:PPV401 3.2 41.4 0.7
OD2 A:ASP107 3.3 33.9 1.0
OPP A:PPV401 3.3 36.8 0.7
OE1 A:GLU111 3.4 41.0 1.0
MG A:MG404 3.4 35.8 1.0
HZ2 A:LYS255 3.4 67.8 1.0
NZ A:LYS255 3.6 56.5 1.0
O11 A:PPV401 3.7 33.6 0.7
HZ3 A:LYS255 3.8 67.8 1.0
NH2 A:ARG336 3.9 32.4 0.6
O32 A:PPV401 4.1 40.9 0.7
O A:HOH538 4.2 47.7 1.0
OE2 A:GLU256 4.2 45.0 1.0
O22 A:PPV401 4.4 37.8 0.7
OD1 A:ASP108 4.4 31.5 0.5
O21 A:PPV401 4.4 26.7 0.7
CG A:GLU111 4.5 40.7 1.0
CG A:ASP107 4.6 29.1 1.0
HG3 A:GLU111 4.6 48.8 1.0
O A:HOH507 4.6 34.0 1.0
MG A:MG402 4.7 43.4 1.0
O A:HOH586 4.8 45.6 1.0
O A:HOH520 4.9 43.6 1.0
CE A:LYS255 4.9 65.5 1.0
HG3 A:GLU256 5.0 62.6 1.0
HG2 A:GLU111 5.0 48.8 1.0

Magnesium binding site 3 out of 6 in 7zrn

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Magnesium binding site 3 out of 6 in the Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:35.8
occ:1.00
 O A:HOH664 2.2 36.9 1.0
O31 A:PPV401 2.3 35.5 0.7
O A:HOH586 2.4 45.6 1.0
OE2 A:GLU111 2.5 35.7 1.0
O A:HOH507 2.6 34.0 1.0
OD2 A:ASP107 2.8 33.9 1.0
OD1 A:ASP107 3.2 29.0 1.0
CG A:ASP107 3.4 29.1 1.0
MG A:MG403 3.4 43.9 1.0
HG3 A:GLU111 3.5 48.8 1.0
CD A:GLU111 3.6 43.9 1.0
P1 A:PPV401 3.6 36.3 0.7
O21 A:PPV401 3.8 26.7 0.7
CG A:GLU111 3.9 40.7 1.0
HG2 A:GLU111 4.1 48.8 1.0
O A:HOH538 4.1 47.7 1.0
HB A:THR205 4.3 24.5 1.0
O11 A:PPV401 4.4 33.6 0.7
HE1 A:TYR176 4.4 25.4 1.0
O A:HOH587 4.4 38.3 1.0
O A:HOH619 4.5 43.3 1.0
O A:THR205 4.5 19.5 1.0
OE1 A:GLU183 4.5 33.9 1.0
HH A:TYR176 4.5 29.0 1.0
OE1 A:GLU111 4.7 41.0 1.0
HH12 A:ARG202 4.7 32.0 1.0
OPP A:PPV401 4.8 36.8 0.7
OE2 A:GLU183 4.8 31.1 1.0
CB A:ASP107 4.9 27.3 1.0
O A:HOH577 4.9 42.0 1.0

Magnesium binding site 4 out of 6 in 7zrn

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Magnesium binding site 4 out of 6 in the Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:28.8
occ:1.00
 HG B:SER252 1.7 34.2 1.0
O32 B:PPV401 2.0 21.7 0.8
O31 B:PPV401 2.1 27.4 0.8
ND2 B:ASN248 2.1 23.5 1.0
OE2 B:GLU256 2.1 28.1 1.0
O B:HOH506 2.2 26.1 1.0
HD21 B:ASN248 2.4 28.2 1.0
OG B:SER252 2.4 28.5 1.0
CD B:GLU256 3.2 32.1 1.0
P1 B:PPV401 3.2 28.5 0.8
CG B:ASN248 3.2 28.9 1.0
P2 B:PPV401 3.2 25.1 0.8
HH22 B:ARG202 3.3 28.4 1.0
CB B:SER252 3.3 27.2 1.0
HB2 B:SER252 3.3 32.7 1.0
OPP B:PPV401 3.4 24.1 0.8
HB3 B:SER252 3.5 32.7 1.0
OE1 B:GLU256 3.6 28.8 1.0
OD1 B:ASN248 3.6 31.8 1.0
NH2 B:ARG202 3.6 23.6 1.0
HH21 B:ARG202 3.7 28.4 1.0
HA B:ASP249 3.9 26.3 1.0
O11 B:PPV401 3.9 27.2 0.8
O B:HOH590 3.9 26.9 1.0
OD1 B:ASP249 4.0 23.9 1.0
O B:HOH643 4.1 28.8 1.0
O12 B:PPV401 4.2 27.2 0.8
O B:ASN248 4.3 24.9 1.0
O22 B:PPV401 4.3 21.4 0.8
HZ1 B:LYS255 4.3 46.0 1.0
O21 B:PPV401 4.4 29.0 0.8
C B:ASN248 4.5 21.4 1.0
CG B:GLU256 4.5 32.7 1.0
HG3 B:GLU256 4.5 39.2 1.0
CB B:ASN248 4.5 22.9 1.0
CZ B:ARG202 4.5 20.8 1.0
HD22 B:ASN264 4.6 26.2 1.0
HB3 B:ASN248 4.6 27.5 1.0
N B:ASP249 4.7 24.1 1.0
CA B:ASP249 4.7 21.9 1.0
HH12 B:ARG202 4.7 28.6 1.0
HE3 B:LYS255 4.7 53.5 1.0
CA B:SER252 4.7 29.1 1.0
MG B:MG405 4.8 29.0 1.0
HG2 B:GLU256 4.9 39.2 1.0
O B:SER252 4.9 35.1 1.0
NH1 B:ARG202 5.0 23.8 1.0
H B:SER252 5.0 35.5 1.0

