Magnesium in PDB 6nr6: Crystal Structure of Staphylococcus Pseudintermedius Sbni in Complex with Adp

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Pseudintermedius Sbni in Complex with Adp, PDB code: 6nr6 was solved by M.M.Verstraete, L.D.Morales, M.J.Kobylarz, S.A.Loutet, H.A.Laakso, D.E.Heinrichs, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.81 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.644, 73.074, 88.372, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Pseudintermedius Sbni in Complex with Adp (pdb code 6nr6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Staphylococcus Pseudintermedius Sbni in Complex with Adp, PDB code: 6nr6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6nr6

Go back to Magnesium Binding Sites List in 6nr6
Magnesium binding site 1 out of 5 in the Crystal Structure of Staphylococcus Pseudintermedius Sbni in Complex with Adp


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 Staphylococcus Pseudintermedius Sbni in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:25.4
occ:1.00
OD1 A:ASN172 2.1 43.6 1.0
OD2 A:ASP173 2.3 43.8 1.0
O A:HOH480 2.4 33.8 1.0
OD1 A:ASP170 2.4 40.2 1.0
O A:PRO94 2.4 44.2 1.0
OD2 A:ASP170 2.5 37.8 1.0
CG A:ASP170 2.8 40.3 1.0
CG A:ASP173 3.2 42.6 1.0
CG A:ASN172 3.3 42.2 1.0
C A:PRO94 3.5 39.5 1.0
OD1 A:ASP173 3.7 42.1 1.0
N A:ASP173 3.8 32.4 1.0
ND2 A:ASN172 3.9 46.0 1.0
CA A:PRO94 4.0 37.0 1.0
CA A:ASP173 4.2 29.6 1.0
C A:ASN172 4.2 36.8 1.0
CB A:ASP173 4.3 35.5 1.0
CB A:ASP170 4.3 41.2 1.0
CB A:PRO94 4.5 40.9 1.0
CB A:ASN172 4.5 38.6 1.0
N A:ASN172 4.6 35.1 1.0
N A:ASN95 4.6 35.5 1.0
CA A:ASN172 4.6 36.7 1.0
O A:ASN172 4.7 37.3 1.0
CA A:ASN95 4.9 32.9 1.0

Magnesium binding site 2 out of 5 in 6nr6

Go back to Magnesium Binding Sites List in 6nr6
Magnesium binding site 2 out of 5 in the Crystal Structure of Staphylococcus Pseudintermedius Sbni in Complex with Adp


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 Staphylococcus Pseudintermedius Sbni in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:40.5
occ:1.00
O A:GLY101 2.3 46.5 1.0
O A:HOH439 2.3 42.4 1.0
O A:HOH417 2.4 59.1 1.0
O A:HOH531 2.5 49.4 1.0
O A:HOH401 2.9 47.0 1.0
CB A:ASP104 3.3 62.1 1.0
C A:GLY101 3.4 50.9 1.0
OD1 A:ASP104 3.9 68.7 1.0
CG A:ASP104 4.1 70.1 1.0
OE1 A:GLU106 4.2 72.2 1.0
CA A:GLY101 4.3 49.7 1.0
O A:HOH403 4.3 55.1 1.0
N A:LEU102 4.4 48.3 1.0
CA A:ASP104 4.4 59.1 1.0
CA A:LEU102 4.4 51.2 1.0
O A:GLU105 4.5 63.1 1.0
N A:ASP104 4.5 48.7 1.0
CB A:SER151 4.5 47.4 1.0
C A:ASP104 4.7 60.8 1.0
C A:LEU102 4.7 52.3 1.0
O A:ASP104 4.8 60.3 1.0
O A:HOH404 4.8 65.9 1.0
OG A:SER151 4.8 41.9 1.0
O A:GLU100 4.9 42.6 1.0

Magnesium binding site 3 out of 5 in 6nr6

Go back to Magnesium Binding Sites List in 6nr6
Magnesium binding site 3 out of 5 in the Crystal Structure of Staphylococcus Pseudintermedius Sbni in Complex with Adp


