Magnesium in PDB 8qws: Crystal Structure of COTB2 Variant V80L in Complex with Alendronate

Protein crystallography data

The structure of Crystal Structure of COTB2 Variant V80L in Complex with Alendronate, PDB code: 8qws was solved by N.Dimos, S.Himpich, M.Ringel, R.Driller, D.T.Major, T.Brueck, B.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.16 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.173, 98.514, 107.417, 90, 90, 90
R / Rfree (%) 17.2 / 20.5

Other elements in 8qws:

The structure of Crystal Structure of COTB2 Variant V80L in Complex with Alendronate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of COTB2 Variant V80L in Complex with Alendronate (pdb code 8qws). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of COTB2 Variant V80L in Complex with Alendronate, PDB code: 8qws:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8qws

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Magnesium binding site 1 out of 7 in the Crystal Structure of COTB2 Variant V80L 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 Variant V80L in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:27.5
occ:1.00
 O15 A:AHD401 2.0 24.3 1.0
O A:HOH553 2.1 32.7 1.0
O11 A:AHD401 2.1 24.7 1.0
OD2 A:ASP110 2.1 27.7 1.0
O A:HOH570 2.1 31.5 1.0
O A:HOH530 2.4 24.7 1.0
CG A:ASP110 3.1 26.3 1.0
P14 A:AHD401 3.2 25.7 1.0
MG A:MG404 3.2 25.9 1.0
P9 A:AHD401 3.3 24.8 1.0
OD1 A:ASP110 3.3 26.5 1.0
C8 A:AHD401 3.5 26.2 1.0
C7 A:AHD401 3.5 24.8 1.0
O16 A:AHD401 3.7 21.4 1.0
O A:HOH633 4.1 30.4 1.0
O10 A:AHD401 4.1 24.1 1.0
O A:HOH513 4.1 43.9 1.0
NH2 A:ARG294 4.2 30.4 1.0
NH1 A:ARG227 4.2 39.8 1.0
OE2 A:GLU228 4.3 25.3 1.0
O A:HOH523 4.4 26.1 1.0
O12 A:AHD401 4.4 29.4 1.0
O A:HOH558 4.4 29.1 1.0
O17 A:AHD401 4.5 27.7 1.0
CB A:ASP110 4.5 29.7 1.0
NE2 A:GLN233 4.5 38.6 1.0
O A:HOH565 4.5 24.3 1.0
C2 A:AHD401 4.6 32.2 1.0
OD1 A:ASP111 4.6 35.9 1.0
O A:ASP110 4.6 31.3 1.0
O A:HOH525 4.6 24.6 1.0
MG A:MG403 4.8 25.9 1.0
O13 A:AHD401 4.9 27.2 1.0

Magnesium binding site 2 out of 7 in 8qws

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Magnesium binding site 2 out of 7 in the Crystal Structure of COTB2 Variant V80L 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 Variant V80L in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:25.9
occ:1.00
 O10 A:AHD401 2.1 24.1 1.0
OD1 A:ASN220 2.1 22.9 1.0
OE2 A:GLU228 2.1 25.3 1.0
O A:HOH509 2.1 24.3 1.0
O16 A:AHD401 2.1 21.4 1.0
OG A:SER224 2.3 23.6 1.0
CD A:GLU228 3.1 22.9 1.0
CG A:ASN220 3.1 23.0 1.0
CB A:SER224 3.2 24.8 1.0
P9 A:AHD401 3.2 24.8 1.0
P14 A:AHD401 3.4 25.7 1.0
OE1 A:GLU228 3.4 26.1 1.0
ND2 A:ASN220 3.5 23.7 1.0
C8 A:AHD401 3.7 26.2 1.0
O13 A:AHD401 3.9 27.2 1.0
O A:HOH565 3.9 24.3 1.0
O11 A:AHD401 3.9 24.7 1.0
NH2 A:ARG177 4.0 21.3 1.0
O A:HOH570 4.1 31.5 1.0
O A:ASN220 4.1 22.5 1.0
O15 A:AHD401 4.3 24.3 1.0
O17 A:AHD401 4.4 27.7 1.0
CG A:GLU228 4.4 27.0 1.0
OD1 A:ASP221 4.4 21.7 1.0
O12 A:AHD401 4.4 29.4 1.0
CB A:ASN220 4.4 20.2 1.0
C A:ASN220 4.5 21.2 1.0
CA A:SER224 4.6 24.0 1.0
MG A:MG402 4.8 27.5 1.0
NH2 A:ARG227 4.9 43.8 1.0
CA A:ASP221 4.9 20.7 1.0
N A:ASP221 4.9 21.4 1.0

