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Mercury in PDB 1g9u: Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis

Protein crystallography data

The structure of Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis, PDB code: 1g9u was solved by A.G.Evdokimov, D.E.Anderson, K.M.Routzahn, D.S.Waugh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.35
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 109.359, 109.359, 101.499, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 23

Other elements in 1g9u:

The structure of Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis (pdb code 1g9u). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 8 binding sites of Mercury where determined in the Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis, PDB code: 1g9u:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Mercury binding site 1 out of 8 in 1g9u

Go back to Mercury Binding Sites List in 1g9u
Mercury binding site 1 out of 8 in the Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2003

b:47.5
occ:1.00
SG A:CYS68 2.2 39.0 1.0
O A:CYS68 3.0 35.4 1.0
O A:ALA73 3.0 43.2 1.0
C A:CYS68 3.5 43.3 1.0
OE1 A:GLN72 3.5 0.8 1.0
N A:ALA73 3.6 45.8 1.0
CB A:PRO90 3.6 27.7 1.0
CB A:CYS68 3.7 45.7 1.0
C A:ALA73 3.7 40.4 1.0
CG A:PRO90 3.9 28.8 1.0
C A:GLN72 3.9 50.7 1.0
N A:LEU69 4.0 44.5 1.0
CA A:ALA73 4.0 38.7 1.0
CA A:CYS68 4.1 41.6 1.0
CA A:GLN72 4.2 63.6 1.0
CA A:LEU69 4.2 36.3 1.0
CB A:LEU93 4.3 42.7 1.0
CB A:ALA73 4.4 25.2 1.0
O A:GLN72 4.6 40.8 1.0
CD A:GLN72 4.8 98.1 1.0
N A:GLN72 4.8 61.4 1.0
N A:HIS74 4.8 54.6 1.0
O A:PRO91 4.9 32.1 1.0

Mercury binding site 2 out of 8 in 1g9u

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Mercury binding site 2 out of 8 in the Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2004

b:29.6
occ:0.20
ND1 A:HIS92 1.5 98.7 1.0
CE1 A:HIS92 1.7 0.6 1.0
NE2 A:GLN72 2.2 66.0 1.0
CG A:HIS92 2.8 92.0 1.0
NE2 A:HIS92 2.9 0.0 1.0
CD A:GLN72 3.3 98.1 1.0
CD2 A:HIS92 3.4 0.0 1.0
O A:PRO91 3.7 32.1 1.0
CB A:HIS92 3.8 69.0 1.0
OE1 A:GLN72 3.8 0.8 1.0
C A:PRO91 4.2 44.4 1.0
CG A:GLN72 4.4 87.8 1.0
CB A:PRO91 4.6 45.5 1.0
N A:HIS92 4.6 45.0 1.0
CA A:HIS92 4.8 51.0 1.0
CA A:PRO91 4.9 48.6 1.0
CD A:PRO91 4.9 47.7 1.0

Mercury binding site 3 out of 8 in 1g9u

Go back to Mercury Binding Sites List in 1g9u
Mercury binding site 3 out of 8 in the Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2005

b:34.1
occ:0.20
ND1 A:HIS348 2.1 39.2 1.0
CE1 A:HIS348 2.8 30.4 1.0
O A:HIS348 2.9 23.9 1.0
CG A:HIS348 3.2 40.1 1.0
CG2 A:ILE330 3.5 18.3 1.0
CB A:HIS348 3.7 26.8 1.0
C A:HIS348 3.9 23.4 1.0
NE2 A:HIS348 3.9 27.7 1.0
CB A:ILE330 4.1 24.5 1.0
CD2 A:HIS348 4.2 33.2 1.0
CG A:PRO368 4.2 25.3 1.0
CA A:HIS348 4.3 21.2 1.0
O A:HOH3172 4.5 85.5 1.0
CA A:ILE330 4.8 30.3 1.0
N A:ALA350 4.8 30.4 1.0

Mercury binding site 4 out of 8 in 1g9u

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Mercury binding site 4 out of 8 in the Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2006

b:0.6
occ:0.10
O A:HOH3064 3.1 55.1 1.0
O A:HOH3051 4.3 47.9 1.0
OE1 A:GLU354 4.4 0.9 1.0
O A:LEU355 4.7 40.0 1.0
CD A:GLU354 4.7 94.2 1.0
CA A:PRO356 4.8 34.8 1.0
N A:GLN357 4.9 33.2 1.0
OE2 A:GLU354 4.9 0.4 1.0

