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Mercury in PDB 6pii: The Evolving Story of Atzt, A Periplasmic Binding Protein

Protein crystallography data

The structure of The Evolving Story of Atzt, A Periplasmic Binding Protein, PDB code: 6pii was solved by T.S.Peat, J.Newman, C.Scott, L.Esquirol, M.Dennis, T.Nebl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.40 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.920, 63.050, 120.436, 90.00, 93.49, 90.00
R / Rfree (%) 15.5 / 18.3

Other elements in 6pii:

The structure of The Evolving Story of Atzt, A Periplasmic Binding Protein also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the The Evolving Story of Atzt, A Periplasmic Binding Protein (pdb code 6pii). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the The Evolving Story of Atzt, A Periplasmic Binding Protein, PDB code: 6pii:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 6pii

Go back to Mercury Binding Sites List in 6pii
Mercury binding site 1 out of 4 in the The Evolving Story of Atzt, A Periplasmic Binding Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of The Evolving Story of Atzt, A Periplasmic Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg402

b:29.3
occ:0.90
HG A:EMC402 0.0 29.3 0.9
C1 A:EMC402 2.3 30.7 0.9
SG A:CYS238 2.4 35.3 1.0
O A:GLN217 2.8 29.4 1.0
C2 A:EMC402 3.0 26.3 0.9
O A:HOH629 3.2 35.7 1.0
CB A:CYS238 3.2 27.6 1.0
OE1 A:GLN135 3.4 31.2 1.0
CD A:GLN135 3.8 32.9 1.0
O A:HOH525 4.0 29.7 1.0
NE2 A:GLN135 4.0 32.3 1.0
C A:GLN217 4.0 27.8 1.0
O A:HOH639 4.0 44.0 1.0
O A:HOH535 4.1 32.4 1.0
CA A:CYS238 4.1 24.0 1.0
CA A:ASN218 4.2 23.4 1.0
N A:ASN218 4.6 24.9 1.0
ND2 A:ASN218 4.6 26.6 1.0
O A:HOH591 4.6 26.7 1.0
CG A:ASN218 4.7 27.8 1.0
CG A:GLN135 4.8 32.1 1.0
ND2 A:ASN169 5.0 23.6 1.0
C A:CYS238 5.0 27.6 1.0

Mercury binding site 2 out of 4 in 6pii

Go back to Mercury Binding Sites List in 6pii
Mercury binding site 2 out of 4 in the The Evolving Story of Atzt, A Periplasmic Binding Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of The Evolving Story of Atzt, A Periplasmic Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg402

b:29.2
occ:0.90
HG B:EMC402 0.0 29.2 0.9
SG B:CYS238 2.3 29.6 1.0
C1 B:EMC402 2.3 17.6 0.9
O B:GLN217 2.8 27.9 1.0
C2 B:EMC402 3.0 25.2 0.9
O B:HOH628 3.2 30.4 1.0
OE1 B:GLN135 3.3 25.9 1.0
CB B:CYS238 3.3 28.8 1.0
CD B:GLN135 3.7 34.1 1.0
O B:HOH560 3.8 26.6 1.0
C B:GLN217 4.0 28.8 1.0
NE2 B:GLN135 4.1 31.6 1.0
CA B:ASN218 4.2 22.9 1.0
CA B:CYS238 4.2 26.8 1.0
O B:HOH568 4.3 47.7 1.0
O B:HOH504 4.3 32.4 1.0
ND2 B:ASN218 4.5 24.7 1.0
N B:ASN218 4.6 24.9 1.0
CG B:ASN218 4.7 28.2 1.0
O B:HOH537 4.7 30.2 1.0
CG B:GLN135 4.7 28.3 1.0
ND2 B:ASN169 5.0 23.9 1.0

Mercury binding site 3 out of 4 in 6pii

Go back to Mercury Binding Sites List in 6pii
Mercury binding site 3 out of 4 in the The Evolving Story of Atzt, A Periplasmic Binding Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of The Evolving Story of Atzt, A Periplasmic Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg402

b:29.0
occ:0.80
HG C:EMC402 0.0 29.0 0.8
C1 C:EMC402 2.3 26.1 0.8
SG C:CYS238 2.4 36.4 1.0
O C:GLN217 2.9 33.0 1.0
O C:HOH631 3.0 38.3 1.0
C2 C:EMC402 3.2 26.4 0.8
CB C:CYS238 3.3 34.2 1.0
OE1 C:GLN135 3.5 30.6 1.0
O C:HOH545 3.9 33.5 1.0
CD C:GLN135 3.9 31.8 1.0
O C:HOH543 3.9 48.8 1.0
O C:HOH535 4.0 38.4 1.0
C C:GLN217 4.1 28.7 1.0
NE2 C:GLN135 4.1 34.0 1.0
CA C:CYS238 4.2 29.8 1.0
CA C:ASN218 4.3 25.8 1.0
ND2 C:ASN218 4.5 30.2 1.0
CA C:CA403 4.5 55.6 1.0
CG C:ASN218 4.6 30.5 1.0
N C:ASN218 4.7 25.8 1.0
CG C:GLN135 4.8 27.7 1.0
OD1 C:ASN218 4.9 28.2 1.0
ND2 C:ASN169 4.9 24.6 1.0
CB C:ASN218 5.0 28.1 1.0

Mercury binding site 4 out of 4 in 6pii

Go back to Mercury Binding Sites List in 6pii
Mercury binding site 4 out of 4 in the The Evolving Story of Atzt, A Periplasmic Binding Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of The Evolving Story of Atzt, A Periplasmic Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg402

b:31.6
occ:0.80
HG D:EMC402 0.0 31.6 0.8
SG D:CYS238 2.3 41.5 1.0
C1 D:EMC402 2.3 30.5 0.8
O D:GLN217 2.9 30.6 1.0
C2 D:EMC402 3.0 25.9 0.8
CB D:CYS238 3.2 36.4 1.0
O D:HOH579 3.3 35.8 1.0
OE1 D:GLN135 3.5 31.2 1.0
O D:HOH551 3.8 34.7 1.0
CD D:GLN135 3.8 41.5 1.0
NE2 D:GLN135 4.0 40.2 1.0
C D:GLN217 4.1 29.6 1.0
CA D:CYS238 4.1 32.1 1.0
O D:HOH537 4.3 38.2 1.0
CA D:ASN218 4.3 27.6 1.0
ND2 D:ASN218 4.5 29.6 1.0
N D:ASN218 4.6 29.2 1.0
CG D:ASN218 4.6 29.4 1.0
O D:HOH563 4.7 35.4 1.0
CG D:GLN135 4.8 36.5 1.0
OD1 D:ASN218 5.0 28.8 1.0
ND2 D:ASN169 5.0 24.8 1.0
C D:CYS238 5.0 30.6 1.0

Reference:

M.Dennis, L.Esquirol, T.Nebl, J.Newman, C.Scott, T.S.Peat. The Evolving Story of Atzt, A Periplasmic Binding Protein Acta Crystallogr.,Sect.D V. 75 995 2019.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798319013883
Page generated: Sun Dec 13 19:15:28 2020

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