Magnesium binding site 3 out of 7 in 8qws

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Magnesium binding site 3 out of 7 in the Crystal Structure of COTB2 Variant V80L 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 Variant V80L in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:25.9
occ:1.00
 O A:HOH525 2.0 24.6 1.0
O A:HOH530 2.0 24.7 1.0
OD1 A:ASP110 2.1 26.5 1.0
O15 A:AHD401 2.1 24.3 1.0
O A:HOH523 2.1 26.1 1.0
O A:HOH514 2.2 27.2 1.0
CG A:ASP110 3.1 26.3 1.0
MG A:MG402 3.2 27.5 1.0
P14 A:AHD401 3.3 25.7 1.0
OD2 A:ASP110 3.4 27.7 1.0
O17 A:AHD401 3.5 27.7 1.0
O A:HOH558 3.7 29.1 1.0
OD2 A:ASP180 4.1 25.8 1.0
O A:HOH633 4.1 30.4 1.0
OD1 A:ASP153 4.2 31.4 1.0
O16 A:AHD401 4.2 21.4 1.0
O A:HOH565 4.3 24.3 1.0
OD1 A:ASP180 4.3 28.9 1.0
O A:ASP180 4.3 26.6 1.0
C2 A:AHD401 4.3 32.2 1.0
O A:HOH570 4.4 31.5 1.0
C7 A:AHD401 4.4 24.8 1.0
CB A:ASP110 4.4 29.7 1.0
O A:HOH620 4.4 37.8 1.0
NH1 A:ARG177 4.5 21.6 1.0
C8 A:AHD401 4.6 26.2 1.0
CG A:ASP180 4.6 29.2 1.0
O A:HOH553 4.8 32.7 1.0
O11 A:AHD401 4.9 24.7 1.0

Magnesium binding site 4 out of 7 in 8qws

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Magnesium binding site 4 out of 7 in the Crystal Structure of COTB2 Variant V80L 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 Variant V80L in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:26.4
occ:1.00
 O16 B:AHD401 2.0 23.2 1.0
O12 B:AHD401 2.0 25.7 1.0
O B:HOH528 2.0 34.9 1.0
O B:HOH562 2.0 29.9 1.0
OD2 B:ASP110 2.1 26.3 1.0
O B:HOH536 2.4 26.6 1.0
CG B:ASP110 3.1 29.6 1.0
P14 B:AHD401 3.1 24.8 1.0
MG B:MG404 3.3 25.3 1.0
P9 B:AHD401 3.3 24.8 1.0
OD1 B:ASP110 3.4 28.6 1.0
C8 B:AHD401 3.5 26.4 1.0
C7 B:AHD401 3.6 23.7 1.0
O17 B:AHD401 3.6 21.7 1.0
O10 B:AHD401 4.1 23.9 1.0
O B:HOH645 4.1 30.3 1.0
NH1 B:ARG227 4.2 41.5 1.0
NH2 B:ARG294 4.2 30.8 1.0
OE2 B:GLU228 4.2 24.7 1.0
O B:HOH503 4.3 39.5 1.0
O15 B:AHD401 4.4 23.8 1.0
O B:HOH530 4.4 26.8 1.0
O11 B:AHD401 4.4 25.4 1.0
O B:HOH569 4.5 26.7 1.0
O B:HOH559 4.5 29.5 1.0
CB B:ASP110 4.5 30.1 1.0
NE2 B:GLN233 4.5 37.7 1.0
C2 B:AHD401 4.5 29.1 1.0
OD1 B:ASP111 4.6 34.2 1.0
O B:HOH522 4.6 25.6 1.0
O B:ASP110 4.7 28.3 1.0
MG B:MG403 4.7 24.0 1.0
O13 B:AHD401 4.9 23.3 1.0

