Atomistry » Magnesium » PDB 4zp1-5a27 » 4zze
Atomistry »
  Magnesium »
    PDB 4zp1-5a27 »
      4zze »

Magnesium in PDB 4zze: Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose

Protein crystallography data

The structure of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose, PDB code: 4zze was solved by F.Fredslund, M.Ejby, J.M.Andersen, D.J.Slotboom, M.A.Hachem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.11 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.880, 91.330, 142.050, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 20.5

Other elements in 4zze:

The structure of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose (pdb code 4zze). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose, PDB code: 4zze:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4zze

Go back to Magnesium Binding Sites List in 4zze
Magnesium binding site 1 out of 9 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:12.3
occ:1.00
 OD2 A:ASP111 2.1 13.3 1.0
O A:HOH1046 2.1 15.1 1.0
O A:HOH843 2.1 14.2 1.0
O A:HOH792 2.1 12.5 1.0
O A:HOH782 2.1 13.0 1.0
O A:HOH740 2.2 11.3 1.0
CG A:ASP111 3.1 14.7 1.0
HD22 A:ASN109 3.5 10.1 1.0
OD1 A:ASP111 3.5 10.6 1.0
HB3 A:ASN109 3.9 13.4 1.0
O A:HOH732 4.0 9.4 1.0
HB3 A:SER113 4.1 15.1 1.0
O A:HOH667 4.1 30.6 1.0
O A:HOH1059 4.2 30.2 1.0
O A:HOH690 4.3 11.1 1.0
O A:HOH822 4.3 15.9 1.0
O6 A:GLC503 4.3 15.7 1.0
ND2 A:ASN109 4.3 8.4 1.0
O A:HOH905 4.4 13.2 1.0
CB A:ASP111 4.4 9.6 1.0
O A:HOH909 4.4 34.0 1.0
O A:HOH1084 4.4 36.4 1.0
HB3 A:ASP111 4.5 11.5 1.0
O A:HOH1065 4.5 42.1 1.0
HB2 A:SER113 4.5 15.1 1.0
O A:HOH1072 4.6 24.9 1.0
HB2 A:ASP111 4.6 11.5 1.0
C5 A:GLC503 4.8 14.6 1.0
CB A:ASN109 4.8 11.2 1.0
CB A:SER113 4.8 12.6 1.0
HD21 A:ASN109 4.8 10.1 1.0
H A:SER113 4.9 11.2 1.0
O5 A:GLC503 5.0 16.7 1.0

Magnesium binding site 2 out of 9 in 4zze

Go back to Magnesium Binding Sites List in 4zze
Magnesium binding site 2 out of 9 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:15.1
occ:1.00
 OD1 A:ASP315 2.0 14.2 1.0
OG A:SER317 2.0 14.4 1.0
O A:HOH685 2.1 16.3 1.0
CG A:ASP315 2.9 13.6 1.0
H A:SER317 3.1 14.3 1.0
HB3 A:SER317 3.1 20.8 1.0
CB A:SER317 3.1 17.3 1.0
OD2 A:ASP315 3.3 21.9 1.0
N A:SER317 3.8 11.9 1.0
HA A:ASP315 3.8 18.0 1.0
HB2 A:SER317 3.8 20.8 1.0
HG3 A:LYS318 3.9 27.2 1.0
CA A:SER317 4.0 16.6 1.0
CB A:ASP315 4.1 16.7 1.0
O A:HOH791 4.2 16.0 1.0
CA A:ASP315 4.3 15.0 1.0
H A:LYS318 4.3 17.6 1.0
C A:ASP315 4.4 17.0 1.0
C A:SER317 4.5 20.5 1.0
H A:ALA316 4.5 15.3 1.0
N A:LYS318 4.5 14.7 1.0
N A:ALA316 4.6 12.7 1.0
HB2 A:ASP315 4.6 20.0 1.0
HD2 A:LYS318 4.6 28.9 1.0
HB2 A:LYS318 4.7 20.1 1.0
CG A:LYS318 4.8 22.6 1.0
HB3 A:ASP315 4.8 20.0 1.0
HA A:SER317 4.8 19.9 1.0
HE3 A:LYS318 4.9 30.0 1.0
O A:ASP315 5.0 14.7 1.0