Magnesium binding site 5 out of 6 in 7zrn

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Magnesium binding site 5 out of 6 in the Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:22.9
occ:1.00
 O B:HOH528 2.2 28.8 1.0
O B:HOH587 2.3 30.9 1.0
O B:HOH578 2.3 33.8 1.0
O12 B:PPV401 2.3 27.2 0.8
OE2 B:GLU111 2.4 27.6 1.0
OD2 B:ASP107 2.5 28.4 1.0
O B:HOH518 2.5 53.2 1.0
CG B:ASP107 3.3 28.2 1.0
OD1 B:ASP107 3.4 24.7 1.0
MG B:MG405 3.5 29.0 1.0
CD B:GLU111 3.5 30.8 1.0
O B:HOH502 3.5 29.6 1.0
P2 B:PPV401 3.5 25.1 0.8
HG3 B:GLU111 3.6 33.7 1.0
O22 B:PPV401 3.7 21.4 0.8
CG B:GLU111 3.9 28.1 1.0
HG2 B:GLU111 3.9 33.7 1.0
O B:HOH570 4.2 32.0 1.0
HB B:THR205 4.3 20.8 1.0
OE1 B:GLU183 4.4 32.8 1.0
O32 B:PPV401 4.4 21.7 0.8
O B:HOH643 4.4 28.8 1.0
O B:HOH590 4.5 26.9 1.0
OE1 B:GLU111 4.6 27.6 1.0
HE1 B:TYR176 4.6 21.0 1.0
O B:THR205 4.6 17.3 1.0
HH12 B:ARG202 4.7 28.6 1.0
H3 B:ACT402 4.7 36.5 1.0
CB B:ASP107 4.7 27.0 1.0
OE2 B:GLU183 4.7 29.2 1.0
OPP B:PPV401 4.7 24.1 0.8
H1 B:ACT402 4.8 36.5 1.0
HH B:TYR176 4.8 26.9 1.0
HB3 B:ASP107 4.9 32.4 1.0

Magnesium binding site 6 out of 6 in 7zrn

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Magnesium binding site 6 out of 6 in the Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of 10-Epi-Cubebol Synthase From Sorangium Cellulosum (Sccubs) in Complex with Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:29.0
occ:1.00
 O B:HOH560 2.0 30.1 1.0
O B:HOH643 2.2 28.8 1.0
O11 B:PPV401 2.2 27.2 0.8
O12 B:PPV401 2.2 27.2 0.8
OE2 B:GLU111 2.2 27.6 1.0
O B:HOH502 2.2 29.6 1.0
HH21 B:ARG336 3.0 42.0 1.0
CD B:GLU111 3.0 30.8 1.0
HZ1 B:LYS255 3.1 46.0 1.0
OE1 B:GLU111 3.2 27.6 1.0
P2 B:PPV401 3.3 25.1 0.8
P1 B:PPV401 3.3 28.5 0.8
MG B:MG404 3.5 22.9 1.0
OPP B:PPV401 3.5 24.1 0.8
OD2 B:ASP107 3.5 28.4 1.0
HH22 B:ARG336 3.6 42.0 1.0
HZ3 B:LYS255 3.6 46.0 1.0
NH2 B:ARG336 3.6 35.0 1.0
NZ B:LYS255 3.7 38.3 1.0
HZ2 B:LYS255 3.8 46.0 1.0
O32 B:PPV401 3.9 21.7 0.8
OD1 B:ASP108 4.0 32.2 1.0
O B:HOH570 4.1 32.0 1.0
O B:HOH503 4.1 53.2 1.0
O31 B:PPV401 4.2 27.4 0.8
O B:HOH518 4.3 53.2 1.0
O21 B:PPV401 4.4 29.0 0.8
OE2 B:GLU256 4.4 28.1 1.0
CG B:GLU111 4.5 28.1 1.0
O22 B:PPV401 4.6 21.4 0.8
HG3 B:GLU111 4.6 33.7 1.0
O B:HOH587 4.7 30.9 1.0
CG B:ASP107 4.8 28.2 1.0
O B:HOH528 4.8 28.8 1.0
O B:HOH679 4.8 36.1 1.0
O B:HOH702 4.8 46.5 1.0
MG B:MG403 4.8 28.8 1.0
CZ B:ARG336 4.9 40.4 1.0
HE B:ARG336 4.9 44.3 1.0
HG2 B:GLU111 4.9 33.7 1.0
HG2 B:GLU256 4.9 39.2 1.0
O B:HOH603 4.9 32.0 1.0

Reference:

J.N.Whitehead, N.G.H.Leferink, G.Komati Reddy, C.W.Levy, S.Hay, E.Takano, N.S.Scrutton. How A 10- Epi-Cubebol Synthase Avoids Premature Reaction Quenching to Form A Tricyclic Product at High Purity. Acs Catalysis V. 12 12123 2022.
ISSN: ESSN 2155-5435
PubMed: 36249875
DOI: 10.1021/ACSCATAL.2C03155
Page generated: Thu Oct 3 17:04:40 2024

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