Magnesium binding site 5 out of 7 in 8qws

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Magnesium binding site 5 out of 7 in the Crystal Structure of COTB2 Variant V80L 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 Variant V80L in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:24.0
occ:1.00
 O10 B:AHD401 2.0 23.9 1.0
OD1 B:ASN220 2.1 22.3 1.0
OE2 B:GLU228 2.1 24.7 1.0
O17 B:AHD401 2.1 21.7 1.0
O B:HOH517 2.2 24.9 1.0
OG B:SER224 2.3 24.4 1.0
CG B:ASN220 3.1 20.7 1.0
CD B:GLU228 3.1 24.5 1.0
CB B:SER224 3.2 23.8 1.0
P9 B:AHD401 3.2 24.8 1.0
P14 B:AHD401 3.3 24.8 1.0
ND2 B:ASN220 3.5 23.2 1.0
OE1 B:GLU228 3.5 25.6 1.0
C8 B:AHD401 3.7 26.4 1.0
O13 B:AHD401 3.8 23.3 1.0
O12 B:AHD401 3.8 25.7 1.0
O B:HOH569 3.9 26.7 1.0
NH2 B:ARG177 3.9 21.4 1.0
O B:HOH562 4.1 29.9 1.0
O B:ASN220 4.1 22.7 1.0
O16 B:AHD401 4.2 23.2 1.0
O15 B:AHD401 4.4 23.8 1.0
OD1 B:ASP221 4.4 23.6 1.0
CG B:GLU228 4.4 26.7 1.0
CB B:ASN220 4.4 18.3 1.0
O11 B:AHD401 4.4 25.4 1.0
C B:ASN220 4.5 21.1 1.0
CA B:SER224 4.6 24.9 1.0
MG B:MG402 4.7 26.4 1.0
NH2 B:ARG227 4.8 43.2 1.0
N B:ASP221 4.9 19.0 1.0
CA B:ASP221 4.9 19.6 1.0
NH1 B:ARG227 5.0 41.5 1.0

Magnesium binding site 6 out of 7 in 8qws

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Magnesium binding site 6 out of 7 in the Crystal Structure of COTB2 Variant V80L 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 Variant V80L in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:25.3
occ:1.00
 OD1 B:ASP110 2.0 28.6 1.0
O B:HOH522 2.1 25.6 1.0
O B:HOH536 2.1 26.6 1.0
O16 B:AHD401 2.2 23.2 1.0
O B:HOH516 2.2 29.4 1.0
O B:HOH530 2.2 26.8 1.0
CG B:ASP110 3.0 29.6 1.0
MG B:MG402 3.3 26.4 1.0
P14 B:AHD401 3.3 24.8 1.0
OD2 B:ASP110 3.3 26.3 1.0
O15 B:AHD401 3.5 23.8 1.0
O B:HOH559 3.7 29.5 1.0
OD1 B:ASP153 4.2 30.7 1.0
OD2 B:ASP180 4.2 26.9 1.0
O B:HOH645 4.2 30.3 1.0
O17 B:AHD401 4.3 21.7 1.0
O B:HOH569 4.3 26.7 1.0
OD1 B:ASP180 4.3 28.9 1.0
C2 B:AHD401 4.3 29.1 1.0
O B:HOH562 4.3 29.9 1.0
CB B:ASP110 4.4 30.1 1.0
O B:HOH630 4.4 42.4 1.0
O B:ASP180 4.4 27.2 1.0
C7 B:AHD401 4.5 23.7 1.0
NH1 B:ARG177 4.6 22.2 1.0
C8 B:AHD401 4.6 26.4 1.0
CG B:ASP180 4.6 32.7 1.0
O B:HOH528 4.8 34.9 1.0
O12 B:AHD401 4.9 25.7 1.0

Magnesium binding site 7 out of 7 in 8qws

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Magnesium binding site 7 out of 7 in the Crystal Structure of COTB2 Variant V80L in Complex with Alendronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of COTB2 Variant V80L in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:46.4
occ:1.00
 O B:HOH547 2.0 50.6 1.0
O B:HOH607 2.0 53.5 1.0
O B:HOH510 2.1 45.6 1.0
O B:HOH524 2.1 42.5 1.0
OG B:SER244 2.3 39.3 1.0
CB B:SER244 3.3 35.6 1.0
OD1 B:ASP242 3.9 35.9 1.0
OD2 B:ASP242 3.9 40.4 1.0
OD2 B:ASP12 4.1 50.5 1.0
OD1 B:ASP12 4.2 45.7 1.0
CG B:ASP242 4.4 36.5 1.0
CG B:ASP12 4.6 48.2 1.0
CA B:SER244 4.6 35.2 1.0
O B:SER244 4.7 40.7 1.0
C B:SER244 4.7 39.5 1.0

Reference:

N.Dimos, S.Himpich, R.Driller, B.Loll. Crystal Structure of COTB2 Variant V80L in Complex with Alendronate To Be Published.
Page generated: Fri Oct 4 17:00:03 2024

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