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Zinc in PDB 5fd6: Zinc-Bound Manganese Uptake Regulator

Protein crystallography data

The structure of Zinc-Bound Manganese Uptake Regulator, PDB code: 5fd6 was solved by D.Bellini, A.M.Hemmings, M.A.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.46 / 2.48
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 94.950, 94.950, 63.020, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Zinc-Bound Manganese Uptake Regulator (pdb code 5fd6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Zinc-Bound Manganese Uptake Regulator, PDB code: 5fd6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5fd6

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Zinc binding site 1 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:53.2
occ:1.00
OE2 A:GLU84 2.0 52.2 1.0
NE2 A:HIS93 2.1 46.7 1.0
NE2 A:HIS91 2.2 56.0 1.0
CD A:GLU84 2.7 57.2 1.0
CE1 A:HIS36 2.8 83.9 1.0
OE1 A:GLU84 2.9 63.2 1.0
NE2 A:HIS36 2.9 87.1 1.0
CE1 A:HIS93 3.0 43.4 1.0
CE1 A:HIS91 3.0 57.1 1.0
CD2 A:HIS93 3.1 49.7 1.0
CD2 A:HIS91 3.3 53.6 1.0
ND1 A:HIS36 3.6 86.8 1.0
CD2 A:HIS36 3.9 90.4 1.0
CG A:GLU84 4.0 57.7 1.0
ND1 A:HIS93 4.1 47.0 1.0
ND1 A:HIS91 4.2 55.9 1.0
CG A:HIS93 4.2 44.7 1.0
CG A:HIS36 4.2 78.0 1.0
CG A:HIS91 4.4 57.0 1.0
NE2 A:HIS74 4.5 51.9 1.0
CD2 A:HIS74 4.7 54.6 1.0
CB A:GLU84 4.8 55.9 1.0
CB A:GLU104 4.9 62.8 1.0

Zinc binding site 2 out of 8 in 5fd6

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Zinc binding site 2 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:58.5
occ:1.00
OD2 A:ASP92 2.0 49.6 1.0
OE2 A:GLU111 2.3 70.2 1.0
NE2 A:HIS90 2.3 66.2 1.0
NE2 A:HIS128 2.3 57.5 1.0
CG A:ASP92 2.6 49.5 1.0
OD1 A:ASP92 2.6 51.8 1.0
CE1 A:HIS90 2.7 67.7 1.0
CD A:GLU111 3.0 72.4 1.0
OE1 A:GLU111 3.1 74.1 1.0
CE1 A:HIS128 3.1 58.1 1.0
CD2 A:HIS128 3.4 55.4 1.0
CD2 A:HIS90 3.6 62.8 1.0
ND1 A:HIS90 4.0 60.6 1.0
CB A:ASP92 4.0 52.6 1.0
ND1 A:HIS128 4.3 54.4 1.0
CG A:HIS90 4.4 62.1 1.0
CG A:HIS128 4.5 55.3 1.0
CG A:GLU111 4.5 69.9 1.0
N A:ASP92 4.5 51.6 1.0
OE1 A:GLN114 4.6 62.1 1.0
C A:HIS91 4.7 53.6 1.0
CA A:ASP92 4.7 52.6 1.0
CD2 A:LEU130 4.9 55.9 1.0

Zinc binding site 3 out of 8 in 5fd6

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Zinc binding site 3 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:57.6
occ:1.00
OE1 B:GLU84 2.2 55.2 1.0
NE2 B:HIS36 2.2 60.5 1.0
NE2 B:HIS91 2.3 80.4 1.0
NE2 B:HIS93 2.3 53.3 1.0
OE2 B:GLU84 2.6 57.7 1.0
CD B:GLU84 2.6 60.8 1.0
CE1 B:HIS91 3.1 82.3 1.0
CE1 B:HIS93 3.1 48.5 1.0
CE1 B:HIS36 3.1 60.7 1.0
CD2 B:HIS91 3.2 79.9 1.0
CD2 B:HIS36 3.3 61.1 1.0
CD2 B:HIS93 3.4 51.9 1.0
CG B:GLU84 4.1 61.1 1.0
ND1 B:HIS91 4.2 84.2 1.0
ND1 B:HIS36 4.2 62.9 1.0
ND1 B:HIS93 4.3 53.4 1.0
CG B:HIS91 4.3 80.3 1.0
CG B:HIS36 4.3 61.2 1.0
CG B:HIS93 4.4 49.6 1.0
CD2 B:HIS74 4.6 61.8 1.0
NE2 B:HIS74 4.6 66.8 1.0
CB B:GLU84 4.7 57.6 1.0