Magnesium binding site 3 out of 9 in 4zze

Go back to Magnesium Binding Sites List in 4zze
Magnesium binding site 3 out of 9 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:37.3
occ:1.00
 O A:HOH713 2.0 29.4 1.0
O A:HOH889 2.1 31.8 1.0
O A:HOH616 2.2 30.7 1.0
O A:HOH952 2.3 35.7 1.0
OE2 A:GLU232 2.5 27.8 1.0
CD A:GLU232 3.3 29.6 1.0
O A:HOH1086 3.5 36.0 1.0
OE1 A:GLU232 3.5 33.0 1.0
H A:GLU232 3.8 18.7 1.0
O A:HOH844 4.1 25.4 1.0
HB2 A:ALA390 4.1 17.8 1.0
HA A:PRO231 4.2 17.9 1.0
HD13 A:ILE320 4.3 34.3 1.0
O A:HOH920 4.3 20.4 1.0
O B:HOH1040 4.3 34.1 1.0
O A:HOH702 4.5 16.0 1.0
O A:HOH1091 4.5 35.4 1.0
HA A:ALA390 4.5 20.7 1.0
HB1 A:ALA390 4.5 17.8 1.0
O A:VAL389 4.6 17.6 1.0
HB2 A:GLU232 4.6 21.8 1.0
O A:HOH857 4.6 37.9 1.0
O B:HOH971 4.6 35.4 1.0
N A:GLU232 4.7 15.6 1.0
HB3 A:PRO231 4.7 21.7 1.0
CB A:ALA390 4.7 14.8 1.0
CG A:GLU232 4.8 23.2 1.0
O B:HOH870 4.9 38.6 1.0
HG21 A:ILE320 4.9 17.0 1.0

Magnesium binding site 4 out of 9 in 4zze

Go back to Magnesium Binding Sites List in 4zze
Magnesium binding site 4 out of 9 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:33.8
occ:1.00
 O A:HOH841 2.2 37.0 1.0
O A:HOH964 2.4 36.5 1.0
O A:HOH794 2.8 32.8 1.0
HZ3 A:LYS301 4.0 54.6 1.0
O A:MET298 4.3 23.8 1.0
HA A:VAL299 4.3 24.9 1.0
O A:VAL299 4.4 21.7 1.0
HZ2 A:LYS301 4.6 54.6 1.0
NZ A:LYS301 4.6 45.5 1.0
HZ1 A:LYS301 4.7 54.6 1.0
O A:HOH935 4.9 17.9 1.0
O A:HOH1052 5.0 32.5 1.0

Magnesium binding site 5 out of 9 in 4zze

Go back to Magnesium Binding Sites List in 4zze
Magnesium binding site 5 out of 9 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:28.8
occ:1.00
 O A:HOH818 2.1 32.4 1.0
OD1 A:ASN300 2.1 23.3 1.0
OD1 A:ASP302 2.1 30.9 1.0
O A:HOH808 2.2 29.0 1.0
O A:HOH704 2.2 30.3 1.0
CG A:ASP302 3.1 36.5 1.0
CG A:ASN300 3.1 22.3 1.0
HD21 A:ASN300 3.2 25.4 1.0
H A:ASP302 3.4 26.5 1.0
OD2 A:ASP302 3.5 37.4 1.0
ND2 A:ASN300 3.6 21.2 1.0
N A:ASP302 4.2 22.1 1.0
HA A:ASN300 4.3 23.7 1.0
CB A:ASP302 4.4 26.6 1.0
CB A:ASN300 4.4 19.1 1.0
HD22 A:ASN300 4.4 25.4 1.0
H A:LYS301 4.5 25.0 1.0
CA A:ASP302 4.6 31.1 1.0
C A:ASP302 4.6 23.4 1.0
C A:ASN300 4.6 21.1 1.0
CA A:ASN300 4.7 19.8 1.0
N A:LYS301 4.7 20.8 1.0
H A:ILE303 4.8 27.3 1.0
N A:ILE303 4.8 22.8 1.0
HB3 A:ASP302 4.8 32.0 1.0
HB2 A:ASN300 4.8 22.9 1.0
O A:HOH935 4.9 17.9 1.0

