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Magnesium in PDB 4zs9: Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose

Protein crystallography data

The structure of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose, PDB code: 4zs9 was solved by F.Fredslund, M.Ejby, J.M.Andersen, D.J.Slotboom, M.Abou Hachem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.00 / 1.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.540, 90.820, 146.750, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 16.7

Other elements in 4zs9:

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

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose (pdb code 4zs9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose, PDB code: 4zs9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 4zs9

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Magnesium binding site 1 out of 15 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose


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 Raffinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:11.3
occ:1.00
 OD2 A:ASP53 2.1 11.5 1.0
O A:HOH726 2.1 14.2 1.0
O A:HOH682 2.1 12.0 1.0
CG A:ASP53 3.2 13.3 1.0
HB2 A:ASP53 3.2 14.2 1.0
CB A:ASP53 3.7 11.9 1.0
O A:VAL102 4.1 10.8 1.0
HA A:PRO103 4.2 12.8 1.0
HB3 A:ASP53 4.2 14.2 1.0
O A:HOH1031 4.2 19.8 1.0
OD1 A:ASP53 4.2 16.8 1.0
O A:HOH689 4.2 11.8 1.0
O A:ARG101 4.3 13.7 1.0
OD2 A:ASP104 4.3 11.2 1.0
HA A:ARG101 4.4 21.5 1.0
H A:ASP53 4.4 13.2 1.0
C A:ARG101 4.7 14.4 1.0
O A:HOH728 4.9 12.8 1.0
C A:VAL102 4.9 9.9 1.0
H A:ASP104 4.9 11.0 1.0
N A:ASP53 5.0 11.0 1.0
HB2 A:ARG101 5.0 25.3 1.0
CA A:ASP53 5.0 10.9 1.0

Magnesium binding site 2 out of 15 in 4zs9

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Magnesium binding site 2 out of 15 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose


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 Raffinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:39.9
occ:1.00
 O A:HOH712 2.1 33.1 1.0
O A:HOH1076 2.1 29.2 1.0
O A:HOH1072 2.1 29.7 1.0
O B:HOH1139 2.2 34.5 1.0
O B:HOH934 2.2 30.4 1.0
O B:HOH1086 2.3 35.9 1.0
O B:HOH1093 4.2 26.2 1.0
O A:HOH817 4.2 13.0 1.0
O A:HOH670 4.2 21.1 1.0
O B:HOH720 4.3 19.6 1.0
O A:HOH1042 4.3 22.1 1.0
OD1 A:ASN145 4.4 14.1 1.0
OD1 B:ASN145 4.4 15.6 1.0
HE3 B:LYS155 4.7 18.4 1.0
HB3 B:PRO152 4.8 15.3 1.0
O A:HOH880 4.8 23.8 1.0
HE3 A:LYS155 4.8 17.9 1.0
HG3 B:LYS155 4.9 18.3 1.0
O B:HOH980 4.9 22.6 1.0
HB3 A:PRO152 4.9 17.4 1.0
HG3 A:LYS155 5.0 19.2 1.0

Magnesium binding site 3 out of 15 in 4zs9

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Magnesium binding site 3 out of 15 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose


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 Raffinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:29.6
occ:1.00
 O A:HOH660 2.0 19.8 1.0
O A:HOH1128 2.1 28.5 1.0
O A:HOH1026 2.2 29.3 1.0
HA2 A:GLY204 3.5 17.0 1.0
O A:ARG201 3.9 13.5 1.0
O A:HOH641 4.4 26.8 1.0
O A:HOH684 4.4 38.6 1.0
HG3 A:ARG201 4.5 16.7 1.0
O A:HOH1100 4.5 35.9 1.0
O A:HOH840 4.5 26.5 1.0
O A:HOH721 4.5 16.5 1.0
CA A:GLY204 4.5 14.1 1.0
HG2 A:ARG201 4.6 16.7 1.0
O A:HOH734 4.7 31.9 1.0
H A:GLY204 4.8 16.0 1.0
HA3 A:GLY204 4.9 17.0 1.0

Magnesium binding site 4 out of 15 in 4zs9

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Magnesium binding site 4 out of 15 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose


