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Magnesium in PDB 6ggj: Crystal Structure of COTB2 in Complex with Alendronate

Enzymatic activity of Crystal Structure of COTB2 in Complex with Alendronate

All present enzymatic activity of Crystal Structure of COTB2 in Complex with Alendronate:
4.2.3.146;

Protein crystallography data

The structure of Crystal Structure of COTB2 in Complex with Alendronate, PDB code: 6ggj was solved by R.Driller, S.Janke, M.Fuchs, E.Warner, A.R.Mhashal, D.T.Major, M.Christmann, T.Brueck, B.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.380, 56.460, 56.930, 91.82, 101.66, 115.93
R / Rfree (%) 18.3 / 23.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of COTB2 in Complex with Alendronate (pdb code 6ggj). 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 COTB2 in Complex with Alendronate, PDB code: 6ggj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6ggj

Go back to Magnesium Binding Sites List in 6ggj
Magnesium binding site 1 out of 6 in the Crystal Structure of COTB2 in Complex with Alendronate


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 COTB2 in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:38.6
occ:1.00
 O A:HOH506 1.8 32.3 1.0
OD2 A:ASP110 2.0 28.6 1.0
O17 A:AHD401 2.1 33.0 1.0
O11 A:AHD401 2.2 32.4 1.0
O A:HOH567 2.5 29.9 1.0
O A:HOH565 2.6 34.4 1.0
CG A:ASP110 3.1 29.7 1.0
P14 A:AHD401 3.1 32.1 1.0
MG A:MG404 3.2 34.7 1.0
P9 A:AHD401 3.4 34.3 1.0
OD1 A:ASP110 3.4 31.2 1.0
O16 A:AHD401 3.5 30.1 1.0
C8 A:AHD401 3.5 37.5 1.0
C7 A:AHD401 3.7 37.7 1.0
O A:HOH593 4.0 27.2 1.0
NH1 A:ARG227 4.1 44.6 1.0
NH2 A:ARG294 4.1 45.9 1.0
OE2 A:GLU228 4.2 31.0 1.0
O10 A:AHD401 4.2 35.9 1.0
CB A:ASP110 4.4 35.6 1.0
O15 A:AHD401 4.4 29.5 1.0
O A:HOH526 4.4 22.4 1.0
O12 A:AHD401 4.5 40.1 1.0
O A:HOH524 4.5 25.2 1.0
O A:HOH544 4.5 30.8 1.0
MG A:MG403 4.6 38.0 1.0
O A:HOH535 4.7 29.8 1.0
NE2 A:GLN233 4.8 36.0 1.0
OD1 A:ASP111 4.8 45.4 1.0
O13 A:AHD401 4.9 32.4 1.0
C2 A:AHD401 5.0 43.6 1.0
O A:ASP110 5.0 39.2 1.0

Magnesium binding site 2 out of 6 in 6ggj

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Magnesium binding site 2 out of 6 in the Crystal Structure of COTB2 in Complex with Alendronate


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 COTB2 in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:38.0
occ:1.00
 O16 A:AHD401 2.0 30.1 1.0
O10 A:AHD401 2.0 35.9 1.0
OE2 A:GLU228 2.1 31.0 1.0
OD1 A:ASN220 2.2 29.4 1.0
O A:HOH522 2.2 31.0 1.0
OG A:SER224 2.5 33.4 0.7
CG A:ASN220 3.1 31.5 1.0
CD A:GLU228 3.1 35.7 1.0
P9 A:AHD401 3.2 34.3 1.0
P14 A:AHD401 3.2 32.1 1.0
ND2 A:ASN220 3.3 34.6 1.0
CB A:SER224 3.4 37.6 0.3
CB A:SER224 3.5 37.7 0.7
OG A:SER224 3.5 36.3 0.3
OE1 A:GLU228 3.5 31.8 1.0
C8 A:AHD401 3.6 37.5 1.0
O11 A:AHD401 3.6 32.4 1.0
O A:HOH526 3.8 22.4 1.0
O13 A:AHD401 3.8 32.4 1.0
O A:HOH506 3.9 32.3 1.0
NH2 A:ARG177 3.9 27.4 1.0
O A:ASN220 4.1 33.8 1.0
O15 A:AHD401 4.2 29.5 1.0
O17 A:AHD401 4.2 33.0 1.0
CG A:GLU228 4.4 37.1 1.0
O12 A:AHD401 4.4 40.1 1.0
CB A:ASN220 4.5 30.8 1.0
OD1 A:ASP221 4.5 26.4 1.0
C A:ASN220 4.5 32.5 1.0
MG A:MG402 4.6 38.6 1.0
NH2 A:ARG227 4.8 44.6 1.0
CA A:SER224 4.8 36.2 0.3
CA A:SER224 4.8 36.1 0.7
NH1 A:ARG227 4.9 44.6 1.0
O A:THR235 5.0 26.4 1.0
N A:ASP221 5.0 31.2 1.0