Magnesium binding site 6 out of 9 in 4zze

Go back to Magnesium Binding Sites List in 4zze
Magnesium binding site 6 out of 9 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:12.9
occ:1.00
 O B:HOH790 2.0 12.1 1.0
O B:HOH877 2.0 14.9 1.0
O B:HOH1054 2.1 18.3 1.0
O B:HOH788 2.1 13.8 1.0
OD2 B:ASP111 2.1 13.0 1.0
O B:HOH772 2.2 10.7 1.0
CG B:ASP111 3.1 10.7 1.0
OD1 B:ASP111 3.5 12.9 1.0
HB3 B:ASN109 3.9 8.1 1.0
O B:HOH738 4.0 9.0 1.0
HB3 B:SER113 4.0 18.4 1.0
O B:HOH678 4.1 31.1 1.0
O B:HOH740 4.1 33.2 1.0
O B:HOH1094 4.1 34.4 1.0
O B:HOH692 4.2 14.4 1.0
OD1 B:ASN109 4.3 11.9 1.0
O6 B:GLC503 4.4 10.8 1.0
O B:HOH923 4.4 11.6 1.0
CB B:ASP111 4.4 10.9 1.0
O B:HOH803 4.5 15.1 1.0
HB3 B:ASP111 4.5 13.0 1.0
O B:HOH1081 4.6 19.3 1.0
HB2 B:SER113 4.6 18.4 1.0
HB2 B:ASP111 4.6 13.0 1.0
CB B:ASN109 4.7 6.7 1.0
CB B:SER113 4.8 15.4 1.0
C5 B:GLC503 4.8 10.7 1.0
H B:SER113 4.9 13.5 1.0

Magnesium binding site 7 out of 9 in 4zze

Go back to Magnesium Binding Sites List in 4zze
Magnesium binding site 7 out of 9 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:13.3
occ:1.00
 O B:HOH640 2.0 10.2 1.0
OD1 B:ASP315 2.1 16.2 1.0
OG B:SER317 2.1 10.3 1.0
CG B:ASP315 3.0 15.7 1.0
H B:SER317 3.1 14.0 1.0
HB3 B:SER317 3.1 16.2 1.0
CB B:SER317 3.2 13.5 1.0
OD2 B:ASP315 3.4 16.9 1.0
HG3 B:LYS318 3.5 24.9 1.0
N B:SER317 3.8 11.6 1.0
HB2 B:SER317 3.9 16.2 1.0
HA B:ASP315 3.9 14.1 1.0
CA B:SER317 4.0 14.9 1.0
H B:LYS318 4.1 17.3 1.0
O B:HOH660 4.2 16.0 1.0
CB B:ASP315 4.2 16.8 1.0
CA B:ASP315 4.4 11.8 1.0
CG B:LYS318 4.4 20.7 1.0
N B:LYS318 4.5 14.4 1.0
H B:ALA316 4.5 14.1 1.0
C B:ASP315 4.5 13.3 1.0
HE3 B:LYS318 4.5 30.6 1.0
N B:ALA316 4.6 11.8 1.0
C B:SER317 4.6 11.8 1.0
HG2 B:LYS318 4.6 24.9 1.0
HB2 B:ASP315 4.7 20.2 1.0
HA B:SER317 4.9 17.9 1.0
HB3 B:ASP315 4.9 20.2 1.0
HB2 B:LYS318 5.0 18.2 1.0
C B:ALA316 5.0 12.7 1.0

