Zinc in PDB 7fir: The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose

The structure of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose, PDB code: 7fir was solved by L.Dai, Z.Chang, J.Yang, W.Liu, Y.Yang, C.-C.Chen, L.Zhang, J.Huang, Y.Sun, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.29 / 2.20
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	205.303, 205.303, 78.649, 90, 90, 90
R / Rfree (%)	17 / 20.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Zinc atom in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose (pdb code 7fir). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose, PDB code: 7fir:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:33.2 occ:1.00 NE2 A:HIS194 2.1 22.7 1.0 O B:HOH713 2.2 7.2 1.0 O A:HOH859 2.3 23.6 1.0 OD2 B:ASP170 2.4 23.3 1.0 OD1 B:ASP170 2.5 20.2 1.0 CG B:ASP170 2.8 20.4 1.0 CD2 A:HIS194 3.0 21.0 1.0 CE1 A:HIS194 3.1 21.4 1.0 CD B:PRO169 3.7 21.8 1.0 CG B:PRO169 4.1 24.5 1.0 ND1 A:HIS194 4.1 23.4 1.0 CG A:HIS194 4.2 21.9 1.0 O B:HOH507 4.2 20.3 1.0 CB B:ASP170 4.2 19.8 1.0 OG B:SER190 4.3 20.4 1.0 OG A:SER193 4.6 27.1 1.0 CD1 B:ILE187 4.6 23.7 1.0 CB B:SER190 4.7 18.1 1.0 CB A:SER193 4.8 21.7 1.0 N B:PRO169 4.9 20.3 1.0 CD B:PRO191 4.9 19.5 1.0 N B:ASP170 5.0 22.8 1.0

Zinc binding site 2 out of 17 in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:23.1 occ:1.00 OD2 A:ASP149 2.0 18.0 1.0 NE2 A:HIS219 2.1 16.0 1.0 O A:HOH865 2.1 10.5 1.0 O A:HOH774 2.3 6.5 1.0 CG A:ASP149 2.8 19.8 1.0 OD1 A:ASP149 2.9 20.1 1.0 CE1 A:HIS219 3.1 17.3 1.0 CD2 A:HIS219 3.1 15.3 1.0 NH2 A:ARG166 3.8 25.1 1.0 CE2 A:PHE268 4.0 19.7 1.0 ND1 A:HIS219 4.2 16.9 1.0 CB A:ASP149 4.2 15.2 1.0 CG A:HIS219 4.2 17.0 1.0 CE2 A:TYR227 4.3 15.9 1.0 O A:HOH843 4.3 25.0 1.0 CZ A:ARG166 4.4 24.1 1.0 NH1 A:ARG166 4.5 17.9 1.0 CZ A:PHE268 4.5 18.0 1.0 CA A:GLY202 4.5 16.6 1.0 CD A:LYS148 4.7 19.9 1.0 O A:HOH787 4.8 22.7 1.0 OH A:TYR227 4.8 22.4 1.0 N A:GLY202 4.8 15.4 1.0 O A:HOH692 4.9 18.9 1.0

Zinc binding site 3 out of 17 in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:30.4 occ:1.00 NE2 B:HIS194 2.0 20.6 1.0 OD2 A:ASP170 2.1 21.3 1.0 O A:HOH847 2.2 8.5 1.0 O B:HOH731 2.2 23.1 1.0 OD1 A:ASP170 2.7 19.0 1.0 CG A:ASP170 2.8 19.1 1.0 CE1 B:HIS194 2.9 19.0 1.0 CD2 B:HIS194 3.0 19.9 1.0 CD A:PRO169 3.7 19.2 1.0 CG A:PRO169 4.0 21.8 1.0 ND1 B:HIS194 4.1 20.8 1.0 O A:HOH684 4.1 19.2 1.0 CG B:HIS194 4.1 22.3 1.0 OG A:SER190 4.2 25.6 1.0 CB A:ASP170 4.2 17.8 1.0 CD1 A:ILE187 4.5 16.0 1.0 OG B:SER193 4.8 31.7 1.0 CB B:SER193 4.8 26.9 1.0 N A:ASP170 4.9 19.2 1.0 CB A:SER190 4.9 19.1 1.0 N A:PRO169 4.9 24.1 1.0

Zinc binding site 4 out of 17 in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:25.5 occ:1.00 OE2 A:GLU92 2.1 24.6 1.0 NE2 A:HIS139 2.1 22.6 1.0 SG A:CYS126 2.2 18.3 1.0 O A:HOH845 2.3 10.0 1.0 CD A:GLU92 3.0 26.9 1.0 CE1 A:HIS139 3.1 24.5 1.0 CD2 A:HIS139 3.1 22.0 1.0 CB A:CYS126 3.1 14.4 1.0 CG A:GLU92 3.5 23.8 1.0 OH A:TYR112 3.7 20.6 1.0 OE1 A:GLU92 4.0 25.9 1.0 ND1 A:HIS139 4.2 28.0 1.0 CG A:HIS139 4.3 26.1 1.0 NH1 A:ARG124 4.4 30.6 1.0 CZ A:TYR112 4.4 17.9 1.0 CE1 A:TYR112 4.4 16.7 1.0 CG1 A:ILE141 4.4 22.9 1.0 CA A:CYS126 4.5 17.8 1.0 OE2 A:GLU88 4.6 43.1 1.0 O A:ARG140 4.7 17.7 1.0 CD A:GLU88 4.8 46.0 1.0 CA A:GLY114 4.8 14.8 1.0 CG A:GLU88 5.0 41.6 1.0

Zinc binding site 5 out of 17 in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:83.9 occ:1.00 O A:HOH601 2.1 33.5 1.0 OE2 A:GLU248 2.7 43.5 1.0 NE2 D:HIS194 2.8 39.2 1.0 O A:HOH604 2.8 31.0 1.0 O A:HOH739 2.9 34.8 1.0 CE1 D:HIS194 3.2 40.4 1.0 CD A:GLU248 3.4 41.8 1.0 OE1 A:GLU248 3.4 42.7 1.0 CD A:PRO249 3.8 20.5 1.0 CD2 D:HIS194 3.9 33.9 1.0 OG D:SER193 4.2 31.5 1.0 O A:HOH836 4.3 26.4 1.0 ND1 D:HIS194 4.3 35.9 1.0 CG A:PRO249 4.4 22.6 1.0 CB D:SER193 4.4 27.1 1.0 CD1 A:TRP196 4.5 22.1 1.0 CG D:HIS194 4.7 31.6 1.0 CG A:GLU248 4.8 33.5 1.0 OE1 A:GLU252 4.8 32.9 1.0 O D:HOH651 4.9 22.0 1.0

Zinc binding site 6 out of 17 in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:31.6 occ:1.00 NE2 A:HIS19 2.0 28.0 1.0 OD1 A:ASP81 2.0 19.1 1.0 O A:HOH868 2.5 38.3 1.0 CE1 A:HIS19 3.0 22.7 1.0 CD2 A:HIS19 3.1 21.6 1.0 CG A:ASP81 3.2 25.8 1.0 O A:HOH807 3.6 44.8 1.0 CB A:ASP81 3.8 27.5 1.0 CA A:ASP81 3.9 19.0 1.0 ND1 A:HIS19 4.1 23.1 1.0 CG A:HIS19 4.2 25.1 1.0 OD2 A:ASP81 4.3 27.4 1.0 O A:ASP81 4.8 23.4 1.0 N A:ASP81 4.8 22.4 1.0 C A:ASP81 4.9 21.3 1.0

Zinc binding site 7 out of 17 in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:39.4 occ:1.00 OD1 B:ASP81 2.1 23.4 1.0 O B:HOH758 2.3 34.5 1.0 NE2 B:HIS19 2.3 27.9 1.0 CD2 B:HIS19 3.2 26.7 1.0 CG B:ASP81 3.2 21.5 1.0 CE1 B:HIS19 3.3 24.1 1.0 O B:HOH773 3.7 39.8 1.0 OD2 B:ASP81 3.8 31.6 1.0 O B:HOH700 4.1 44.1 1.0 CG B:HIS19 4.4 27.8 1.0 ND1 B:HIS19 4.4 27.4 1.0 CB B:ASP81 4.4 20.6 1.0 CA B:ASP81 4.8 22.1 1.0 O B:HOH735 4.9 39.4 1.0

Zinc binding site 8 out of 17 in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:33.9 occ:1.00 OE2 B:GLU92 2.2 30.2 1.0 NE2 B:HIS139 2.2 32.5 1.0 O B:HOH741 2.3 11.6 1.0 SG B:CYS126 2.3 25.6 1.0 CD2 B:HIS139 3.1 32.8 1.0 CB B:CYS126 3.1 22.4 1.0 CD B:GLU92 3.1 28.4 1.0 CE1 B:HIS139 3.2 30.5 1.0 CG B:GLU92 3.5 27.8 1.0 OH B:TYR112 3.7 24.2 1.0 OE1 B:GLU92 4.2 31.0 1.0 CG B:HIS139 4.3 33.6 1.0 ND1 B:HIS139 4.3 35.7 1.0 CE1 B:TYR112 4.4 21.3 1.0 CZ B:TYR112 4.4 25.1 1.0 CA B:CYS126 4.4 22.8 1.0 CG1 B:ILE141 4.6 25.5 1.0 NH1 B:ARG124 4.8 38.2 1.0 O B:ARG140 4.9 26.6 1.0 CA B:GLY114 4.9 19.8 1.0

Zinc binding site 9 out of 17 in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:24.9 occ:1.00 OD2 B:ASP149 2.0 17.7 1.0 NE2 B:HIS219 2.1 17.8 1.0 O B:HOH753 2.2 12.8 1.0 O B:HOH656 2.2 8.2 1.0 CG B:ASP149 2.8 17.7 1.0 OD1 B:ASP149 3.0 15.4 1.0 CE1 B:HIS219 3.0 20.0 1.0 CD2 B:HIS219 3.1 18.9 1.0 NH1 B:ARG166 3.7 24.9 1.0 CE2 B:PHE268 3.9 19.9 1.0 ND1 B:HIS219 4.1 17.8 1.0 CG B:HIS219 4.2 15.8 1.0 CB B:ASP149 4.2 13.6 1.0 O B:HOH704 4.2 33.4 1.0 CZ B:ARG166 4.3 21.8 1.0 NH2 B:ARG166 4.3 20.4 1.0 CZ B:PHE268 4.3 17.4 1.0 CA B:GLY202 4.4 18.5 1.0 CE2 B:TYR227 4.4 17.9 1.0 N B:GLY202 4.7 19.4 1.0 O B:HOH571 4.8 25.4 1.0 CD B:LYS148 4.8 25.3 1.0 OH B:TYR227 4.9 22.8 1.0

Zinc binding site 10 out of 17 in the The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Crystal Structure of Beta-1,2-Mannobiose Phosphorylase in Complex with 1,4-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:66.5 occ:1.00 CE1 C:HIS194 2.4 40.3 1.0 OE1 B:GLU248 2.5 46.0 1.0 OE2 B:GLU248 2.6 43.3 1.0 NE2 C:HIS194 2.7 44.6 1.0 CD B:GLU248 2.8 42.1 1.0 O C:HOH822 3.3 38.7 1.0 O B:HOH697 3.5 25.9 1.0 ND1 C:HIS194 3.6 39.7 1.0 O B:HOH502 3.7 43.5 1.0 CD2 C:HIS194 4.0 40.2 1.0 CG B:GLU248 4.3 33.0 1.0 CD1 B:TRP196 4.4 24.5 1.0 CG C:HIS194 4.4 38.3 1.0 CD B:PRO249 4.5 19.5 1.0 O C:HOH796 4.5 26.4 1.0 CA B:GLU248 4.9 27.3 1.0 CB B:GLU248 5.0 26.1 1.0 NZ B:LYS247 5.0 47.3 1.0

L.Dai, Z.Chang, J.Yang, W.Liu, Y.Yang, C.C.Chen, L.Zhang, J.W.Huang, Y.Sun, R.T.Guo. Structural Investigation of A Thermostable 1,2-Beta-Mannobiose Phosphorylase From Thermoanaerobacter Sp. X-514. Biochem.Biophys.Res.Commun. V. 579 54 2021.
ISSN: ESSN 1090-2104
PubMed: 34587555
DOI: 10.1016/J.BBRC.2021.09.046