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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Sun Sep 29 00:12:53 2024

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