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Zinc in PDB 7fip: The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.

Protein crystallography data

The structure of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp., PDB code: 7fip 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) 35.38 / 2.39
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 206.317, 206.317, 78.424, 90, 90, 90
R / Rfree (%) 18.7 / 23.9

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. (pdb code 7fip). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp., PDB code: 7fip:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 7fip

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Zinc binding site 1 out of 16 in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:28.5
occ:1.00
OD2 A:ASP149 2.1 20.9 1.0
NE2 A:HIS219 2.1 19.9 1.0
O A:HOH537 2.5 4.1 1.0
CG A:ASP149 2.8 23.9 1.0
CD2 A:HIS219 3.0 16.1 1.0
OD1 A:ASP149 3.0 22.1 1.0
CE1 A:HIS219 3.2 13.2 1.0
NH1 A:ARG166 3.5 28.8 1.0
CE2 A:PHE268 4.0 18.6 1.0
O A:HOH603 4.0 27.3 1.0
CG A:HIS219 4.1 15.1 1.0
CZ A:ARG166 4.2 28.4 1.0
ND1 A:HIS219 4.2 15.4 1.0
CB A:ASP149 4.3 17.8 1.0
CZ A:PHE268 4.3 17.7 1.0
CE2 A:TYR227 4.3 20.4 1.0
NH2 A:ARG166 4.3 20.2 1.0
CD A:LYS148 4.5 26.0 1.0
CA A:GLY202 4.5 17.7 1.0
O A:HOH551 4.8 20.8 1.0
N A:GLY202 4.9 17.1 1.0

Zinc binding site 2 out of 16 in 7fip

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Zinc binding site 2 out of 16 in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:50.6
occ:1.00
NE2 A:HIS194 2.1 30.7 1.0
O B:HOH632 2.2 20.3 1.0
OD2 B:ASP170 2.2 40.8 1.0
OD1 B:ASP170 2.8 30.5 1.0
CG B:ASP170 2.8 32.4 1.0
CE1 A:HIS194 2.9 24.3 1.0
CD2 A:HIS194 3.2 25.2 1.0
CD B:PRO169 3.5 31.8 1.0
O B:HOH525 3.9 30.4 1.0
CG B:PRO169 4.0 35.0 1.0
ND1 A:HIS194 4.0 31.1 1.0
OG B:SER190 4.0 27.9 1.0
CG A:HIS194 4.2 27.5 1.0
CB B:ASP170 4.3 29.7 1.0
CD1 B:ILE187 4.5 31.2 1.0
N B:PRO169 4.8 31.1 1.0
CB A:SER193 4.9 25.6 1.0
N B:ASP170 4.9 29.8 1.0
CB B:SER190 5.0 23.2 1.0

Zinc binding site 3 out of 16 in 7fip

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Zinc binding site 3 out of 16 in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:43.7
occ:1.00
NE2 B:HIS194 2.0 29.0 1.0
OD2 A:ASP170 2.2 25.0 1.0
O A:HOH670 2.4 18.1 1.0
O A:HOH720 2.7 25.4 1.0
OD1 A:ASP170 2.7 25.4 1.0
CE1 B:HIS194 2.7 20.0 1.0
CG A:ASP170 2.8 22.7 1.0
CD2 B:HIS194 3.1 23.2 1.0
CD A:PRO169 3.5 25.3 1.0
CG A:PRO169 3.9 22.6 1.0
ND1 B:HIS194 3.9 24.1 1.0
OG A:SER190 4.1 25.7 1.0
O A:HOH596 4.1 17.9 1.0
CG B:HIS194 4.1 24.2 1.0
CB A:ASP170 4.2 28.0 1.0
OG B:SER193 4.7 33.1 1.0
CD1 A:ILE187 4.7 17.5 1.0
N A:PRO169 4.7 32.0 1.0
CB B:SER193 4.8 35.0 1.0
N A:ASP170 4.8 27.3 1.0
CD A:PRO191 4.9 15.9 1.0
O A:HOH757 5.0 31.5 1.0

Zinc binding site 4 out of 16 in 7fip

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Zinc binding site 4 out of 16 in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:72.3
occ:1.00
OE1 A:GLU248 2.1 50.1 1.0
NE2 D:HIS194 2.4 41.3 1.0
CE1 D:HIS194 2.6 50.5 1.0
OE2 A:GLU248 2.6 52.5 1.0
CD A:GLU248 2.7 48.2 1.0
O A:HOH704 3.2 35.8 1.0
CD2 D:HIS194 3.6 42.3 1.0
ND1 D:HIS194 3.8 49.2 1.0
O D:HOH614 4.1 38.1 1.0
CD1 A:TRP196 4.2 28.9 1.0
CG A:GLU248 4.2 35.6 1.0
CG D:HIS194 4.3 40.9 1.0
NZ A:LYS247 4.4 49.7 1.0
CD A:PRO249 4.5 25.9 1.0
NE1 A:TRP196 4.8 25.7 1.0

Zinc binding site 5 out of 16 in 7fip

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Zinc binding site 5 out of 16 in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:36.2
occ:1.00
OD1 A:ASP81 1.9 12.7 1.0
NE2 A:HIS19 2.0 31.8 1.0
CE1 A:HIS19 2.9 28.2 1.0
CG A:ASP81 3.1 24.6 1.0
CD2 A:HIS19 3.2 22.6 1.0
CB A:ASP81 3.8 22.1 1.0
CA A:ASP81 3.9 24.9 1.0
ND1 A:HIS19 4.1 27.6 1.0
OD2 A:ASP81 4.1 25.8 1.0
CG A:HIS19 4.2 28.9 1.0
O A:ASP81 4.7 23.3 1.0
C A:ASP81 4.9 24.6 1.0
N A:ASP81 4.9 25.8 1.0