Zinc binding site 4 out of 8 in 5fd6

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Zinc binding site 4 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:60.0
occ:1.00
OD2 B:ASP92 2.1 55.1 1.0
NE2 B:HIS128 2.3 54.9 1.0
NE2 B:HIS90 2.4 69.1 1.0
OE2 B:GLU111 2.5 66.3 1.0
OD1 B:ASP92 2.5 52.4 1.0
OE1 B:GLU111 2.6 55.9 1.0
CG B:ASP92 2.6 54.9 1.0
CD B:GLU111 2.9 67.0 1.0
CE1 B:HIS90 3.1 78.4 1.0
CD2 B:HIS128 3.3 54.0 1.0
CE1 B:HIS128 3.3 56.3 1.0
CD2 B:HIS90 3.5 73.2 1.0
CB B:ASP92 4.1 55.2 1.0
ND1 B:HIS90 4.3 78.1 1.0
CG B:GLU111 4.4 67.4 1.0
ND1 B:HIS128 4.4 54.7 1.0
CG B:HIS128 4.4 56.5 1.0
OE1 B:GLN114 4.5 64.7 1.0
CG B:HIS90 4.6 83.3 1.0
N B:ASP92 4.6 55.8 1.0
CA B:ASP92 4.9 55.5 1.0
NE2 B:GLN114 4.9 57.5 1.0
C B:HIS91 5.0 62.9 1.0

Zinc binding site 5 out of 8 in 5fd6

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Zinc binding site 5 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:58.8
occ:1.00
NE2 C:HIS93 2.1 54.7 1.0
OE1 C:GLU84 2.2 65.2 1.0
NE2 C:HIS36 2.3 63.5 1.0
NE2 C:HIS91 2.3 58.0 1.0
CD C:GLU84 2.8 64.6 1.0
OE2 C:GLU84 2.9 66.5 1.0
CE1 C:HIS93 3.0 52.7 1.0
CD2 C:HIS36 3.0 66.8 1.0
CD2 C:HIS93 3.1 56.1 1.0
CD2 C:HIS91 3.2 54.3 1.0
CE1 C:HIS36 3.3 61.9 1.0
CE1 C:HIS91 3.3 60.8 1.0
NE2 C:HIS74 4.0 77.0 1.0
CG C:GLU84 4.1 63.2 1.0
ND1 C:HIS93 4.2 50.3 1.0
CG C:HIS36 4.2 67.2 1.0
CD2 C:HIS74 4.2 77.5 1.0
CG C:HIS93 4.2 53.0 1.0
ND1 C:HIS36 4.3 62.9 1.0
CG C:HIS91 4.4 57.0 1.0
ND1 C:HIS91 4.4 57.6 1.0
CB C:GLU84 4.9 59.2 1.0
CE1 C:HIS74 5.0 74.1 1.0