Magnesium binding site 3 out of 6 in 6ggj

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Magnesium binding site 3 out of 6 in the Crystal Structure of COTB2 in Complex with Alendronate


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 COTB2 in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:34.7
occ:1.00
 O17 A:AHD401 2.0 33.0 1.0
O A:HOH544 2.0 30.8 1.0
O A:HOH538 2.2 32.9 1.0
OD1 A:ASP110 2.2 31.2 1.0
O A:HOH524 2.3 25.2 1.0
O A:HOH565 2.3 34.4 1.0
CG A:ASP110 3.1 29.7 1.0
MG A:MG402 3.2 38.6 1.0
P14 A:AHD401 3.3 32.1 1.0
OD2 A:ASP110 3.3 28.6 1.0
O15 A:AHD401 3.5 29.5 1.0
O A:HOH535 4.0 29.8 1.0
O A:HOH526 4.0 22.4 1.0
O A:HOH593 4.1 27.2 1.0
OD2 A:ASP180 4.1 25.8 1.0
O16 A:AHD401 4.1 30.1 1.0
O A:HOH578 4.2 41.4 1.0
OD1 A:ASP180 4.3 28.3 1.0
O A:HOH506 4.3 32.3 1.0
O A:ASP180 4.3 23.2 1.0
OD1 A:ASP153 4.4 27.1 1.0
CB A:ASP110 4.5 35.6 1.0
NH1 A:ARG177 4.5 21.5 1.0
C7 A:AHD401 4.5 37.7 1.0
CG A:ASP180 4.6 28.3 1.0
C8 A:AHD401 4.6 37.5 1.0
C2 A:AHD401 5.0 43.6 1.0

Magnesium binding site 4 out of 6 in 6ggj

Go back to Magnesium Binding Sites List in 6ggj
Magnesium binding site 4 out of 6 in the Crystal Structure of COTB2 in Complex with Alendronate


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 COTB2 in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:31.6
occ:1.00
 O B:HOH546 2.0 30.2 1.0
O15 B:AHD401 2.0 25.9 1.0
O10 B:AHD401 2.1 27.9 1.0
OD2 B:ASP110 2.2 25.2 1.0
O B:HOH512 2.2 25.9 1.0
CG B:ASP110 3.2 28.3 1.0
P14 B:AHD401 3.2 25.5 1.0
MG B:MG403 3.3 29.5 1.0
P9 B:AHD401 3.4 26.0 1.0
OD1 B:ASP110 3.4 30.8 1.0
C8 B:AHD401 3.6 22.0 1.0
O16 B:AHD401 3.8 25.8 1.0
C7 B:AHD401 3.8 20.8 1.0
NH2 B:ARG227 3.8 43.1 1.0
O B:HOH597 4.0 24.9 1.0
NH2 B:ARG294 4.1 32.1 1.0
OE2 B:GLU228 4.2 33.1 1.0
O11 B:AHD401 4.2 25.6 1.0
O B:HOH530 4.3 32.3 1.0
NE2 B:GLN233 4.4 31.9 1.0
O B:HOH503 4.4 21.6 1.0
O17 B:AHD401 4.4 27.0 1.0
O B:HOH542 4.4 22.2 1.0
O12 B:AHD401 4.4 29.3 1.0
O B:HOH547 4.5 25.6 1.0
OD1 B:ASP111 4.5 40.5 1.0
CB B:ASP110 4.5 32.1 1.0
O B:HOH524 4.7 25.8 1.0
MG B:MG404 4.8 26.4 1.0
O B:ASP110 4.9 35.8 1.0
C2 B:AHD401 5.0 25.7 1.0