Zinc binding site 6 out of 16 in 7fip

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Zinc binding site 6 out of 16 in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:32.0
occ:1.00
OE2 A:GLU92 2.0 23.6 1.0
NE2 A:HIS139 2.1 29.4 1.0
SG A:CYS126 2.3 22.1 1.0
CD A:GLU92 3.0 28.1 1.0
CE1 A:HIS139 3.0 32.2 1.0
CD2 A:HIS139 3.1 31.2 1.0
CB A:CYS126 3.2 21.3 1.0
CG A:GLU92 3.5 29.2 1.0
OH A:TYR112 3.8 18.6 1.0
OE1 A:GLU92 4.0 32.2 1.0
ND1 A:HIS139 4.2 31.5 1.0
CG A:HIS139 4.2 30.6 1.0
CE1 A:TYR112 4.4 17.8 1.0
CZ A:TYR112 4.4 22.2 1.0
CA A:CYS126 4.4 21.2 1.0
NH1 A:ARG124 4.5 25.5 1.0
CG1 A:ILE141 4.5 25.1 1.0
CA A:GLY114 4.8 17.7 1.0
O A:ARG140 4.9 23.8 1.0

Zinc binding site 7 out of 16 in 7fip

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Zinc binding site 7 out of 16 in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:39.8
occ:1.00
OD1 B:ASP81 2.0 22.3 1.0
NE2 B:HIS19 2.2 38.3 1.0
O B:HOH536 2.4 26.2 1.0
CD2 B:HIS19 3.1 30.0 1.0
CG B:ASP81 3.1 22.2 1.0
CE1 B:HIS19 3.3 28.8 1.0
OD2 B:ASP81 3.7 31.1 1.0
CG B:HIS19 4.3 33.3 1.0
ND1 B:HIS19 4.3 32.3 1.0
CB B:ASP81 4.4 21.6 1.0
CA B:ASP81 4.7 24.5 1.0

Zinc binding site 8 out of 16 in 7fip

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Zinc binding site 8 out of 16 in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:43.9
occ:1.00
NE2 B:HIS139 2.0 42.4 1.0
OE2 B:GLU92 2.3 31.0 1.0
SG B:CYS126 2.5 29.9 1.0
CE1 B:HIS139 2.8 41.0 1.0
CD2 B:HIS139 3.1 39.6 1.0
CD B:GLU92 3.1 27.8 1.0
CB B:CYS126 3.4 30.0 1.0
CG B:GLU92 3.5 29.8 1.0
ND1 B:HIS139 4.0 43.5 1.0
CG B:HIS139 4.1 46.1 1.0
OH B:TYR112 4.1 20.0 1.0
OE1 B:GLU92 4.2 34.9 1.0
NH1 B:ARG124 4.2 41.2 1.0
CG1 B:ILE141 4.4 28.1 1.0
CA B:CYS126 4.7 30.2 1.0
CE1 B:TYR112 4.7 25.5 1.0
CD B:ARG124 4.8 38.9 1.0
CG B:ARG124 4.8 30.0 1.0
CZ B:TYR112 4.8 26.9 1.0
CA B:GLY114 5.0 22.6 1.0

Zinc binding site 9 out of 16 in 7fip

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Zinc binding site 9 out of 16 in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:33.5
occ:1.00
NE2 B:HIS219 2.0 20.7 1.0
OD2 B:ASP149 2.1 22.4 1.0
O B:HOH553 2.2 15.4 1.0
O B:HOH674 2.3 12.0 1.0
CG B:ASP149 2.9 24.9 1.0
CE1 B:HIS219 3.0 21.2 1.0
CD2 B:HIS219 3.0 22.7 1.0
OD1 B:ASP149 3.1 23.1 1.0
NH1 B:ARG166 3.5 32.7 1.0
CE2 B:PHE268 4.0 22.8 1.0
CZ B:ARG166 4.0 33.1 1.0
ND1 B:HIS219 4.1 22.8 1.0
NH2 B:ARG166 4.1 25.4 1.0
CG B:HIS219 4.1 22.0 1.0
CB B:ASP149 4.2 22.3 1.0
CA B:GLY202 4.3 26.8 1.0
CZ B:PHE268 4.3 23.2 1.0
CE2 B:TYR227 4.4 17.0 1.0
N B:GLY202 4.5 25.1 1.0
O B:HOH517 4.5 23.7 1.0
CD B:LYS148 4.6 25.6 1.0
C B:ILE201 5.0 26.1 1.0
OH B:TYR227 5.0 25.3 1.0

Zinc binding site 10 out of 16 in 7fip

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Zinc binding site 10 out of 16 in the The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Native Structure of Beta-1,2-Mannobiose Phosphorylase From Thermoanaerobacter Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:62.8
occ:1.00
OE1 B:GLU248 2.1 44.8 1.0
NE2 C:HIS194 2.4 54.2 1.0
O B:HOH670 2.6 29.7 1.0
CD B:GLU248 2.7 42.0 1.0
OE2 B:GLU248 2.8 38.9 1.0
CE1 C:HIS194 2.8 53.2 1.0
O B:HOH666 2.9 34.8 1.0
CD2 C:HIS194 3.6 45.1 1.0
ND1 C:HIS194 3.9 54.1 1.0
O C:HOH615 4.1 38.7 1.0
CG B:GLU248 4.2 38.2 1.0
CD1 B:TRP196 4.3 31.4 1.0
CG C:HIS194 4.3 47.3 1.0
CD B:PRO249 4.7 32.0 1.0
CB C:SER193 4.9 32.5 1.0

Reference:

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
Page generated: Thu Mar 31 05:22:07 2022

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