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 Staphylococcus Pseudintermedius Sbni in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:36.2
occ:1.00
O1B A:ADP304 2.2 45.2 1.0
OD1 A:ASP58 2.3 41.3 1.0
O1A A:ADP304 2.3 54.4 1.0
O A:HOH514 2.6 52.2 1.0
H5'1 A:ADP304 2.8 91.2 1.0
CG A:ASP58 3.3 37.1 1.0
PA A:ADP304 3.5 56.2 1.0
PB A:ADP304 3.5 39.2 1.0
OD2 A:ASP58 3.5 47.6 1.0
C5' A:ADP304 3.6 76.0 1.0
O5' A:ADP304 3.8 64.8 1.0
H5'2 A:ADP304 3.8 91.2 1.0
NH2 A:ARG62 3.8 38.0 1.0
O3A A:ADP304 3.9 53.2 1.0
O3B A:ADP304 4.2 35.8 1.0
N A:GLY59 4.4 30.8 1.0
O A:HOH445 4.5 50.5 1.0
CB A:ASP58 4.6 28.1 1.0
O2B A:ADP304 4.7 37.9 1.0
O2A A:ADP304 4.8 53.0 1.0
O A:HOH420 4.9 43.2 1.0
CA A:ASP58 4.9 28.0 1.0
C4' A:ADP304 4.9 86.5 1.0
C A:ASP58 4.9 30.0 1.0
CZ A:ARG62 5.0 36.4 1.0

Magnesium binding site 4 out of 5 in 6nr6

Go back to Magnesium Binding Sites List in 6nr6
Magnesium binding site 4 out of 5 in the Crystal Structure of Staphylococcus Pseudintermedius Sbni in Complex with Adp


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 Staphylococcus Pseudintermedius Sbni in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:45.4
occ:1.00
OD1 B:ASP173 2.3 51.8 1.0
OD1 B:ASN172 2.4 62.4 1.0
O B:HOH429 2.4 66.2 1.0
O B:PRO94 2.4 55.5 1.0
OD1 B:ASP170 2.5 60.5 1.0
OD2 B:ASP170 2.5 53.6 1.0
CG B:ASP170 2.8 57.8 1.0
CG B:ASP173 3.1 52.9 1.0
CG B:ASN172 3.4 61.2 1.0
C B:PRO94 3.5 53.6 1.0
OD2 B:ASP173 3.6 55.0 1.0
CA B:PRO94 3.8 50.5 1.0
ND2 B:ASN172 3.9 63.2 1.0
N B:ASP173 4.0 52.4 1.0
O B:HOH406 4.1 60.3 1.0
CB B:PRO94 4.1 50.2 1.0
CB B:ASP173 4.2 49.8 1.0
CA B:ASP173 4.2 49.9 1.0
C B:ASN172 4.3 56.9 1.0
CB B:ASP170 4.4 57.2 1.0
CB B:ASN172 4.6 59.2 1.0
N B:ASN172 4.7 55.0 1.0
N B:ASN95 4.7 55.4 1.0
O B:ASN172 4.7 55.4 1.0
CA B:ASN172 4.7 57.7 1.0

Magnesium binding site 5 out of 5 in 6nr6

Go back to Magnesium Binding Sites List in 6nr6
Magnesium binding site 5 out of 5 in the Crystal Structure of Staphylococcus Pseudintermedius Sbni in Complex with Adp


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 Staphylococcus Pseudintermedius Sbni in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:61.3
occ:1.00
O2A B:ADP303 2.1 83.5 1.0
O B:HOH438 2.3 64.2 1.0
OD1 B:ASP58 2.4 68.4 1.0
O B:HOH427 2.5 54.8 1.0
O B:HOH414 2.5 63.9 1.0
O3B B:ADP303 2.6 72.9 1.0
CG B:ASP58 3.6 64.5 1.0
PA B:ADP303 3.6 82.4 1.0
PB B:ADP303 3.7 72.4 1.0
O B:HOH433 3.9 59.9 1.0
O2B B:ADP303 4.0 72.3 1.0
OD2 B:ASP58 4.1 66.3 1.0
O3A B:ADP303 4.1 77.1 1.0
NH2 B:ARG26 4.3 83.1 1.0
C5' B:ADP303 4.4 0.6 1.0
O B:HOH416 4.4 55.5 1.0
N B:GLY59 4.5 57.8 1.0
O5' B:ADP303 4.5 92.0 1.0
NH2 B:ARG62 4.6 64.6 1.0
O1A B:ADP303 4.6 82.3 1.0
CB B:ASP58 4.8 58.9 1.0
CA B:ASP58 4.8 57.3 1.0

Reference:

M.M.Verstraete, M.J.Kobylarz, S.A.Loutet, L.D.Morales, H.A.Laakso, D.E.Heinrichs, M.E.P.Murphy. Crystal Structure of Staphylococcus Pseudintermedius Sbni in Complex with Adp To Be Published.
Page generated: Mon Dec 14 23:41:29 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy