Zinc in PDB 6i5r: BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose

The structure of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose, PDB code: 6i5r was solved by M.Abou Hachem, M.Ejby, A.Guskov, D.J.Slotboom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.83 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.560, 74.500, 102.370, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose (pdb code 6i5r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose, PDB code: 6i5r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:67.3 occ:1.00 OD2 A:ASP313 1.9 29.2 1.0 O A:HOH911 2.4 31.3 1.0 CG A:ASP313 3.0 24.2 1.0 OD1 A:ASP313 3.4 32.0 1.0 O A:HOH731 3.6 35.2 1.0 CB A:ASP313 4.2 26.9 1.0 HB2 A:ASP313 4.2 32.0 1.0 O A:HOH650 4.4 30.6 1.0 HB3 A:ASP313 4.6 32.0 1.0

Zinc binding site 2 out of 14 in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:37.0 occ:1.00 O A:HOH1008 1.7 33.7 1.0 O A:HOH798 1.8 29.3 1.0 NE2 A:HIS257 2.0 22.9 1.0 O A:HOH724 2.0 16.4 1.0 O A:HOH697 2.2 28.5 1.0 O A:HOH1069 2.3 29.9 1.0 CE1 A:HIS257 2.7 20.6 1.0 HE1 A:HIS257 2.7 24.6 1.0 CD2 A:HIS257 3.2 19.0 1.0 HD2 A:HIS257 3.6 22.5 1.0 ND1 A:HIS257 3.9 25.2 1.0 O A:HOH820 4.0 22.9 1.0 O A:HOH1060 4.0 34.9 1.0 O A:HOH694 4.0 27.1 1.0 CG A:HIS257 4.2 17.1 1.0 HE1 A:PHE235 4.3 20.1 1.0 O A:HOH1057 4.3 32.3 1.0 OD1 A:ASP250 4.4 30.2 1.0 HD1 A:HIS257 4.6 30.0 1.0 HB A:THR230 4.7 22.8 1.0 O A:HOH674 4.8 27.2 1.0 HG22 A:THR230 4.8 21.0 1.0 O A:HOH996 5.0 30.9 1.0 HG21 A:THR230 5.0 21.0 1.0

Zinc binding site 3 out of 14 in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:20.1 occ:1.00 OE2 A:GLU449 2.0 16.4 1.0 O A:HOH918 2.1 20.1 1.0 CD A:GLU449 2.6 19.3 1.0 OE1 A:GLU449 2.6 17.9 1.0 HZ2 A:LYS453 3.0 26.1 1.0 HZ1 A:LYS453 3.3 26.1 1.0 NZ A:LYS453 3.6 22.0 1.0 HH22 A:ARG441 3.8 19.4 1.0 O A:HOH682 4.0 19.7 1.0 HZ3 A:LYS453 4.0 26.1 1.0 CG A:GLU449 4.1 23.4 1.0 O A:HOH696 4.1 28.0 1.0 HG2 A:GLU449 4.2 27.9 1.0 HG3 A:GLU449 4.5 27.9 1.0 HH12 A:ARG441 4.5 19.4 1.0 NH2 A:ARG441 4.5 16.4 1.0 HE3 A:LYS453 4.7 24.9 1.0 CE A:LYS453 4.8 21.0 1.0 OD2 A:ASP431 4.9 20.4 1.0 HH21 A:ARG441 4.9 19.4 1.0 HB3 A:GLU449 4.9 20.4 1.0

Zinc binding site 4 out of 14 in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:20.8 occ:1.00 OD1 A:ASP155 2.0 17.3 1.0 OD2 A:ASP155 2.4 34.4 1.0 CG A:ASP155 2.6 22.1 1.0 O A:HOH761 3.6 27.9 1.0 HE2 A:TYR154 3.8 22.4 1.0 CB A:ASP155 4.1 17.1 1.0 O A:HOH1047 4.1 28.9 1.0 HA A:ASP155 4.3 22.5 1.0 CE2 A:TYR154 4.3 18.9 1.0 HB3 A:ASP155 4.5 20.2 1.0 OH A:TYR154 4.6 36.1 1.0 HB2 A:ASP155 4.6 20.2 1.0 CZ A:TYR154 4.8 22.8 1.0 CA A:ASP155 4.8 18.9 1.0 HH A:TYR154 4.9 43.1 1.0 O A:HOH978 5.0 22.5 1.0

Zinc binding site 5 out of 14 in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:19.9 occ:1.00 O A:HOH666 2.1 16.4 1.0 O A:HOH819 2.1 16.6 1.0 OD1 A:ASP215 2.1 16.4 1.0 CG A:ASP215 3.0 24.4 1.0 HE22 A:GLN430 3.1 19.4 1.0 HZ2 A:LYS427 3.1 32.5 1.0 OD2 A:ASP215 3.2 28.8 1.0 HZ1 A:LYS427 3.6 32.5 1.0 NZ A:LYS427 3.7 27.3 1.0 O A:VAL213 3.9 16.4 1.0 NE2 A:GLN430 3.9 16.4 1.0 HZ3 A:LYS427 3.9 32.5 1.0 O A:HOH634 4.1 26.0 1.0 H A:ASP215 4.2 19.4 1.0 CB A:ASP215 4.3 20.0 1.0 OE1 A:GLN430 4.4 16.4 1.0 O A:HOH905 4.4 28.0 1.0 HE21 A:GLN430 4.5 19.4 1.0 HB2 A:ASP215 4.6 23.8 1.0 CD A:GLN430 4.6 21.5 1.0 N A:ASP215 4.7 16.4 1.0 HA A:ASP215 4.7 20.9 1.0 HD2 A:LYS427 4.8 31.6 1.0 CA A:ASP215 4.9 17.6 1.0 C A:VAL213 5.0 20.5 1.0

Zinc binding site 6 out of 14 in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:23.8 occ:0.77 O A:HOH627 1.7 32.3 1.0 OE1 A:GLU138 2.1 21.1 1.0 O A:HOH901 2.1 31.1 1.0 OE2 A:GLU138 2.3 32.5 1.0 CD A:GLU138 2.5 22.7 1.0 O A:HOH758 3.9 33.9 1.0 CG A:GLU138 4.1 22.0 1.0 O A:HOH824 4.1 36.3 1.0 HG A:SER140 4.3 32.3 1.0 OG A:SER140 4.3 27.1 1.0 HG2 A:GLU138 4.4 26.2 1.0 HG3 A:GLU138 4.5 26.2 1.0 HB3 A:GLU138 4.6 25.7 1.0 CB A:GLU138 4.8 21.6 1.0 HG2 A:GLU141 4.8 25.2 1.0 HB2 A:GLU138 4.9 25.7 1.0

Zinc binding site 7 out of 14 in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:17.5 occ:0.44 O A:HOH982 2.0 30.1 1.0 O A:HOH1068 2.1 29.1 1.0 O A:HOH845 2.1 27.5 1.0 O A:HOH987 2.1 30.3 1.0 OD1 A:ASP195 2.2 17.4 1.0 O A:HOH640 2.4 18.2 1.0 CG A:ASP195 3.0 17.9 1.0 OD2 A:ASP195 3.1 18.1 1.0 HG23 A:ILE182 3.5 19.4 1.0 HB3 A:GLU191 4.0 19.4 1.0 HG12 A:ILE182 4.2 28.6 1.0 O A:HOH1092 4.2 31.0 1.0 O A:GLU191 4.2 17.2 1.0 O A:GLU184 4.3 25.0 1.0 HB3 A:PRO186 4.4 26.4 1.0 CG2 A:ILE182 4.4 16.4 1.0 CB A:ASP195 4.4 16.4 1.0 HB3 A:ALA194 4.4 21.4 1.0 HA A:ASP195 4.5 23.3 1.0 HA A:ILE182 4.5 21.8 1.0 HG21 A:ILE182 4.6 19.4 1.0 HD12 A:LEU198 4.6 22.5 1.0 H A:ASP195 4.7 19.4 1.0 O A:HOH1089 4.7 33.3 1.0 HA A:GLU191 4.7 23.1 1.0 HA A:PRO186 4.7 24.1 1.0 O A:HOH998 4.7 34.4 1.0 HD3 A:PRO186 4.8 21.0 1.0 N A:ASP195 4.8 16.4 1.0 H A:LYS183 4.8 31.3 1.0 CA A:ASP195 4.8 19.6 1.0 H A:GLU184 4.8 27.4 1.0 CB A:GLU191 4.9 16.4 1.0 HB3 A:ASP195 4.9 19.4 1.0 HB2 A:ASP195 4.9 19.4 1.0 C A:GLU191 5.0 17.1 1.0

Zinc binding site 8 out of 14 in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn510 b:21.5 occ:0.62 HG A:SER127 1.8 29.5 1.0 OD2 A:ASP125 2.1 33.3 1.0 OD2 A:ASP408 2.1 27.9 1.0 O A:HOH635 2.1 16.8 1.0 OD1 A:ASP408 2.2 28.7 1.0 OD1 A:ASN412 2.3 24.0 1.0 OG A:SER127 2.3 24.8 1.0 OD1 A:ASP125 2.3 33.2 1.0 CG A:ASP408 2.5 23.7 1.0 CG A:ASP125 2.6 23.9 1.0 HB3 A:SER127 2.9 26.1 1.0 CB A:SER127 3.1 21.9 1.0 HD21 A:ASN412 3.2 29.0 1.0 CG A:ASN412 3.3 21.9 1.0 H A:SER127 3.6 27.4 1.0 ND2 A:ASN412 3.6 24.4 1.0 HB2 A:SER127 3.7 26.1 1.0 HB3 A:ALA411 3.8 26.0 1.0 CB A:ASP408 4.0 22.9 1.0 CB A:ASP125 4.0 19.0 1.0 HB3 A:ASP125 4.2 22.6 1.0 N A:SER127 4.3 23.0 1.0 O A:ASP408 4.3 22.1 1.0 CA A:SER127 4.3 22.6 1.0 HB1 A:ALA411 4.3 26.0 1.0 HB2 A:ASP408 4.4 27.3 1.0 HB3 A:ASP408 4.4 27.3 1.0 HB2 A:ASP125 4.4 22.6 1.0 HD22 A:ASN412 4.5 29.0 1.0 CB A:ALA411 4.5 21.9 1.0 HA A:ASP408 4.6 30.7 1.0 HA A:ASN412 4.6 19.4 1.0 CB A:ASN412 4.7 21.8 1.0 H A:ASN412 4.8 19.9 1.0 CA A:ASP408 4.8 25.8 1.0 N A:ASN412 4.8 16.8 1.0 CA A:ASN412 5.0 16.4 1.0 HA A:SER127 5.0 26.9 1.0

Zinc binding site 9 out of 14 in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn511 b:0.6 occ:1.00 O A:HOH601 1.6 33.9 1.0 OE1 A:GLU178 1.9 27.3 1.0 OE2 A:GLU178 2.2 30.0 1.0 CD A:GLU178 2.4 21.2 1.0 O A:HOH700 2.7 36.0 1.0 O A:HOH907 3.7 31.4 1.0 CG A:GLU178 3.9 24.5 1.0 HG2 A:GLU178 4.2 29.1 1.0 O A:HOH686 4.3 27.4 1.0 HG3 A:GLU178 4.3 29.1 1.0 HA A:GLU178 4.6 24.2 1.0 HB2 A:GLU178 4.6 21.6 1.0 CB A:GLU178 4.8 18.2 1.0

Zinc binding site 10 out of 14 in the BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of BLMNBP1 Binding Protein of An Abc Transporter From Bifidobacterium Animalis Subsp. Lactis ATCC27673 in Complex with Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn512 b:76.2 occ:1.00 O A:HOH850 1.7 32.4 1.0 O A:HOH838 1.8 28.6 1.0 O A:HOH1051 2.0 34.0 1.0 OE1 A:GLU214 2.2 21.6 1.0 O A:HOH764 2.5 30.7 1.0 CD A:GLU214 3.1 23.9 1.0 OE2 A:GLU214 3.3 17.2 1.0 O A:HOH905 3.5 28.0 1.0 HE1 A:TRP216 3.6 19.4 1.0 O A:SER99 3.7 16.5 1.0 O A:HOH1054 3.7 31.1 1.0 HB2 A:SER99 3.9 27.0 1.0 O A:HOH1005 4.1 32.8 1.0 HA A:ASN100 4.1 21.6 1.0 HA A:GLU214 4.1 19.4 1.0 HD1 A:TRP216 4.2 19.5 1.0 O6 A:BMA501 4.3 21.1 1.0 NE1 A:TRP216 4.3 16.4 1.0 C A:SER99 4.3 19.9 1.0 CG A:GLU214 4.5 17.7 1.0 HB3 A:GLU214 4.6 19.6 1.0 HO6 A:BMA501 4.6 25.1 1.0 CD1 A:TRP216 4.6 16.4 1.0 CB A:SER99 4.7 22.7 1.0 H62 A:BMA501 4.7 23.9 1.0 N A:ASN100 4.8 17.0 1.0 CA A:ASN100 4.9 18.2 1.0 C6 A:BMA501 4.9 20.1 1.0 CB A:GLU214 4.9 16.6 1.0 HG3 A:GLU214 4.9 21.0 1.0 CA A:GLU214 4.9 16.4 1.0 H61 A:BMA501 5.0 23.9 1.0 OG A:SER99 5.0 28.4 1.0 HB2 A:ASN100 5.0 26.8 1.0

M.Ejby, A.Guskov, M.J.Pichler, G.C.Zanten, E.Schoof, W.Saburi, D.J.Slotboom, M.Abou Hachem. Two Binding Proteins of the Abc Transporter That Confers Growth of Bifidobacterium Animalis Subsp. Lactis ATCC27673 on Beta-Mannan Possess Distinct Manno-Oligosaccharide-Binding Profiles. Mol.Microbiol. V. 112 114 2019.
ISSN: ESSN 1365-2958
PubMed: 30947380
DOI: 10.1111/MMI.14257