Zinc binding site 6 out of 8 in 5fd6

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Zinc binding site 6 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:46.6
occ:1.00
OD2 C:ASP92 2.0 47.4 1.0
NE2 C:HIS90 2.0 45.2 1.0
NE2 C:HIS128 2.1 50.5 1.0
OE2 C:GLU111 2.1 47.4 1.0
CG C:ASP92 2.7 47.7 1.0
CE1 C:HIS90 2.8 46.3 1.0
CE1 C:HIS128 2.8 44.4 1.0
OD1 C:ASP92 2.8 52.5 1.0
CD C:GLU111 2.9 50.4 1.0
OE1 C:GLU111 2.9 52.5 1.0
CD2 C:HIS90 3.2 48.4 1.0
CD2 C:HIS128 3.4 48.0 1.0
ND1 C:HIS90 4.0 46.5 1.0
ND1 C:HIS128 4.0 45.5 1.0
CB C:ASP92 4.1 48.1 1.0
CG C:HIS90 4.2 48.3 1.0
CG C:HIS128 4.3 47.5 1.0
CG C:GLU111 4.3 50.3 1.0
OE1 C:GLN114 4.3 48.4 1.0
N C:ASP92 4.6 44.4 1.0
CD2 C:LEU130 4.8 44.2 1.0
C C:HIS91 4.8 45.0 1.0
CA C:ASP92 4.9 45.7 1.0

Zinc binding site 7 out of 8 in 5fd6

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Zinc binding site 7 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:65.2
occ:1.00
OE2 D:GLU84 1.9 53.5 1.0
NE2 D:HIS91 2.2 76.0 1.0
NE2 D:HIS93 2.3 56.2 1.0
NE2 D:HIS36 2.4 65.6 1.0
CD D:GLU84 2.9 57.5 1.0
CE1 D:HIS91 3.0 76.0 1.0
CD2 D:HIS36 3.1 62.6 1.0
OE1 D:GLU84 3.2 66.1 1.0
CE1 D:HIS93 3.3 55.8 1.0
CD2 D:HIS93 3.3 53.0 1.0
CD2 D:HIS91 3.3 77.2 1.0
CE1 D:HIS36 3.5 64.2 1.0
NE2 D:HIS74 4.0 71.3 1.0
ND1 D:HIS91 4.2 74.1 1.0
CG D:GLU84 4.2 59.2 1.0
CD2 D:HIS74 4.3 69.0 1.0
CG D:HIS36 4.3 66.8 1.0
ND1 D:HIS93 4.4 56.6 1.0
CG D:HIS91 4.4 72.5 1.0
CG D:HIS93 4.4 55.1 1.0
ND1 D:HIS36 4.4 68.1 1.0
CB D:GLU84 4.6 59.3 1.0
CG D:GLU104 4.8 67.6 1.0
OE2 D:GLU104 4.8 73.2 1.0
CD D:GLU104 5.0 74.4 1.0

Zinc binding site 8 out of 8 in 5fd6

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Zinc binding site 8 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:54.7
occ:1.00
OD2 D:ASP92 2.0 57.3 1.0
NE2 D:HIS90 2.1 57.8 1.0
NE2 D:HIS128 2.3 55.4 1.0
OE2 D:GLU111 2.4 65.6 1.0
CG D:ASP92 2.7 59.4 1.0
OE1 D:GLU111 2.8 68.0 1.0
OD1 D:ASP92 2.9 61.7 1.0
CD D:GLU111 3.0 61.1 1.0
CD2 D:HIS90 3.0 61.2 1.0
CE1 D:HIS128 3.0 57.9 1.0
CE1 D:HIS90 3.2 65.7 1.0
CD2 D:HIS128 3.5 55.9 1.0
CB D:ASP92 4.2 56.7 1.0
CG D:HIS90 4.2 63.7 1.0
ND1 D:HIS90 4.2 60.5 1.0
ND1 D:HIS128 4.3 59.0 1.0
CG D:GLU111 4.5 55.8 1.0
CG D:HIS128 4.5 55.6 1.0
OE1 D:GLN114 4.6 68.8 1.0
N D:ASP92 4.7 56.9 1.0
C D:HIS91 4.9 58.6 1.0
CA D:ASP92 5.0 57.9 1.0
NE2 D:GLN114 5.0 59.3 1.0

Reference:

D.Bellini, A.Lebedev, R.Keegan, J.Todd, A.M.Hemmings, A.W.Johnston, M.A.Walsh. Structure of A Zinc-Bound Manganese Uptake Regulator, Mur To Be Published.
Page generated: Wed Dec 16 06:13:45 2020

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