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 Raffinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:48.5
occ:1.00
 O A:HOH1129 2.0 36.2 1.0
O A:HOH1133 2.1 52.3 1.0
O A:HOH655 2.2 26.7 1.0
O A:HOH1011 2.2 31.0 1.0
O A:HOH786 2.2 30.9 1.0
O A:HOH1043 2.3 35.9 1.0
HE1 A:MET298 3.4 56.1 1.0
HA A:GLU60 3.7 15.4 1.0
SD A:MET298 4.1 46.1 1.0
OE1 A:GLN295 4.1 22.8 1.0
CE A:MET298 4.1 46.8 1.0
O A:HOH816 4.3 24.9 1.0
O A:ALA59 4.3 15.2 1.0
O A:HOH1120 4.3 39.7 1.0
HG3 A:GLN295 4.3 24.8 1.0
O A:HOH884 4.5 27.1 1.0
HG3 A:GLU60 4.6 17.0 1.0
CA A:GLU60 4.6 12.8 1.0
HE3 A:MET298 4.7 56.1 1.0
HE2 A:MET298 4.7 56.1 1.0
O A:HOH769 4.7 25.8 1.0
O A:HOH983 4.8 16.0 1.0
CD A:GLN295 4.8 22.3 1.0
HB1 A:ALA59 4.9 18.2 1.0
C A:ALA59 4.9 13.4 1.0

Magnesium binding site 5 out of 15 in 4zs9

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Magnesium binding site 5 out of 15 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose


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 Raffinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:45.8
occ:1.00
 O A:HOH700 2.0 29.9 1.0
O A:HOH1066 2.2 24.7 1.0
O A:HOH1027 2.2 31.2 1.0
HA A:ASP264 4.0 20.4 1.0
OD1 A:ASP264 4.1 19.4 1.0
O A:HOH878 4.2 36.8 1.0
O A:HOH794 4.2 35.1 1.0
O A:HOH804 4.5 30.1 1.0
O A:HOH840 4.5 26.5 1.0
O A:HOH1009 4.6 35.1 1.0
O A:HOH658 4.6 36.5 1.0
CG A:ASP264 4.7 18.0 1.0
HH21 A:ARG201 4.7 22.8 1.0
CA A:ASP264 4.9 17.0 1.0
O A:HOH1107 4.9 38.6 1.0
HB3 A:ASP264 4.9 20.2 1.0
NH2 A:ARG201 5.0 19.0 1.0

Magnesium binding site 6 out of 15 in 4zs9

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Magnesium binding site 6 out of 15 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose


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 Raffinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:72.3
occ:1.00
 O A:HOH667 1.9 24.0 1.0
O A:HOH763 2.1 33.0 1.0
HB2 A:ASP191 3.7 19.5 1.0
HG3 A:GLU192 4.0 21.0 1.0
O A:HOH736 4.1 22.2 1.0
OG1 A:THR189 4.3 13.4 1.0
O A:HOH1022 4.4 27.0 1.0
HG21 A:THR189 4.4 14.8 1.0
HB3 A:ASP191 4.4 19.5 1.0
CB A:ASP191 4.5 16.2 1.0
OD2 A:ASP191 4.6 23.5 1.0
HG1 A:THR189 4.6 16.1 1.0
CG A:GLU192 4.8 17.5 1.0
HB3 A:ASN314 4.9 14.6 1.0

Magnesium binding site 7 out of 15 in 4zs9

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Magnesium binding site 7 out of 15 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose


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 Raffinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:66.5
occ:1.00
 O B:HOH1054 2.0 30.8 1.0
O A:HOH1116 2.1 31.4 1.0
O A:HOH1038 2.1 31.9 1.0
O A:HOH702 2.1 30.6 1.0
O A:HOH1063 2.2 32.3 1.0
O A:HOH616 2.4 42.1 1.0
O A:HOH962 3.4 31.4 1.0
O A:HOH1092 3.5 27.1 1.0
H A:GLU232 3.5 16.7 1.0
O B:HOH617 3.8 35.9 1.0
O A:HOH1111 3.9 38.2 1.0
O A:HOH930 4.0 26.0 1.0
HA A:PRO231 4.0 16.4 1.0
O A:HOH1106 4.2 38.2 1.0
HB2 A:GLU232 4.2 21.1 1.0
HB2 A:ALA390 4.3 19.3 1.0
OE2 A:GLU232 4.3 26.8 1.0
O B:HOH1069 4.3 32.5 1.0
N A:GLU232 4.4 13.9 1.0
HB3 A:PRO231 4.4 19.7 1.0
O A:HOH835 4.4 31.7 1.0
HG3 A:GLU232 4.5 28.2 1.0
HD13 A:ILE320 4.5 21.4 1.0
O A:HOH751 4.6 13.8 1.0
O B:HOH1173 4.7 35.6 1.0
O A:VAL389 4.7 14.0 1.0
HB1 A:ALA390 4.7 19.3 1.0
HA A:ALA390 4.7 15.5 1.0
CA A:PRO231 4.8 13.6 1.0
O A:HOH941 4.8 29.0 1.0
O B:HOH937 4.9 43.9 1.0
CB A:ALA390 4.9 16.1 1.0
CB A:GLU232 4.9 17.6 1.0
CG A:GLU232 5.0 23.5 1.0