Mercury binding site 5 out of 8 in 1g9u

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Mercury binding site 5 out of 8 in the Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2007

b:47.0
occ:0.20
ND1 A:HIS363 2.5 15.6 1.0
OE2 A:GLU365 3.4 49.8 1.0
CG A:HIS363 3.4 19.4 1.0
CE1 A:HIS363 3.4 13.3 1.0
CB A:HIS363 3.7 13.3 1.0
CG2 A:ILE343 3.8 8.1 1.0
NH1 A:ARG383 4.0 70.2 1.0
CD1 A:ILE343 4.5 32.2 1.0
O A:HOH3217 4.5 73.6 1.0
NE2 A:HIS363 4.5 17.6 1.0
CD2 A:HIS363 4.6 20.1 1.0
CD A:GLU365 4.6 55.2 1.0
CG1 A:ILE343 4.8 10.3 1.0
CD A:ARG383 4.9 32.1 1.0
CB A:ILE343 4.9 20.2 1.0
OG A:SER345 5.0 57.4 1.0

Mercury binding site 6 out of 8 in 1g9u

Go back to Mercury Binding Sites List in 1g9u
Mercury binding site 6 out of 8 in the Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2008

b:92.8
occ:0.20
CD2 A:HIS348 2.2 33.2 1.0
NE2 A:HIS348 2.7 27.7 1.0
CG A:HIS348 3.2 40.1 1.0
O A:HOH3153 3.4 40.9 1.0
CD A:PRO368 3.6 25.7 1.0
CE1 A:HIS348 3.7 30.4 1.0
CG A:PRO368 3.7 25.3 1.0
O A:ASN347 3.8 20.5 1.0
CA A:HIS348 3.8 21.2 1.0
ND1 A:HIS348 3.9 39.2 1.0
CB A:HIS348 4.0 26.8 1.0
CB A:PRO368 4.2 27.8 1.0
C A:ASN347 4.6 25.2 1.0
N A:PRO368 4.6 32.6 1.0
N A:HIS348 4.7 17.8 1.0
O A:HOH3048 4.7 33.3 1.0
C A:HIS348 4.9 23.4 1.0

Mercury binding site 7 out of 8 in 1g9u

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Mercury binding site 7 out of 8 in the Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2009

b:96.7
occ:0.20
CB A:CYS100 3.0 29.6 1.0
SG A:CYS100 3.1 37.0 1.0
CA A:CYS100 3.6 31.8 1.0
ND2 A:ASN80 4.0 30.5 1.0
C A:CYS100 4.4 32.4 1.0
O A:CYS100 4.6 24.3 1.0
CB A:ASN120 4.6 33.0 1.0
CG A:ASN80 4.8 37.6 1.0
N A:CYS100 4.8 28.4 1.0
OD1 A:ASN120 4.9 64.0 1.0
CG A:ASN120 4.9 46.5 1.0

Mercury binding site 8 out of 8 in 1g9u

Go back to Mercury Binding Sites List in 1g9u
Mercury binding site 8 out of 8 in the Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of Yopm-Leucine Rich Effector Protein From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2010

b:0.9
occ:0.20
SG A:CYS100 2.7 37.0 1.0
CB A:CYS100 4.2 29.6 1.0
OG A:SER99 4.4 28.9 1.0
OD2 A:ASP119 4.5 99.5 1.0
ND2 A:ASN120 4.7 31.6 1.0
CB A:SER99 4.9 28.8 1.0

Reference:

A.G.Evdokimov, D.E.Anderson, K.M.Routzahn, D.S.Waugh. Unusual Molecular Architecture of the Yersinia Pestis Cytotoxin Yopm: A Leucine-Rich Repeat Protein with the Shortest Repeating Unit. J.Mol.Biol. V. 312 807 2001.
ISSN: ISSN 0022-2836
PubMed: 11575934
DOI: 10.1006/JMBI.2001.4973
Page generated: Wed Oct 28 18:39:28 2020

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