Magnesium binding site 8 out of 9 in 4zze

Go back to Magnesium Binding Sites List in 4zze
Magnesium binding site 8 out of 9 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:22.1
occ:1.00
 O B:HOH1064 2.1 25.4 1.0
O B:HOH915 2.1 22.9 1.0
O B:HOH631 2.1 20.5 1.0
O B:HOH824 2.1 23.2 1.0
OE1 B:GLU232 2.1 21.0 1.0
O B:HOH924 2.3 25.2 1.0
CD B:GLU232 3.1 19.1 1.0
OE2 B:GLU232 3.3 25.2 1.0
H B:GLU232 3.6 15.2 1.0
HA B:PRO231 4.0 18.2 1.0
O B:HOH807 4.1 20.5 1.0
O B:HOH1020 4.2 32.0 1.0
O B:HOH672 4.2 11.3 1.0
O A:HOH820 4.3 32.1 1.0
HB2 B:ALA390 4.3 22.1 1.0
HB2 B:GLU232 4.3 21.8 1.0
HD13 B:ILE320 4.3 26.1 1.0
HA B:ALA390 4.4 14.7 1.0
O B:HOH960 4.4 16.6 1.0
O B:HOH987 4.4 33.5 1.0
O A:HOH1004 4.4 29.9 1.0
N B:GLU232 4.4 12.7 1.0
CG B:GLU232 4.5 20.2 1.0
O B:VAL389 4.5 16.4 1.0
HB3 B:PRO231 4.6 24.0 1.0
HB1 B:ALA390 4.6 22.1 1.0
O B:HOH1095 4.6 31.9 1.0
CB B:ALA390 4.8 18.4 1.0
CA B:PRO231 4.8 15.1 1.0
CB B:GLU232 4.9 18.1 1.0
HG3 B:GLU232 4.9 24.2 1.0

Magnesium binding site 9 out of 9 in 4zze

Go back to Magnesium Binding Sites List in 4zze
Magnesium binding site 9 out of 9 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Panose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg507

b:37.2
occ:1.00
 O B:HOH761 2.0 27.2 1.0
O B:HOH973 2.3 39.2 1.0
O B:HOH618 2.4 38.4 1.0
HZ1 B:LYS351 3.2 46.8 1.0
NZ B:LYS351 4.0 39.0 1.0
OE2 B:GLU355 4.0 19.5 1.0
HZ3 B:LYS351 4.1 46.8 1.0
HD1 B:TYR371 4.1 29.7 1.0
OE1 B:GLU355 4.2 21.8 1.0
O B:HOH809 4.3 32.1 1.0
HZ2 B:LYS351 4.4 46.8 1.0
CD B:GLU355 4.5 24.8 1.0
O B:HOH1046 4.6 32.0 1.0
HE1 B:TYR371 4.7 34.1 1.0
CD1 B:TYR371 4.7 24.8 1.0
HE2 B:LYS351 4.7 41.9 1.0
CE B:LYS351 4.9 34.9 1.0
O B:HOH698 4.9 36.0 1.0
CE1 B:TYR371 5.0 28.4 1.0

Reference:

M.Ejby, F.Fredslund, J.M.Andersen, A.Vujicic Zagar, J.R.Henriksen, T.L.Andersen, B.Svensson, D.J.Slotboom, M.Abou Hachem. An Atp Binding Cassette Transporter Mediates the Uptake of Alpha-(1,6)-Linked Dietary Oligosaccharides in Bifidobacterium and Correlates with Competitive Growth on These Substrates. J. Biol. Chem. V. 291 20220 2016.
ISSN: ESSN 1083-351X
PubMed: 27502277
DOI: 10.1074/JBC.M116.746529
Page generated: Mon Dec 14 19:58:52 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