Magnesium binding site 8 out of 15 in 4zs9

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Magnesium binding site 8 out of 15 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose


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 Raffinose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:9.2
occ:1.00
 OD2 B:ASP53 2.0 9.5 1.0
O B:HOH717 2.1 9.5 1.0
O B:HOH738 2.1 10.9 1.0
CG B:ASP53 3.1 9.3 1.0
HB2 B:ASP53 3.3 10.9 1.0
CB B:ASP53 3.7 9.1 1.0
OD1 B:ASP53 4.1 11.7 1.0
HA B:PRO103 4.1 10.8 1.0
O B:HOH756 4.1 10.5 1.0
O B:VAL102 4.1 10.1 1.0
OD2 B:ASP104 4.2 9.6 1.0
HB3 B:ASP53 4.3 10.9 1.0
O B:ARG101 4.3 13.1 1.0
H B:ASP53 4.3 10.0 1.0
HA B:ARG101 4.4 20.5 1.0
O B:HOH675 4.7 12.3 1.0
C B:ARG101 4.7 13.6 1.0
N B:ASP53 4.9 8.3 1.0
C B:VAL102 4.9 9.6 1.0
CA B:ASP53 4.9 8.7 1.0
H B:ASP104 4.9 9.0 1.0

Magnesium binding site 9 out of 15 in 4zs9

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Magnesium binding site 9 out of 15 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose


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 Raffinose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:61.3
occ:1.00
 O B:HOH1176 1.8 32.3 1.0
O B:HOH608 2.0 36.1 1.0
O B:HOH1067 2.3 32.4 1.0
O B:HOH813 2.3 31.6 1.0
O B:HOH1174 2.3 37.2 1.0
O B:HOH1130 3.2 25.1 1.0
OE2 B:GLU232 4.1 26.6 1.0
O B:HOH1070 4.4 20.1 1.0
HA B:ALA390 4.5 15.9 1.0
O B:HOH872 4.5 34.7 1.0
O B:HOH835 4.5 30.2 1.0
O B:VAL389 4.5 13.9 1.0
O B:HOH943 4.5 25.1 1.0
HB2 B:GLU232 4.9 20.9 1.0
O B:HOH1013 4.9 23.0 1.0
O B:HOH1097 4.9 32.8 1.0
CD B:GLU232 5.0 26.3 1.0

Magnesium binding site 10 out of 15 in 4zs9

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Magnesium binding site 10 out of 15 in the Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Raffinose and Panose Binding Protein From Bifidobacterium Animalis Subsp. Lactis Bl-04, Bound with Raffinose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:28.9
occ:1.00
 O B:HOH727 2.1 16.6 1.0
O B:HOH1146 2.1 21.0 1.0
O B:HOH1062 2.1 26.5 1.0
O B:HOH1091 2.4 33.5 1.0
O B:HOH605 3.0 21.5 1.0
O B:HOH713 3.9 27.6 1.0
HA B:ASP264 3.9 16.3 1.0
OD1 B:ASP264 4.1 17.8 1.0
O B:HOH1045 4.3 33.3 1.0
O B:HOH748 4.4 23.1 1.0
O B:HOH734 4.4 26.0 1.0
O B:ALA263 4.6 13.6 1.0
HH21 B:ARG201 4.8 22.4 1.0
O B:LYS261 4.8 12.4 1.0
CA B:ASP264 4.8 13.6 1.0
CG B:ASP264 5.0 15.3 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 00:09:39 2024

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