Magnesium binding site 5 out of 6 in 6ggj

Go back to Magnesium Binding Sites List in 6ggj
Magnesium binding site 5 out of 6 in the Crystal Structure of COTB2 in Complex with Alendronate


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 COTB2 in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:29.5
occ:1.00
 O B:HOH553 2.0 29.3 1.0
OD1 B:ASP110 2.1 30.8 1.0
O B:HOH524 2.1 25.8 1.0
O B:HOH512 2.2 25.9 1.0
O15 B:AHD401 2.2 25.9 1.0
O B:HOH542 2.2 22.2 1.0
CG B:ASP110 3.1 28.3 1.0
P14 B:AHD401 3.3 25.5 1.0
O17 B:AHD401 3.3 27.0 1.0
MG B:MG402 3.3 31.6 1.0
OD2 B:ASP110 3.4 25.2 1.0
O B:HOH547 4.0 25.6 1.0
OD2 B:ASP180 4.0 20.5 1.0
O B:HOH503 4.1 21.6 1.0
O16 B:AHD401 4.2 25.8 1.0
OD1 B:ASP180 4.2 24.3 1.0
O B:HOH581 4.3 28.2 1.0
O B:HOH597 4.3 24.9 1.0
OD1 B:ASP153 4.3 32.3 1.0
O B:ASP180 4.4 21.6 1.0
CB B:ASP110 4.4 32.1 1.0
C7 B:AHD401 4.5 20.8 1.0
CG B:ASP180 4.5 24.8 1.0
NH1 B:ARG177 4.5 20.8 1.0
O B:HOH546 4.5 30.2 1.0
C8 B:AHD401 4.6 22.0 1.0
C2 B:AHD401 4.7 25.7 1.0
O10 B:AHD401 5.0 27.9 1.0

Magnesium binding site 6 out of 6 in 6ggj

Go back to Magnesium Binding Sites List in 6ggj
Magnesium binding site 6 out of 6 in the Crystal Structure of COTB2 in Complex with Alendronate


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 COTB2 in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:26.4
occ:1.00
 O11 B:AHD401 2.0 25.6 1.0
O B:HOH543 2.1 20.3 1.0
OD1 B:ASN220 2.1 21.0 1.0
O16 B:AHD401 2.1 25.8 1.0
OE2 B:GLU228 2.3 33.1 1.0
OG B:SER224 2.5 26.6 1.0
CG B:ASN220 3.1 21.7 1.0
P9 B:AHD401 3.2 26.0 1.0
CD B:GLU228 3.3 26.0 1.0
P14 B:AHD401 3.3 25.5 1.0
CB B:SER224 3.5 30.5 1.0
ND2 B:ASN220 3.5 25.6 1.0
OE1 B:GLU228 3.6 28.3 1.0
C8 B:AHD401 3.6 22.0 1.0
O13 B:AHD401 3.7 23.4 1.0
O10 B:AHD401 3.8 27.9 1.0
NH2 B:ARG177 3.8 23.1 1.0
O B:HOH503 4.0 21.6 1.0
O B:ASN220 4.0 22.4 1.0
O B:HOH546 4.2 30.2 1.0
O15 B:AHD401 4.2 25.9 1.0
O17 B:AHD401 4.3 27.0 1.0
O12 B:AHD401 4.4 29.3 1.0
CB B:ASN220 4.4 23.6 1.0
C B:ASN220 4.4 24.2 1.0
OD1 B:ASP221 4.5 22.2 1.0
NH2 B:ARG227 4.5 43.1 1.0
CG B:GLU228 4.6 29.2 1.0
MG B:MG402 4.8 31.6 1.0
CA B:SER224 4.9 25.3 1.0
N B:ASP221 4.9 25.8 1.0
CZ B:ARG177 5.0 19.9 1.0
CA B:ASP221 5.0 25.7 1.0

Reference:

R.Driller, S.Janke, M.Fuchs, E.Warner, A.R.Mhashal, D.T.Major, M.Christmann, T.Bruck, B.Loll. Towards A Comprehensive Understanding of the Structural Dynamics of A Bacterial Diterpene Synthase During Catalysis. Nat Commun V. 9 3971 2018.
ISSN: ESSN 2041-1723
PubMed: 30266969
DOI: 10.1038/S41467-018-06325-8
Page generated: Tue Oct 1 01:10:24 2024

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